Starting phenix.real_space_refine on Mon May 12 09:38:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u58_41914/05_2025/8u58_41914.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u58_41914/05_2025/8u58_41914.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8u58_41914/05_2025/8u58_41914.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u58_41914/05_2025/8u58_41914.map" model { file = "/net/cci-nas-00/data/ceres_data/8u58_41914/05_2025/8u58_41914.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u58_41914/05_2025/8u58_41914.cif" } resolution = 2.45 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= 0.027 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 56 5.16 5 C 5962 2.51 5 N 1362 2.21 5 O 1504 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 8884 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 565, 4428 Classifications: {'peptide': 565} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 544} Chain breaks: 4 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 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 Restraints were copied for chains: C Time building chain proxies: 8.14, per 1000 atoms: 0.92 Number of scatterers: 8884 At special positions: 0 Unit cell: (130.491, 99.5598, 69.5952, 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 56 16.00 O 1504 8.00 N 1362 7.00 C 5962 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 901 " - " ASN A 309 " " NAG C 901 " - " ASN C 309 " Time building additional restraints: 2.23 Conformation dependent library (CDL) restraints added in 1.2 seconds 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2116 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 0 sheets defined 89.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'C' and resid 38 through 40 No H-bonds generated for 'chain 'C' and resid 38 through 40' Processing helix chain 'C' and resid 41 through 62 Processing helix chain 'C' and resid 66 through 80 removed outlier: 3.612A pdb=" N LYS C 71 " --> pdb=" O SER C 67 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLY C 72 " --> pdb=" O THR C 68 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU C 73 " --> pdb=" O GLN C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 93 Processing helix chain 'C' and resid 94 through 98 removed outlier: 3.508A pdb=" N VAL C 98 " --> pdb=" O PHE C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 125 Processing helix chain 'C' and resid 129 through 141 Proline residue: C 138 - end of helix Processing helix chain 'C' and resid 149 through 159 removed outlier: 3.507A pdb=" N ILE C 153 " --> pdb=" O LEU C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 165 Processing helix chain 'C' and resid 166 through 196 removed outlier: 4.134A pdb=" N TYR C 170 " --> pdb=" O LEU C 166 " (cutoff:3.500A) Proline residue: C 174 - end of helix Proline residue: C 182 - end of helix Processing helix chain 'C' and resid 202 through 216 Processing helix chain 'C' and resid 217 through 233 removed outlier: 3.587A pdb=" N VAL C 223 " --> pdb=" O ILE C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 264 removed outlier: 4.223A pdb=" N ASN C 243 " --> pdb=" O VAL C 239 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N PHE C 244 " --> pdb=" O TYR C 240 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N SER C 253 " --> pdb=" O GLY C 249 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N GLY C 254 " --> pdb=" O ASN C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 288 Processing helix chain 'C' and resid 288 through 302 Processing helix chain 'C' and resid 306 through 322 Processing helix chain 'C' and resid 326 through 337 removed outlier: 4.170A pdb=" N ALA C 330 " --> pdb=" O ALA C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 367 removed outlier: 3.673A pdb=" N ALA C 355 " --> pdb=" O THR C 351 " (cutoff:3.500A) Proline residue: C 356 - end of helix Processing helix chain 'C' and resid 368 through 370 No H-bonds generated for 'chain 'C' and resid 368 through 370' Processing helix chain 'C' and resid 371 through 404 Processing helix chain 'C' and resid 405 through 409 Processing helix chain 'C' and resid 411 through 436 removed outlier: 4.101A pdb=" N PHE C 434 " --> pdb=" O MET C 430 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 472 removed outlier: 3.914A pdb=" N LEU C 445 " --> pdb=" O VAL C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 503 removed outlier: 4.197A pdb=" N ILE C 491 " --> pdb=" O SER C 487 " (cutoff:3.500A) Proline residue: C 492 - end of helix Processing helix chain 'C' and resid 511 through 515 Processing helix chain 'C' and resid 516 through 542 Processing helix chain 'C' and resid 654 through 682 Processing helix chain 'C' and resid 688 through 712 removed outlier: 5.656A pdb=" N GLY C 704 " --> pdb=" O ASN C 700 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N PHE C 705 " --> pdb=" O PHE C 701 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE C 706 " --> pdb=" O GLY C 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 40 No H-bonds generated for 'chain 'A' and resid 38 through 40' Processing helix chain 'A' and resid 41 through 62 Processing helix chain 