Starting phenix.real_space_refine on Sun May 11 18:27:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jez_36204/05_2025/8jez_36204_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jez_36204/05_2025/8jez_36204.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jez_36204/05_2025/8jez_36204.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jez_36204/05_2025/8jez_36204.map" model { file = "/net/cci-nas-00/data/ceres_data/8jez_36204/05_2025/8jez_36204_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jez_36204/05_2025/8jez_36204_neut.cif" } resolution = 2.6 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 ------------------------------------------------------------------------------- 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= 0.013 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 58 5.16 5 C 5508 2.51 5 N 1248 2.21 5 O 1466 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 8282 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 3883 Classifications: {'peptide': 513} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 479} Chain breaks: 2 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 230 Unusual residues: {'AV0': 2, 'CLR': 2, 'LBN': 1, 'PLM': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PLM:plan-1': 1, 'LBN:plan-3': 1} Unresolved non-hydrogen planarities: 4 Restraints were copied for chains: C, D Time building chain proxies: 7.81, per 1000 atoms: 0.94 Number of scatterers: 8282 At special positions: 0 Unit cell: (76.692, 108.564, 77.688, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 58 16.00 P 2 15.00 O 1466 8.00 N 1248 7.00 C 5508 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 Atom "HETATM 8036 O5 NAG D 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3895 O5 NAG B 1 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG B 1 " - " ASN A 144 " " NAG D 1 " - " ASN C 144 " Time building additional restraints: 2.57 Conformation dependent library (CDL) restraints added in 1.0 seconds 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1856 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 2 sheets defined 74.7% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'A' and resid 40 through 70 removed outlier: 3.914A pdb=" N SER A 57 " --> pdb=" O LEU A 53 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N GLY A 58 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA A 61 " --> pdb=" O SER A 57 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N VAL A 62 " --> pdb=" O GLY A 58 " (cutoff:3.500A) Proline residue: A 63 - end of helix Processing helix chain 'A' and resid 75 through 101 Processing helix chain 'A' and resid 111 through 113 No H-bonds generated for 'chain 'A' and resid 111 through 113' Processing helix chain 'A' and resid 114 through 123 Processing helix chain 'A' and resid 124 through 128 Processing helix chain 'A' and resid 131 through 136 Processing helix chain 'A' and resid 145 through 173 Proline residue: A 151 - end of helix removed outlier: 3.543A pdb=" N VAL A 166 " --> pdb=" O VAL A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 181 removed outlier: 3.851A pdb=" N ASN A 181 " --> pdb=" O GLY A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 198 Proline residue: A 190 - end of helix Processing helix chain 'A' and resid 199 through 208 Processing helix chain 'A' and resid 210 through 227 Processing helix chain 'A' and resid 250 through 255 removed outlier: 3.621A pdb=" N MET A 254 " --> pdb=" O GLN A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 274 Processing helix chain 'A' and resid 285 through 289 Processing helix chain 'A' and resid 317 through 346 removed outlier: 4.202A pdb=" N SER A 326 " --> pdb=" O LEU A 322 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ALA A 327 " --> pdb=" O GLY A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 374 Processing helix chain 'A' and resid 382 through 393 Processing helix chain 'A' and resid 396 through 413 removed outlier: 3.783A pdb=" N VAL A 400 " --> pdb=" O SER A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 422 Processing helix chain 'A' and resid 424 through 445 removed outlier: 3.631A pdb=" N THR A 434 " --> pdb=" O GLY A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 449 Processing helix chain 'A' and resid 454 through 478 Proline residue: A 472 - end of helix Processing helix chain 'A' and resid 486 through 498 Processing helix chain 'A' and resid 499 through 515 Processing helix chain 'A' and resid 541 through 545 Processing helix chain 'A' and resid 549 through 554 Processing helix chain 'A' and resid 556 through 561 removed outlier: 3.508A pdb=" N LYS A 560 " --> pdb=" O THR A 557 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 70 removed outlier: 3.914A pdb=" N SER C 57 " --> pdb=" O LEU C 53 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N GLY C 58 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA C 61 " --> pdb=" O SER C 57 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N VAL C 62 " --> pdb=" O GLY C 58 " (cutoff:3.500A) Proline residue: C 63 - end of helix Processing helix chain 'C' and resid 75 through 101 Processing helix chain 'C' and resid 111 through 113 No H-bonds generated for 'chain 'C' and resid 111 through 113' Processing helix chain 'C' and resid 114 through 123 Processing helix chain 'C' and resid 124 through 128 Processing helix chain 'C' and resid 131 through 136 Processing helix chain 'C' and resid 145 through 173 Proline residue: C 151 - end of helix removed outlier: 3.543A pdb=" N VAL C 166 " --> pdb=" O VAL C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 181 removed outlier: 3.851A pdb=" N ASN C 181 " --> pdb=" O GLY C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 198 Proline residue: C 190 - end of helix Processing helix chain 'C' and resid 199 through 208 Processing helix chain 'C' and resid 210 through 227 Processing helix chain 'C' and resid 250 through 255 removed outlier: 3.621A pdb=" N MET C 254 " --> pdb=" O GLN C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 274 Processing helix chain 'C' and resid 285 through 289 Processing helix chain 'C' and resid 317 through 346 removed outlier: 4.202A pdb=" N SER C 326 " --> pdb=" O LEU C 322 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ALA C 327 " --> pdb=" O GLY C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 374 Processing helix chain 'C' and resid 382 through 393 Processing helix chain 'C' and resid 396 through 413 removed outlier: 3.783A pdb=" N VAL C 400 " --> pdb=" O SER C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 422 Processing helix chain 'C' and resid 424 through 445 removed outlier: 3.631A pdb=" N THR C 434 " --> pdb=" O GLY C 430 " (cutoff:3.500A) Processing helix chain 'C' and resid 446 through 449 Processing helix chain 'C' and resid 454 through 478 Proline residue: C 472 - end of helix Processing helix chain 'C' and resid 486 through 498 Processing helix chain 'C' and resid 499 through 515 Processing helix chain 'C' and resid 541 through 545 Processing helix chain 'C' and resid 549 through 554 Processing helix chain 'C' and resid 556 through 561 removed outlier: 3.508A pdb=" N LYS C 560 " --> pdb=" O THR C 557 " (cutoff:3.500A) Processing sheet with id=1, first strand: chain 'A' and resid 108 through 109 Processing sheet with id=2, first strand: chain 'C' and resid 108 through 109 518 hydrogen bonds defined for protein. 1494 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.21 Time building geometry restraints manager: 2.