'A' and resid 66 through 80 removed outlier: 3.603A pdb=" N LYS A 71 " --> pdb=" O SER A 67 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N GLY A 72 " --> pdb=" O THR A 68 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU A 73 " --> pdb=" O GLN A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 93 Processing helix chain 'A' and resid 94 through 98 removed outlier: 3.522A pdb=" N VAL A 98 " --> pdb=" O PHE A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 125 Processing helix chain 'A' and resid 129 through 141 Proline residue: A 138 - end of helix Processing helix chain 'A' and resid 149 through 159 removed outlier: 3.505A pdb=" N ILE A 153 " --> pdb=" O LEU A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 165 Processing helix chain 'A' and resid 166 through 196 removed outlier: 4.134A pdb=" N TYR A 170 " --> pdb=" O LEU A 166 " (cutoff:3.500A) Proline residue: A 174 - end of helix Proline residue: A 182 - end of helix Processing helix chain 'A' and resid 202 through 216 Processing helix chain 'A' and resid 217 through 233 removed outlier: 3.582A pdb=" N VAL A 223 " --> pdb=" O ILE A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 264 removed outlier: 4.219A pdb=" N ASN A 243 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N PHE A 244 " --> pdb=" O TYR A 240 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N SER A 253 " --> pdb=" O GLY A 249 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N GLY A 254 " --> pdb=" O ASN A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 288 Processing helix chain 'A' and resid 288 through 302 Processing helix chain 'A' and resid 306 through 322 Processing helix chain 'A' and resid 326 through 337 removed outlier: 4.176A pdb=" N ALA A 330 " --> pdb=" O ALA A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 367 removed outlier: 3.681A pdb=" N ALA A 355 " --> pdb=" O THR A 351 " (cutoff:3.500A) Proline residue: A 356 - end of helix Processing helix chain 'A' and resid 368 through 370 No H-bonds generated for 'chain 'A' and resid 368 through 370' Processing helix chain 'A' and resid 371 through 404 Processing helix chain 'A' and resid 405 through 409 Processing helix chain 'A' and resid 411 through 436 removed outlier: 4.099A pdb=" N PHE A 434 " --> pdb=" O MET A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 472 removed outlier: 3.911A pdb=" N LEU A 445 " --> pdb=" O VAL A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 503 removed outlier: 4.196A pdb=" N ILE A 491 " --> pdb=" O SER A 487 " (cutoff:3.500A) Proline residue: A 492 - end of helix Processing helix chain 'A' and resid 511 through 515 Processing helix chain 'A' and resid 516 through 542 Processing helix chain 'A' and resid 654 through 682 Processing helix chain 'A' and resid 688 through 712 removed outlier: 5.652A pdb=" N GLY A 704 " --> pdb=" O ASN A 700 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N PHE A 705 " --> pdb=" O PHE A 701 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE A 706 " --> pdb=" O GLY A 702 " (cutoff:3.500A) 732 hydrogen bonds defined for protein. 2160 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: 3.00 Time building geometry restraints manager: 2.58 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: 2350 1.34 - 1.45: 1673 1.45 - 1.57: 4981 1.57 - 1.69: 0 1.69 - 1.81: 90 Bond restraints: 9094 Sorted by residual: bond pdb=" C1 NAG A 901 " pdb=" O5 NAG A 901 " ideal model delta sigma weight residual 1.406 1.457 -0.051 2.00e-02 2.50e+03 6.45e+00 bond pdb=" C1 NAG C 901 " pdb=" O5 NAG C 901 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 6.12e+00 bond pdb=" CB TYR C 320 " pdb=" CG TYR C 320 " ideal model delta sigma weight residual 1.512 1.465 0.047 2.20e-02 2.07e+03 4.59e+00 bond pdb=" CB TYR A 320 " pdb=" CG TYR A 320 " ideal model delta sigma weight residual 1.512 1.465 0.047 2.20e-02 2.07e+03 4.49e+00 bond pdb=" C PRO A 372 " pdb=" N LYS A 373 " ideal model delta sigma weight residual 1.337 1.305 0.032 1.61e-02 3.86e+03 4.03e+00 ... (remaining 9089 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 11528 1.89 - 3.78: 708 3.78 - 5.68: 92 5.68 - 7.57: 18 7.57 - 9.46: 10 Bond angle restraints: 12356 Sorted by residual: angle pdb=" CA TYR C 451 " pdb=" CB TYR C 451 " pdb=" CG TYR C 451 " ideal model delta sigma weight residual 113.90 104.44 9.46 1.80e+00 3.09e-01 2.76e+01 angle pdb=" CA TYR A 451 " pdb=" CB TYR A 451 " pdb=" CG TYR A 451 " ideal model delta sigma weight residual 113.90 104.47 9.43 1.80e+00 3.09e-01 2.75e+01 angle pdb=" CA TYR A 689 " pdb=" CB TYR A 689 " pdb=" CG TYR A 689 " ideal model delta sigma weight residual 113.90 106.06 7.84 1.80e+00 3.09e-01 1.90e+01 angle pdb=" CA TYR C 689 " pdb=" CB TYR C 689 " pdb=" CG TYR C 689 " ideal model delta sigma weight residual 113.90 106.08 7.82 1.80e+00 3.09e-01 1.89e+01 angle pdb=" CA TYR C 320 " pdb=" CB TYR C 320 " pdb=" CG TYR C 320 " ideal model delta sigma weight residual 113.90 106.76 7.14 1.80e+00 3.09e-01 1.57e+01 ... (remaining 12351 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.92: 4953 16.92 - 33.83: 323 33.83 - 50.75: 36 50.75 - 67.66: 10 67.66 - 84.58: 4 Dihedral angle restraints: 