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1198 1.30 - 1.44: 2218 1.44 - 1.57: 4984 1.57 - 1.71: 8 1.71 - 1.85: 88 Bond restraints: 8496 Sorted by residual: bond pdb=" C MET A 161 " pdb=" O MET A 161 " ideal model delta sigma weight residual 1.236 1.312 -0.076 1.15e-02 7.56e+03 4.31e+01 bond pdb=" C MET C 161 " pdb=" O MET C 161 " ideal model delta sigma weight residual 1.236 1.312 -0.076 1.15e-02 7.56e+03 4.31e+01 bond pdb=" C VAL A 169 " pdb=" O VAL A 169 " ideal model delta sigma weight residual 1.237 1.166 0.071 1.17e-02 7.31e+03 3.65e+01 bond pdb=" C VAL C 169 " pdb=" O VAL C 169 " ideal model delta sigma weight residual 1.237 1.166 0.071 1.17e-02 7.31e+03 3.65e+01 bond pdb=" C LEU A 329 " pdb=" O LEU A 329 " ideal model delta sigma weight residual 1.237 1.300 -0.063 1.19e-02 7.06e+03 2.80e+01 ... (remaining 8491 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.77: 10164 2.77 - 5.53: 1394 5.53 - 8.30: 38 8.30 - 11.07: 2 11.07 - 13.83: 2 Bond angle restraints: 11600 Sorted by residual: angle pdb=" CA VAL C 353 " pdb=" C VAL C 353 " pdb=" O VAL C 353 " ideal model delta sigma weight residual 121.05 114.79 6.26 1.04e+00 9.25e-01 3.63e+01 angle pdb=" CA VAL A 353 " pdb=" C VAL A 353 " pdb=" O VAL A 353 " ideal model delta sigma weight residual 121.05 114.79 6.26 1.04e+00 9.25e-01 3.63e+01 angle pdb=" N LEU A 524 " pdb=" CA LEU A 524 " pdb=" C LEU A 524 " ideal model delta sigma weight residual 111.82 105.25 6.57 1.16e+00 7.43e-01 3.21e+01 angle pdb=" N LEU C 524 " pdb=" CA LEU C 524 " pdb=" C LEU C 524 " ideal model delta sigma weight residual 111.82 105.25 6.57 1.16e+00 7.43e-01 3.21e+01 angle pdb=" N VAL C 276 " pdb=" CA VAL C 276 " pdb=" C VAL C 276 " ideal model delta sigma weight residual 111.00 104.90 6.10 1.09e+00 8.42e-01 3.13e+01 ... (remaining 11595 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.34: 5312 29.34 - 58.69: 144 58.69 - 88.03: 28 88.03 - 117.37: 18 117.37 - 146.72: 10 Dihedral angle restraints: 5512 sinusoidal: 2606 harmonic: 2906 Sorted by residual: dihedral pdb=" C1 LBN A 602 " pdb=" O1 LBN A 602 " pdb=" P1 LBN A 602 " pdb=" O3 LBN A 602 " ideal model delta sinusoidal sigma weight residual -84.60 62.12 -146.72 1 3.00e+01 1.11e-03 1.96e+01 dihedral pdb=" C1 LBN C 602 " pdb=" O1 LBN C 602 " pdb=" P1 LBN C 602 " pdb=" O3 LBN C 602 " ideal model delta sinusoidal sigma weight residual -84.60 62.12 -146.72 1 3.00e+01 1.11e-03 1.96e+01 dihedral pdb=" CCD AV0 A 603 " pdb=" CCS AV0 A 603 " pdb=" OBZ AV0 A 603 " pdb=" OCB AV0 A 603 " ideal model delta sinusoidal sigma weight residual 298.59 166.03 132.56 1 3.00e+01 1.11e-03 1.79e+01 ... (remaining 5509 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.183: 1372 0.183 - 0.365: 58 0.365 - 0.547: 0 0.547 - 0.730: 0 0.730 - 0.912: 2 Chirality restraints: 1432 Sorted by residual: chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -3.31 0.91 2.00e-02 2.50e+03 2.08e+03 chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -3.31 0.91 2.00e-02 2.50e+03 2.08e+03 chirality pdb=" CG LEU A 106 " pdb=" CB LEU A 106 " pdb=" CD1 LEU A 106 " pdb=" CD2 LEU A 106 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.70e+00 ... (remaining 1429 not shown) Planarity restraints: 1356 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 2 " -0.358 2.00e-02 2.50e+03 3.09e-01 1.19e+03 pdb=" C7 NAG B 2 " 0.117 2.00e-02 2.50e+03 pdb=" C8 NAG B 2 " -0.096 2.00e-02 2.50e+03 pdb=" N2 NAG B 2 " 0.536 2.00e-02 2.50e+03 pdb=" O7 NAG B 2 " -0.198 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 2 " -0.358 2.00e-02 2.50e+03 3.09e-01 1.19e+03 pdb=" C7 NAG D 2 " 0.117 2.00e-02 2.50e+03 pdb=" C8 NAG D 2 " -0.096 2.00e-02 2.50e+03 pdb=" N2 NAG D 2 " 0.536 2.00e-02 2.50e+03 pdb=" O7 NAG D 2 " -0.198 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 1 " 0.330 2.00e-02 2.50e+03 2.87e-01 1.03e+03 pdb=" C7 NAG B 1 " -0.105 2.00e-02 2.50e+03 pdb=" C8 NAG B 1 " 0.057 2.00e-02 2.50e+03 pdb=" N2 NAG B 1 " -0.494 2.00e-02 2.50e+03 pdb=" O7 NAG B 1 " 0.211 2.00e-02 2.50e+03 ... (remaining 1353 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 2006 2.84 - 3.35: 8852 3.35 - 3.87: 14738 3.87 - 4.38: 17431 4.38 - 4.90: 28567 Nonbonded interactions: 71594 Sorted by model distance: nonbonded pdb=" O ILE C 160 " pdb=" OG SER C 164 " model vdw 2.325 3.040 nonbonded pdb=" O ILE A 160 " pdb=" OG SER A 164 " model vdw 2.325 3.040 nonbonded pdb=" O ILE A 510 " pdb=" OG1 THR A 514 " model vdw 2.373 3.040 nonbonded pdb=" O ILE C 510 " pdb=" OG1 THR C 514 " model vdw 2.373 3.040 nonbonded pdb=" O VAL C 460 " pdb=" OG SER C 464 " model vdw 2.445 3.040 ... (remaining 71589 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 24.390 Find NCS groups from input model: 0.150 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:11.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 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 : 0.016 0.275 8500 Z= 1.145 Angle : 1.889 35.290 11612 Z= 1.314 Chirality : 0.096 0.912 1432 Planarity : 0.020 0.309 1354 Dihedral : 17.037 146.716 3656 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.48 % Allowed : 4.76 % Favored : 94.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.01 (0.25), residues: 1014 helix: 0.18 (0.18), residues: 674 sheet: -3.79 (1.03), residues: 20 loop : 0.23 (0.37), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.010 TRP A 127 HIS 0.012 0.006 HIS C 147 PHE 0.049 0.010 PHE A 502 TYR 0.039 0.010 TYR C 227 ARG 0.023 0.003 ARG C 344 Details of bonding type rmsd link_NAG-ASN : bond 0.09566 ( 2) link_NAG-ASN : angle 22.85647 ( 6) link_BETA1-4 : bond 0.27457 ( 2) link_BETA1-4 : angle 14.66948 ( 6) hydrogen bonds : bond 0.18386 ( 518) hydrogen bonds : angle 6.82562 ( 1494) covalent geometry : bond 0.01573 ( 8496) covalent geometry : angle 1.78592 (11600) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 146 time to evaluate : 0.749 Fit side-chains REVERT: A 181 ASN cc_start: 0.8570 (m-40) cc_final: 0.8348 (m-40) REVERT: A 229 ARG cc_start: 0.7455 (ptm160) cc_final: 0.5998 (ptt-90) REVERT: A 325 PHE cc_start: 0.7778 (t80) cc_final: 0.7576 (t80) REVERT: A 381 SER cc_start: 0.8560 (OUTLIER) cc_final: 0.8081 (p) REVERT: A 393 LYS cc_start: 0.7428 (mmtp) cc_final: 0.7115 (mptt) REVERT: A 465 MET cc_start: 0.8754 (mtp) cc_final: 0.8539 (mtm) REVERT: A 488 GLU cc_start: 0.6727 (tt0) cc_final: 0.5627 (mp0) REVERT: A 545 ASP cc_start: 0.7131 (m-30) cc_final: 0.6911 (m-30) REVERT: A 552 ILE cc_start: 0.5865 (mm) cc_final: 0.5595 (mp) REVERT: A 561 TYR cc_start: 0.5500 (m-80) cc_final: 0.5104 (m-80) REVERT: A 565 CYS cc_start: 0.6931 (m) cc_final: 0.6133 (t) REVERT: C 181 ASN cc_start: 0.8571 (m-40) cc_final: 0.8349 (m-40) REVERT: C 229 ARG cc_start: 0.7453 (ptm160) cc_final: 0.5999 (ptt-90) REVERT: C 325 PHE cc_start: 0.7782 (t80) cc_final: 0.7581 (t80) REVERT: C 381 SER cc_start: 0.8562 (OUTLIER) cc_final: 0.8082 (p) REVERT: C 393 LYS cc_start: 0.7426 (mmtp) cc_final: 0.7114 (mptt) REVERT: C 465 MET cc_start: 0.8754 (mtp) cc_final: 0.8538 (mtm) REVERT: C 488 GLU cc_start: 0.6726 (tt0) cc_final: 0.5625 (mp0) REVERT: C 545 ASP cc_start: 0.7133 (m-30) cc_final: 0.6912 (m-30) REVERT: C 552 ILE cc_start: 0.5870 (mm) cc_final: 0.5599 (mp) REVERT: C 561 TYR cc_start: 0.5501 (m-80) cc_final: 0.5102 (m-80) REVERT: C 565 CYS cc_start: 0.6931 (m) cc_final: 0.6132 (t) outliers start: 4 outliers final: 0 residues processed: 150 average time/residue: 1.0683 time to fit residues: 