5326 sinusoidal: 2050 harmonic: 3276 Sorted by residual: dihedral pdb=" CA ASN A 63 " pdb=" C ASN A 63 " pdb=" N VAL A 64 " pdb=" CA VAL A 64 " ideal model delta harmonic sigma weight residual 180.00 157.15 22.85 0 5.00e+00 4.00e-02 2.09e+01 dihedral pdb=" CA ASN C 63 " pdb=" C ASN C 63 " pdb=" N VAL C 64 " pdb=" CA VAL C 64 " ideal model delta harmonic sigma weight residual 180.00 157.24 22.76 0 5.00e+00 4.00e-02 2.07e+01 dihedral pdb=" CA MET A 179 " pdb=" C MET A 179 " pdb=" N LEU A 180 " pdb=" CA LEU A 180 " ideal model delta harmonic sigma weight residual -180.00 -159.59 -20.41 0 5.00e+00 4.00e-02 1.67e+01 ... (remaining 5323 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 964 0.046 - 0.091: 419 0.091 - 0.137: 92 0.137 - 0.183: 21 0.183 - 0.228: 6 Chirality restraints: 1502 Sorted by residual: chirality pdb=" C1 NAG C 901 " pdb=" ND2 ASN C 309 " pdb=" C2 NAG C 901 " pdb=" O5 NAG C 901 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" C1 NAG A 901 " pdb=" ND2 ASN A 309 " pdb=" C2 NAG A 901 " pdb=" O5 NAG A 901 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CA TYR C 451 " pdb=" N TYR C 451 " pdb=" C TYR C 451 " pdb=" CB TYR C 451 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.10e+00 ... (remaining 1499 not shown) Planarity restraints: 1478 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 320 " 0.096 2.00e-02 2.50e+03 4.85e-02 4.71e+01 pdb=" CG TYR C 320 " -0.057 2.00e-02 2.50e+03 pdb=" CD1 TYR C 320 " -0.049 2.00e-02 2.50e+03 pdb=" CD2 TYR C 320 " -0.032 2.00e-02 2.50e+03 pdb=" CE1 TYR C 320 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR C 320 " -0.016 2.00e-02 2.50e+03 pdb=" CZ TYR C 320 " 0.009 2.00e-02 2.50e+03 pdb=" OH TYR C 320 " 0.052 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 320 " -0.096 2.00e-02 2.50e+03 4.85e-02 4.70e+01 pdb=" CG TYR A 320 " 0.057 2.00e-02 2.50e+03 pdb=" CD1 TYR A 320 " 0.048 2.00e-02 2.50e+03 pdb=" CD2 TYR A 320 " 0.033 2.00e-02 2.50e+03 pdb=" CE1 TYR A 320 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR A 320 " 0.014 2.00e-02 2.50e+03 pdb=" CZ TYR A 320 " -0.008 2.00e-02 2.50e+03 pdb=" OH TYR A 320 " -0.052 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 901 " -0.066 2.00e-02 2.50e+03 5.47e-02 3.74e+01 pdb=" C7 NAG A 901 " 0.004 2.00e-02 2.50e+03 pdb=" C8 NAG A 901 " -0.046 2.00e-02 2.50e+03 pdb=" N2 NAG A 901 " 0.091 2.00e-02 2.50e+03 pdb=" O7 NAG A 901 " 0.017 2.00e-02 2.50e+03 ... (remaining 1475 not shown) Histogram of nonbonded interaction distances: 2.52 - 2.99: 4804 2.99 - 3.47: 10323 3.47 - 3.95: 16113 3.95 - 4.42: 19101 4.42 - 4.90: 29395 Nonbonded interactions: 79736 Sorted by model distance: nonbonded pdb=" O SER A 101 " pdb=" OG SER A 105 " model vdw 2.518 3.040 nonbonded pdb=" O SER C 101 " pdb=" OG SER C 105 " model vdw 2.519 3.040 nonbonded pdb=" OE2 GLU A 299 " pdb=" OG SER A 314 " model vdw 2.545 3.040 nonbonded pdb=" O ILE C 400 " pdb=" OG SER C 404 " model vdw 2.545 3.040 nonbonded pdb=" O ILE A 400 " pdb=" OG SER A 404 " model vdw 2.546 3.040 ... (remaining 79731 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } 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: 1.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 26.500 Find NCS groups from input model: 0.170 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:11.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 39.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7031 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 : 0.007 0.052 9096 Z= 0.365 Angle : 1.061 9.462 12362 Z= 0.604 Chirality : 0.053 0.228 1502 Planarity : 0.009 0.095 1476 Dihedral : 11.796 84.578 3210 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.71 (0.22), residues: 1110 helix: -0.36 (0.15), residues: 902 sheet: None (None), residues: 0 loop : -0.19 (0.44), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.006 TRP A 100 HIS 0.007 0.003 HIS A 505 PHE 0.054 0.007 PHE A 694 TYR 0.096 0.009 TYR A 320 ARG 0.004 0.001 ARG A 687 Details of bonding type rmsd link_NAG-ASN : bond 0.00968 ( 2) link_NAG-ASN : angle 5.06188 ( 6) hydrogen bonds : bond 0.11708 ( 732) hydrogen bonds : angle 6.64466 ( 2160) covalent geometry : bond 0.00737 ( 9094) covalent geometry : angle 1.05572 (12356) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 1.062 Fit side-chains REVERT: A 193 TRP cc_start: 0.6946 (t-100) cc_final: 0.6717 (t-100) outliers start: 0 outliers final: 1 residues processed: 202 average time/residue: 0.9503 time to fit residues: 207.8733 Evaluate side-chains 78 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 77 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 710 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 chunk 57 optimal weight: 0.6980 chunk 45 optimal weight: 5.9990 chunk 87 optimal weight: 0.5980 chunk 33 optimal weight: 0.7980 chunk 53 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 101 optimal weight: 7.