171.7288 Evaluate side-chains 128 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 126 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain C residue 381 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 6.9990 chunk 77 optimal weight: 0.4980 chunk 42 optimal weight: 5.9990 chunk 26 optimal weight: 0.0270 chunk 52 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 79 optimal weight: 6.9990 chunk 30 optimal weight: 6.9990 chunk 48 optimal weight: 10.0000 chunk 59 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 overall best weight: 1.5044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN A 181 ASN A 287 GLN C 76 GLN C 181 ASN C 287 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.144445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.120821 restraints weight = 8664.491| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 1.34 r_work: 0.3208 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8500 Z= 0.145 Angle : 0.668 6.933 11612 Z= 0.322 Chirality : 0.045 0.249 1432 Planarity : 0.005 0.034 1354 Dihedral : 15.144 130.458 1954 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.67 % Allowed : 9.76 % Favored : 88.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.89 (0.26), residues: 1014 helix: 1.54 (0.19), residues: 694 sheet: None (None), residues: 0 loop : 0.82 (0.38), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 41 HIS 0.002 0.001 HIS C 354 PHE 0.015 0.002 PHE A 361 TYR 0.009 0.001 TYR A 402 ARG 0.007 0.001 ARG A 555 Details of bonding type rmsd link_NAG-ASN : bond 0.00047 ( 2) link_NAG-ASN : angle 4.40410 ( 6) link_BETA1-4 : bond 0.00537 ( 2) link_BETA1-4 : angle 1.82407 ( 6) hydrogen bonds : bond 0.05530 ( 518) hydrogen bonds : angle 4.83343 ( 1494) covalent geometry : bond 0.00305 ( 8496) covalent geometry : angle 0.65995 (11600) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 138 time to evaluate : 0.819 Fit side-chains REVERT: A 32 LEU cc_start: 0.7394 (OUTLIER) cc_final: 0.7058 (tp) REVERT: A 251 ILE cc_start: 0.7147 (tt) cc_final: 0.6615 (tp) REVERT: A 255 PHE cc_start: 0.7927 (OUTLIER) cc_final: 0.7537 (p90) REVERT: A 262 MET cc_start: 0.7967 (mmm) cc_final: 0.7455 (mpt) REVERT: A 269 TYR cc_start: 0.7866 (t80) cc_final: 0.7641 (t80) REVERT: A 488 GLU cc_start: 0.7543 (tt0) cc_final: 0.6680 (mp0) REVERT: A 545 ASP cc_start: 0.7502 (m-30) cc_final: 0.7221 (m-30) REVERT: A 555 ARG cc_start: 0.7036 (mtm110) cc_final: 0.6117 (mtm180) REVERT: A 561 TYR cc_start: 0.5477 (m-80) cc_final: 0.5029 (m-80) REVERT: C 32 LEU cc_start: 0.7394 (OUTLIER) cc_final: 0.7066 (tp) REVERT: C 251 ILE cc_start: 0.7155 (tt) cc_final: 0.6622 (tp) REVERT: C 255 PHE cc_start: 0.7924 (OUTLIER) cc_final: 0.7529 (p90) REVERT: C 262 MET cc_start: 0.7960 (mmm) cc_final: 0.7450 (mpt) REVERT: C 269 TYR cc_start: 0.7862 (t80) cc_final: 0.7637 (t80) REVERT: C 488 GLU cc_start: 0.7533 (tt0) cc_final: 0.6670 (mp0) REVERT: C 545 ASP cc_start: 0.7513 (m-30) cc_final: 0.7241 (m-30) REVERT: C 555 ARG cc_start: 0.7028 (mtm110) cc_final: 0.6108 (mtm180) REVERT: C 561 TYR cc_start: 0.5490 (m-80) cc_final: 0.5038 (m-80) outliers start: 14 outliers final: 2 residues processed: 142 average time/residue: 1.0520 time to fit residues: 159.8514 Evaluate side-chains 126 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 120 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 255 PHE Chi-restraints excluded: chain C residue 567 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 96 optimal weight: 2.9990 chunk 66 optimal weight: 8.9990 chunk 89 optimal weight: 0.8980 chunk 47 optimal weight: 9.9990 chunk 62 optimal weight: 6.9990 chunk 98 optimal weight: 0.1980 chunk 93 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 chunk 95 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 97 optimal weight: 5.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 GLN C 287 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.145320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.122937 restraints weight = 8852.899| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 1.29 r_work: 0.3242 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8500 Z= 0.141 Angle : 0.626 7.475 11612 Z= 0.301 Chirality : 0.045 0.380 1432 Planarity : 0.005 0.039 1354 Dihedral : 13.860 128.354 1952 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.81 % Allowed : 9.76 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 2.23 (0.26), residues: 1014 helix: 1.77 (0.19), residues: 694 sheet: None (None), residues: 0 loop : 1.04 (0.38), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 149 HIS 0.002 0.001 HIS A 354 PHE 0.017 0.002 PHE A 325 TYR 0.009 0.002 TYR A 307 ARG 0.005 0.001 ARG A 126 Details of bonding type rmsd link_NAG-ASN : bond 0.00159 ( 2) link_NAG-ASN : angle 3.43702 ( 6) link_BETA1-4 : bond 0.00564 ( 2) link_BETA1-4 : angle 1.67804 ( 6) hydrogen bonds : bond 0.05257 ( 518) hydrogen bonds : angle 4.64932 ( 1494) covalent geometry : bond 0.00304 ( 8496) covalent geometry : angle 0.62037 (11600) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 134 time to evaluate : 0.809 Fit side-chains REVERT: A 32 LEU cc_start: 0.7454 (OUTLIER) cc_final: 0.7155 (tp) REVERT: A 262 MET cc_start: 0.8032 (mmm) cc_final: 0.7486 (mpt) REVERT: A 488 GLU cc_start: 0.7675 (tt0) cc_final: 0.6703 (mp0) REVERT: A 550 MET cc_start: 0.7311 (tpt) cc_final: 0.6775 (mmt) REVERT: A 561 TYR cc_start: 0.5538 (m-80) cc_final: 0.5067 (m-80) REVERT: C 32 LEU cc_start: 0.7454 (OUTLIER) cc_final: 0.7156 (tp) REVERT: C 262 MET cc_start: 0.8024 (mmm) cc_final: 0.7473 (mpt) REVERT: C 488 GLU cc_start: 0.7673 (tt0) cc_final: 0.6695 (mp0) REVERT: C 550 MET cc_start: 0.7317 (tpt) cc_final: 0.6782 (mmt) REVERT: C 561 TYR cc_start: 0.5557 (m-80) cc_final: 0.5086 (m-80) outliers start: 32 outliers final: 24 residues processed: 144 average time/residue: 0.9313 time to fit residues: 144.6294 Evaluate side-chains 152 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 126 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 275 ASP Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 255 PHE Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 275 ASP Chi-restraints excluded: chain C residue 381 SER Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 465 MET Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 567 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 39 optimal weight: 9.9990 chunk 94 optimal weight: 9.9990 chunk 52 optimal weight: 9.9990 chunk 33 optimal weight: 10.0000 chunk 38 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 chunk 96 optimal weight: 6.9990 chunk 40 optimal weight: 0.8980 chunk 59 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN A 287 GLN C 50 GLN C 287 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.140460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.117560 restraints weight = 8863.598| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 1.35 r_work: 0.3159 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 8500 Z= 0.193 Angle : 0.695 7.502 11612 Z= 0.335 Chirality : 0.048 0.373 1432 Planarity : 0.005 0.046 1354 Dihedral : 13.921 133.788 1952 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 3.81 % Allowed : 10.95 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.66 (0.26), residues: 1014 helix: 1.38 (0.19), residues: 704 sheet: None (None), residues: 0 loop : 0.70 (0.38), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP C 149 HIS 0.002 0.001 HIS A 147 PHE 0.019 0.002 PHE C 325 TYR 