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 143 GLN ** C 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 167 GLN ** C 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 654 GLN ** C 658 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 143 GLN ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 167 GLN A 654 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.133105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.098217 restraints weight = 16604.099| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 2.25 r_work: 0.3374 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.4297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9096 Z= 0.194 Angle : 0.693 8.469 12362 Z= 0.356 Chirality : 0.046 0.173 1502 Planarity : 0.005 0.034 1476 Dihedral : 4.933 34.849 1224 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 2.64 % Allowed : 10.16 % Favored : 87.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.88 (0.25), residues: 1110 helix: 1.51 (0.17), residues: 898 sheet: None (None), residues: 0 loop : 0.40 (0.46), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 396 HIS 0.004 0.001 HIS A 310 PHE 0.022 0.002 PHE C 221 TYR 0.028 0.002 TYR C 455 ARG 0.006 0.001 ARG A 295 Details of bonding type rmsd link_NAG-ASN : bond 0.00483 ( 2) link_NAG-ASN : angle 1.93598 ( 6) hydrogen bonds : bond 0.05334 ( 732) hydrogen bonds : angle 4.91716 ( 2160) covalent geometry : bond 0.00441 ( 9094) covalent geometry : angle 0.69197 (12356) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 115 time to evaluate : 1.095 Fit side-chains revert: symmetry clash REVERT: C 112 SER cc_start: 0.8986 (m) cc_final: 0.8723 (t) REVERT: C 130 ARG cc_start: 0.7702 (ptt180) cc_final: 0.7499 (ptp90) REVERT: C 242 GLU cc_start: 0.8274 (tp30) cc_final: 0.8035 (tp30) REVERT: C 382 VAL cc_start: 0.8020 (t) cc_final: 0.7789 (t) REVERT: A 37 MET cc_start: 0.7539 (ttm) cc_final: 0.7217 (ttm) REVERT: A 112 SER cc_start: 0.9018 (m) cc_final: 0.8775 (t) REVERT: A 193 TRP cc_start: 0.8145 (t-100) cc_final: 0.7704 (t-100) REVERT: A 242 GLU cc_start: 0.8305 (tp30) cc_final: 0.8057 (tp30) REVERT: A 382 VAL cc_start: 0.8047 (t) cc_final: 0.7835 (t) REVERT: A 540 MET cc_start: 0.6282 (mmm) cc_final: 0.5981 (tmt) outliers start: 26 outliers final: 3 residues processed: 132 average time/residue: 0.8431 time to fit residues: 122.2585 Evaluate side-chains 84 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 81 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 239 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 110 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 43 optimal weight: 7.9990 chunk 30 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 chunk 107 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 44 optimal weight: 7.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 145 ASN ** C 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 412 HIS A 658 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.131368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.095069 restraints weight = 16908.738| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 2.31 r_work: 0.3342 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.6147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9096 Z= 0.180 Angle : 0.646 11.349 12362 Z= 0.323 Chirality : 0.042 0.154 1502 Planarity : 0.004 0.037 1476 Dihedral : 4.615 30.559 1222 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 2.74 % Allowed : 10.16 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 2.45 (0.25), residues: 1110 helix: 1.88 (0.17), residues: 898 sheet: None (None), residues: 0 loop : 0.73 (0.46), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 193 HIS 0.003 0.001 HIS C 716 PHE 0.025 0.002 PHE C 221 TYR 0.033 0.002 TYR C 455 ARG 0.006 0.001 ARG C 235 Details of bonding type rmsd link_NAG-ASN : bond 0.00444 ( 2) link_NAG-ASN : angle 1.70611 ( 6) hydrogen bonds : bond 0.05293 ( 732) hydrogen bonds : angle 4.71797 ( 2160) covalent geometry : bond 0.00412 ( 9094) covalent geometry : angle 0.64482 (12356) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 98 time to evaluate : 1.009 Fit side-chains REVERT: C 145 ASN cc_start: 0.9184 (OUTLIER) cc_final: 0.8966 (t0) REVERT: C 234 ASP cc_start: 0.8008 (m-30) cc_final: 0.7295 (t0) REVERT: C 338 MET cc_start: 0.8520 (mtt) cc_final: 0.8185 (mtm) REVERT: C 352 PHE cc_start: 0.6814 (m-10) cc_final: 0.6273 (t80) REVERT: C 401 LEU cc_start: 0.7740 (OUTLIER) cc_final: 0.7479 (tp) REVERT: C 452 SER cc_start: 0.9038 (t) cc_final: 0.8608 (p) REVERT: C 519 GLU cc_start: 0.7788 (mm-30) cc_final: 0.6960 (mp0) REVERT: C 540 MET cc_start: 0.6330 (mmm) cc_final: 0.5996 (tmt) REVERT: A 37 MET cc_start: 0.7909 (ttm) cc_final: 0.7499 (ttp) REVERT: A 193 TRP cc_start: 0.8225 (t-100) cc_final: 0.7925 (m-90) REVERT: A 234 ASP cc_start: 0.8009 (m-30) cc_final: 0.7310 (t0) REVERT: A 299 GLU cc_start: 0.8405 (mt-10) cc_final: 0.8125 (mt-10) REVERT: A 338 MET cc_start: 0.8448 (mtt) cc_final: 0.8113 (mtm) REVERT: A 352 PHE cc_start: 0.6845 (m-10) cc_final: 0.6277 (t80) REVERT: A 401 LEU cc_start: 0.7721 (OUTLIER) cc_final: 0.7483 (tp) REVERT: A 519 GLU cc_start: 0.7795 (mm-30) cc_final: 0.6891 (mp0) REVERT: A 540 MET cc_start: 0.6389 (mmm) cc_final: 0.6178 (tmt) outliers start: 27 outliers final: 7 residues processed: 119 average time/residue: 0.9468 time to fit residues: 122.6269 Evaluate side-chains 82 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 145 ASN Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 395 ILE Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 401 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 11 optimal weight: 0.5980 chunk 49 optimal weight: 5.9990 chunk 54 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 chunk 106 optimal weight: 3.9990 chunk 103 optimal weight: 8.9990 chunk 97 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 chunk 87 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 412 HIS ** A 145 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 = 0.4078 r_free = 0.4078 target = 0.131166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.094943 restraints weight = 17038.802| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 2.31 r_work: 0.3337 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.6804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9096 Z= 0.165 Angle : 0.612 13.109 12362 Z= 0.303 Chirality : 0.042 0.387 1502 Planarity : 0.004 0.034 1476 Dihedral : 4.420 29.777 1222 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 2.54 % Allowed : 10.67 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.67 (0.25), residues: 1110 helix: 2.05 (0.17), residues: 898 sheet: None (None), residues: 0 loop : 0.68 (0.44), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 396 HIS 0.004 0.001 HIS A 716 PHE 0.023 0.002 PHE A 221 TYR 0.019 0.001 TYR C 455 ARG 0.003 0.000 ARG A 295 Details of bonding type rmsd link_NAG-ASN : bond 0.00447 ( 2) link_NAG-ASN : angle 1.41293 ( 6) hydrogen bonds : bond 0.04824 ( 732) hydrogen bonds : angle 4.58823 ( 2160) covalent geometry : bond 0.00383 ( 9094) covalent geometry : angle 0.61135 (12356) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 79 time to evaluate : 1.023 Fit side-chains REVERT: C 37 MET cc_start: 0.7963 (ttm) cc_final: 0.7562 (ttm) REVERT: C 338 MET cc_start: 0.8490 (mtt) cc_final: 0.8147 (mtm) REVERT: C 352 PHE cc_start: 0.6716 (m-10) cc_final: 0.6028 (t80) REVERT: C 401 LEU cc_start: 0.7725 (OUTLIER) cc_final: 0.7494 (mp) REVERT: C 402 LEU cc_start: 0.7055 (OUTLIER) cc_final: 0.6712 (tt) REVERT: C 452 SER cc_start: 0.8989 (t) cc_final: 0.8588 (p) REVERT: C 521 MET cc_start: 0.5666 (tpt) cc_final: 0.5224 (mmm) REVERT: C 540 MET cc_start: 0.6583 (mmm) cc_final: 0.6154 (tmt) REVERT: A 37 MET cc_start: 0.8034 (ttm) cc_final: 0.7579 (ttm) REVERT: A 193 TRP cc_start: 0.8212 (t-100) cc_final: 0.7908 (m-90) REVERT: A 338 MET cc_start: 0.8513 (mtt) cc_final: 0.8153 (mtm) REVERT: A 352 PHE cc_start: 0.6710 (m-10) cc_final: 0.6012 (t80) REVERT: A 401 LEU cc_start: 0.7742 (OUTLIER) cc_final: 0.7474 (tp) REVERT: A 402 LEU cc_start: 0.7008 (OUTLIER) cc_final: 0.6686 (tt) outliers start: 25 outliers final: 8 residues processed: 99 average time/residue: 0.8424 time to fit residues: 92.2288 Evaluate side-chains 89 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 402 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 10 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 47 optimal weight: 6.9990 chunk 6 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 90 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 91 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: ** C 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.130664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.094787 restraints weight = 17054.825| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 2.31 r_work: 0.3333 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.7250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9096 Z= 0.156 Angle : 0.588 8.610 12362 Z= 0.291 Chirality : 0.043 0.325 1502 Planarity : 0.004 0.034 1476 Dihedral : 4.350 28.437 1222 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 3.35 % Allowed : 9.65 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.76 (0.25), residues: 1110 helix: 2.13 (0.17), residues: 900 sheet: None (None), residues: 0 loop : 0.66 (0.44), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 363 HIS 0.004 0.001 HIS C 716 PHE 0.023 0.002 PHE A 221 TYR 0.018 0.002 TYR C 455 ARG 0.002 0.000 ARG C 235 Details of bonding type rmsd link_NAG-ASN : bond 0.00376 ( 2) link_NAG-ASN : angle 1.36987 ( 6) hydrogen bonds : bond 0.04672 ( 732) hydrogen bonds : angle 4.53989 ( 2160) covalent geometry : bond 0.00357 ( 9094) covalent geometry : angle 0.58708 (12356) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 85 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 338 MET cc_start: 0.8517 (mtt) cc_final: 0.8187 (mtm) REVERT: C 352 PHE cc_start: 0.6669 (m-10) cc_final: 0.5978 (t80) REVERT: C 401 LEU cc_start: 0.7765 (OUTLIER) cc_final: 0.7564 (mp) REVERT: C 402 LEU cc_start: 0.6936 (OUTLIER) cc_final: 0.6595 (tt) REVERT: C 452 SER cc_start: 0.9009 (t) cc_final: 0.8625 (p) REVERT: C 519 GLU cc_start: 0.7836 (mm-30) cc_final: 0.6998 (mp0) REVERT: C 521 MET cc_start: 0.5640 (OUTLIER) cc_final: 0.5109 (mmm) REVERT: C 540 MET cc_start: 0.6633 (mmm) cc_final: 0.6424 (ptp) REVERT: A 193 TRP cc_start: 0.8188 (t-100) cc_final: 0.7912 (m-90) REVERT: A 338 MET cc_start: 0.8516 (mtt) cc_final: 0.8168 (mtm) REVERT: A 352 PHE cc_start: 0.6633 (m-10) cc_final: 0.5945 (t80) REVERT: A 402 LEU cc_start: 0.6972 (OUTLIER) cc_final: 0.6642 (tt) REVERT: A 452 SER cc_start: 0.9022 (t) cc_final: 0.8641 (p) outliers start: 33 outliers final: 11 residues processed: 108 average time/residue: 0.8609 time to fit residues: 102.2254 Evaluate side-chains 99 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 84 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain C residue 521 MET Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 402 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 6.9990 chunk 33 optimal weight: 0.6980 chunk 46 optimal weight: 9.9990 chunk 20 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 92 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 106 optimal weight: 0.5980 chunk 74 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.130441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.094502 restraints weight = 17116.596| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 2.32 r_work: 0.3324 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.7612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9096 Z= 0.157 Angle : 0.591 9.028 12362 Z= 0.294 Chirality : 0.043 0.336 1502 Planarity : 0.004 0.033 1476 Dihedral : 4.278 27.047 1222 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 3.25 % Allowed : 9.45 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 2.80 (0.25), residues: 1110 helix: 2.16 (0.17), residues: 898 sheet: None (None), residues: 0 loop : 0.65 (0.44), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 460 HIS 0.004 0.001 HIS A 716 PHE 0.024 0.002 PHE C 221 TYR 0.044 0.002 TYR C 455 ARG 0.001 0.000 ARG C 235 Details of bonding type rmsd link_NAG-ASN : bond 0.00369 ( 2) link_NAG-ASN : angle 1.29936 ( 6) hydrogen bonds : bond 0.04609 ( 732) hydrogen bonds : angle 4.54583 ( 2160) covalent geometry : bond 0.00359 ( 9094) covalent geometry : angle 0.59077 (12356) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 88 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 338 MET cc_start: 0.8515 (mtt) cc_final: 0.8225 (mtp) REVERT: C 352 PHE cc_start: 0.6717 (m-10) cc_final: 0.5980 (t80) REVERT: C 402 LEU cc_start: 0.6852 (OUTLIER) cc_final: 0.6524 (tt) REVERT: C 452 SER cc_start: 0.9067 (t) cc_final: 0.8614 (p) REVERT: C 521 MET cc_start: 0.5381 (OUTLIER) cc_final: 0.5043 (mmm) REVERT: C 667 ILE cc_start: 0.8272 (mp) cc_final: 0.8060 (pt) REVERT: A 193 TRP cc_start: 0.8181 (t-100) cc_final: 0.7921 (m-90) REVERT: A 234 ASP cc_start: 0.8292 (m-30) cc_final: 0.7691 (t0) REVERT: A 338 MET cc_start: 0.8490 (mtt) cc_final: 0.8177 (mtm) REVERT: A 352 PHE cc_start: 0.6670 (m-10) cc_final: 0.5949 (t80) REVERT: A 402 LEU cc_start: 0.6897 (OUTLIER) cc_final: 0.6597 (tt) REVERT: A 452 SER cc_start: 0.9050 (t) cc_final: 0.8589 (p) REVERT: A 455 TYR cc_start: 0.7314 (m-80) cc_final: 0.6569 (m-80) outliers start: 32 outliers final: 12 residues processed: 108 average time/residue: 0.8138 time to fit residues: 97.1732 Evaluate side-chains 99 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 84 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain C residue 521 MET Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 673 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 88 optimal weight: 0.5980 chunk 96 optimal weight: 10.0000 chunk 1 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 chunk 94 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 80 optimal weight: 0.7980 chunk 99 optimal weight: 9.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.130246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.094289 restraints weight = 17106.741| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 2.29 r_work: 0.3324 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.7856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9096 Z= 0.156 Angle : 0.589 10.645 12362 Z= 0.292 Chirality : 0.042 0.338 1502 Planarity : 0.004 0.033 1476 Dihedral : 4.260 25.624 1222 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 2.54 % Allowed : 10.47 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 2.79 (0.25), residues: 1110 helix: 2.14 (0.17), residues: 898 sheet: None (None), residues: 0 loop : 0.70 (0.44), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 460 HIS 0.004 0.001 HIS A 716 PHE 0.022 0.002 PHE C 221 TYR 0.017 0.001 TYR A 451 ARG 0.001 0.000 ARG C 295 Details of bonding type rmsd link_NAG-ASN : bond 0.00345 ( 2) link_NAG-ASN : angle 1.30595 ( 6) hydrogen bonds : bond 0.04541 ( 732) hydrogen bonds : angle 4.54317 ( 2160) covalent geometry : bond 0.00358 ( 9094) covalent geometry : angle 0.58834 (12356) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 86 time to evaluate : 1.069 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 234 ASP cc_start: 0.8341 (m-30) cc_final: 0.7822 (t0) REVERT: C 297 MET cc_start: 0.8715 (mmt) cc_final: 0.8440 (mmt) REVERT: C 352 PHE cc_start: 0.6769 (m-10) cc_final: 0.6028 (t80) REVERT: C 452 SER cc_start: 0.9128 (t) cc_final: 0.8702 (p) REVERT: C 455 TYR cc_start: 0.7551 (m-80) cc_final: 0.6581 (m-80) REVERT: C 521 MET cc_start: 0.5388 (OUTLIER) cc_final: 0.4621 (mmm) REVERT: C 667 ILE cc_start: 0.8245 (mp) cc_final: 0.8029 (pt) REVERT: A 193 TRP cc_start: 0.8167 (t-100) cc_final: 0.7957 (m-90) REVERT: A 352 PHE cc_start: 0.6720 (m-10) cc_final: 0.5983 (t80) REVERT: A 402 LEU cc_start: 0.6956 (OUTLIER) cc_final: 0.6689 (tt) REVERT: A 452 SER cc_start: 0.9071 (t) cc_final: 0.8717 (p) REVERT: A 667 ILE cc_start: 0.8343 (mt) cc_final: 0.8131 (mm) outliers start: 25 outliers final: 10 residues processed: 105 average time/residue: 0.8152 time to fit residues: 94.6385 Evaluate side-chains 92 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain C residue 521 MET Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 419 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 57 optimal weight: 1.9990 chunk 53 optimal weight: 7.9990 chunk 73 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 96 optimal weight: 8.9990 chunk 94 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 68 optimal weight: 0.7980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 409 GLN ** A 145 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 = 0.4048 r_free = 0.4048 target = 0.129182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.093160 restraints weight = 17312.308| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 2.29 r_work: 0.3302 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.8096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9096 Z= 0.179 Angle : 0.617 11.008 12362 Z= 0.304 Chirality : 0.043 0.340 1502 Planarity : 0.004 0.033 1476 Dihedral : 4.241 23.584 1222 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 2.03 % Allowed : 11.48 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 2.75 (0.25), residues: 1110 helix: 2.11 (0.17), residues: 898 sheet: None (None), residues: 0 loop : 0.72 (0.44), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 460 HIS 0.004 0.001 HIS A 716 PHE 0.023 0.002 PHE C 221 TYR 0.016 0.001 TYR C 451 ARG 0.001 0.000 ARG C 130 Details of bonding type rmsd link_NAG-ASN : bond 0.00322 ( 2) link_NAG-ASN : angle 1.23223 ( 6) hydrogen bonds : bond 0.04678 ( 732) hydrogen bonds : angle 4.60551 ( 2160) covalent geometry : bond 0.00419 ( 9094) covalent geometry : angle 0.61616 (12356) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 84 time to evaluate : 0.974 Fit side-chains revert: symmetry clash REVERT: C 211 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8716 (mm) REVERT: C 297 MET cc_start: 0.8749 (mmt) cc_final: 0.8458 (mmt) REVERT: C 352 PHE cc_start: 0.6759 (m-10) cc_final: 0.6001 (t80) REVERT: C 409 GLN cc_start: 0.8505 (tp40) cc_final: 0.8113 (tt0) REVERT: C 452 SER cc_start: 0.9121 (t) cc_final: 0.8695 (p) REVERT: C 455 TYR cc_start: 0.7340 (m-80) cc_final: 0.6741 (m-80) REVERT: C 521 MET cc_start: 0.5386 (OUTLIER) cc_final: 0.4629 (mmm) REVERT: C 667 ILE cc_start: 0.8288 (mp) cc_final: 0.8054 (pt) REVERT: A 193 TRP cc_start: 0.8182 (t-100) cc_final: 0.7972 (m-90) REVERT: A 211 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8712 (mm) REVERT: A 234 ASP cc_start: 0.8353 (m-30) cc_final: 0.7840 (t0) REVERT: A 352 PHE cc_start: 0.6739 (m-10) cc_final: 0.6006 (t80) REVERT: A 402 LEU cc_start: 0.6898 (OUTLIER) cc_final: 0.6664 (tt) REVERT: A 452 SER cc_start: 0.9139 (t) cc_final: 0.8740 (p) outliers start: 20 outliers final: 9 residues processed: 98 average time/residue: 0.9089 time to fit residues: 97.9681 Evaluate side-chains 92 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 79 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain C residue 521 MET Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 419 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 89 optimal weight: 0.0770 chunk 80 optimal weight: 0.8980 chunk 108 optimal weight: 0.9990 chunk 100 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 58 optimal weight: 0.5980 chunk 72 optimal weight: 0.8980 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.130253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.094767 restraints weight = 17133.864| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 2.29 r_work: 0.3331 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.8252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9096 Z= 0.148 Angle : 0.606 10.965 12362 Z= 0.296 Chirality : 0.042 0.342 1502 Planarity : 0.004 0.032 1476 Dihedral : 4.179 22.906 1222 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 1.73 % Allowed : 12.20 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 2.78 (0.25), residues: 1110 helix: 2.14 (0.17), residues: 900 sheet: None (None), residues: 0 loop : 0.70 (0.45), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 363 HIS 0.004 0.001 HIS A 716 PHE 0.020 0.001 PHE A 221 TYR 0.016 0.001 TYR C 451 ARG 0.001 0.000 ARG A 235 Details of bonding type rmsd link_NAG-ASN : bond 0.00349 ( 2) link_NAG-ASN : angle 1.34687 ( 6) hydrogen bonds : bond 0.04455 ( 732) hydrogen bonds : angle 4.53510 ( 2160) covalent geometry : bond 0.00337 ( 9094) covalent geometry : angle 0.60521 (12356) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 0.995 Fit side-chains revert: symmetry clash REVERT: C 234 ASP cc_start: 0.8283 (m-30) cc_final: 0.7823 (t0) REVERT: C 297 MET cc_start: 0.8721 (mmt) cc_final: 0.8469 (mmt) REVERT: C 352 PHE cc_start: 0.6769 (m-10) cc_final: 0.6029 (t80) REVERT: C 409 GLN cc_start: 0.8487 (tp40) cc_final: 0.8174 (tt0) REVERT: C 452 SER cc_start: 0.9123 (t) cc_final: 0.8691 (p) REVERT: C 455 TYR cc_start: 0.7384 (m-80) cc_final: 0.6832 (m-80) REVERT: C 521 MET cc_start: 0.5286 (OUTLIER) cc_final: 0.4536 (mmm) REVERT: A 352 PHE cc_start: 0.6728 (m-10) cc_final: 0.6041 (t80) REVERT: A 402 LEU cc_start: 0.6802 (OUTLIER) cc_final: 0.6533 (tt) REVERT: A 452 SER cc_start: 0.9140 (t) cc_final: 0.8744 (p) REVERT: A 667 ILE cc_start: 0.8316 (mt) cc_final: 0.8090 (mm) outliers start: 17 outliers final: 8 residues processed: 97 average time/residue: 0.9605 time to fit residues: 102.1263 Evaluate side-chains 90 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 80 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain C residue 521 MET Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 419 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 74 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 40 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 102 optimal weight: 20.0000 chunk 39 optimal weight: 0.9990 chunk 84 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 658 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.129753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.094086 restraints weight = 17117.642| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 2.30 r_work: 0.3322 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.8389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9096 Z= 0.162 Angle : 0.628 11.616 12362 Z= 0.305 Chirality : 0.043 0.343 1502 Planarity : 0.004 0.032 1476 Dihedral : 4.171 21.826 1222 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 1.63 % Allowed : 11.89 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 2.78 (0.25), residues: 1110 helix: 2.13 (0.17), residues: 898 sheet: None (None), residues: 0 loop : 0.75 (0.45), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 460 HIS 0.004 0.001 HIS A 716 PHE 0.021 0.001 PHE C 221 TYR 0.016 0.001 TYR C 451 ARG 0.001 0.000 ARG C 235 Details of bonding type rmsd link_NAG-ASN : bond 0.00321 ( 2) link_NAG-ASN : angle 1.28917 ( 6) hydrogen bonds : bond 0.04546 ( 732) hydrogen bonds : angle 4.56173 ( 2160) covalent geometry : bond 0.00374 ( 9094) covalent geometry : angle 0.62726 (12356) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 82 time to evaluate : 1.060 Fit side-chains REVERT: C 211 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8725 (mm) REVERT: C 297 MET cc_start: 0.8739 (mmt) cc_final: 0.8467 (mmt) REVERT: C 352 PHE cc_start: 0.6751 (m-10) cc_final: 0.5991 (t80) REVERT: C 409 GLN cc_start: 0.8521 (tp40) cc_final: 0.8304 (tt0) REVERT: C 452 SER cc_start: 0.9141 (t) cc_final: 0.8708 (p) REVERT: C 455 TYR cc_start: 0.7306 (m-80) cc_final: 0.6810 (m-80) REVERT: C 521 MET cc_start: 0.5285 (OUTLIER) cc_final: 0.4764 (mmm) REVERT: A 211 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8705 (mm) REVERT: A 234 ASP cc_start: 0.8292 (m-30) cc_final: 0.7846 (t0) REVERT: A 352 PHE cc_start: 0.6720 (m-10) cc_final: 0.5972 (t80) REVERT: A 402 LEU cc_start: 0.6818 (OUTLIER) cc_final: 0.6556 (tt) REVERT: A 452 SER cc_start: 0.9155 (t) cc_final: 0.8768 (p) outliers start: 16 outliers final: 9 residues processed: 91 average time/residue: 0.9514 time to fit residues: 94.8072 Evaluate side-chains 92 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 79 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain C residue 521 MET Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 673 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 54 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 72 optimal weight: 0.3980 chunk 50 optimal weight: 10.0000 chunk 74 optimal weight: 0.5980 chunk 99 optimal weight: 20.0000 chunk 79 optimal weight: 0.8980 chunk 82 optimal weight: 0.2980 chunk 76 optimal weight: 2.9990 chunk 96 optimal weight: 8.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.130941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.095617 restraints weight = 17005.528| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 2.30 r_work: 0.3346 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.8502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9096 Z= 0.143 Angle : 0.626 11.505 12362 Z= 0.302 Chirality : 0.042 0.340 1502 Planarity : 0.004 0.033 1476 Dihedral : 4.133 21.159 1222 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 1.42 % Allowed : 12.30 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 2.80 (0.25), residues: 1110 helix: 2.16 (0.17), residues: 900 sheet: None (None), residues: 0 loop : 0.64 (0.45), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 460 HIS 0.004 0.001 HIS A 716 PHE 0.019 0.001 PHE A 221 TYR 0.022 0.001 TYR C 407 ARG 0.002 0.000 ARG C 235 Details of bonding type rmsd link_NAG-ASN : bond 0.00342 ( 2) link_NAG-ASN : angle 1.37120 ( 6) hydrogen bonds : bond 0.04392 ( 732) hydrogen bonds : angle 4.50199 ( 2160) covalent geometry : bond 0.00322 ( 9094) covalent geometry : angle 0.62550 (12356) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7086.26 seconds wall clock time: 122 minutes 35.32 seconds (7355.32 seconds total)