0.013 0.002 TYR A 307 ARG 0.007 0.001 ARG A 555 Details of bonding type rmsd link_NAG-ASN : bond 0.00219 ( 2) link_NAG-ASN : angle 2.81496 ( 6) link_BETA1-4 : bond 0.00256 ( 2) link_BETA1-4 : angle 1.40403 ( 6) hydrogen bonds : bond 0.06135 ( 518) hydrogen bonds : angle 4.86217 ( 1494) covalent geometry : bond 0.00454 ( 8496) covalent geometry : angle 0.69126 (11600) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 116 time to evaluate : 0.922 Fit side-chains REVERT: A 250 GLN cc_start: 0.7294 (OUTLIER) cc_final: 0.6994 (mm-40) REVERT: A 255 PHE cc_start: 0.7906 (OUTLIER) cc_final: 0.6395 (p90) REVERT: A 262 MET cc_start: 0.8149 (mmm) cc_final: 0.7547 (mpt) REVERT: A 488 GLU cc_start: 0.7554 (tt0) cc_final: 0.6669 (mp0) REVERT: A 490 ASP cc_start: 0.8086 (m-30) cc_final: 0.7612 (m-30) REVERT: A 555 ARG cc_start: 0.7039 (mtm110) cc_final: 0.5981 (mtm180) REVERT: C 250 GLN cc_start: 0.7298 (OUTLIER) cc_final: 0.6992 (mm-40) REVERT: C 255 PHE cc_start: 0.7907 (OUTLIER) cc_final: 0.6389 (p90) REVERT: C 262 MET cc_start: 0.8139 (mmm) cc_final: 0.7535 (mpt) REVERT: C 488 GLU cc_start: 0.7555 (tt0) cc_final: 0.6673 (mp0) REVERT: C 490 ASP cc_start: 0.8092 (m-30) cc_final: 0.7627 (m-30) REVERT: C 555 ARG cc_start: 0.7028 (mtm110) cc_final: 0.5975 (mtm180) outliers start: 32 outliers final: 16 residues processed: 128 average time/residue: 1.1039 time to fit residues: 151.1448 Evaluate side-chains 124 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 104 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 250 GLN Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 250 GLN Chi-restraints excluded: chain C residue 255 PHE Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 381 SER Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 567 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 79 optimal weight: 5.9990 chunk 93 optimal weight: 6.9990 chunk 8 optimal weight: 0.6980 chunk 69 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 88 optimal weight: 9.9990 chunk 80 optimal weight: 6.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN A 150 HIS A 287 GLN C 50 GLN C 150 HIS C 287 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.144914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.122732 restraints weight = 8702.870| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 1.29 r_work: 0.3232 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8500 Z= 0.138 Angle : 0.606 7.223 11612 Z= 0.293 Chirality : 0.044 0.350 1432 Planarity : 0.005 0.045 1354 Dihedral : 13.283 132.131 1952 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 3.57 % Allowed : 12.14 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 2.00 (0.26), residues: 1014 helix: 1.54 (0.19), residues: 710 sheet: None (None), residues: 0 loop : 1.07 (0.40), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 149 HIS 0.001 0.001 HIS C 354 PHE 0.014 0.002 PHE C 361 TYR 0.009 0.001 TYR C 42 ARG 0.005 0.001 ARG A 126 Details of bonding type rmsd link_NAG-ASN : bond 0.00098 ( 2) link_NAG-ASN : angle 2.28865 ( 6) link_BETA1-4 : bond 0.00360 ( 2) link_BETA1-4 : angle 1.25392 ( 6) hydrogen bonds : bond 0.05066 ( 518) hydrogen bonds : angle 4.61423 ( 1494) covalent geometry : bond 0.00306 ( 8496) covalent geometry : angle 0.60305 (11600) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 112 time to evaluate : 0.840 Fit side-chains REVERT: A 250 GLN cc_start: 0.7224 (OUTLIER) cc_final: 0.6973 (mm-40) REVERT: A 262 MET cc_start: 0.8031 (mmm) cc_final: 0.7480 (mpt) REVERT: A 488 GLU cc_start: 0.7590 (tt0) cc_final: 0.6718 (mp0) REVERT: A 550 MET cc_start: 0.7279 (tpt) cc_final: 0.6829 (mmt) REVERT: A 554 LYS cc_start: 0.6274 (mtpt) cc_final: 0.6025 (mttt) REVERT: C 250 GLN cc_start: 0.7222 (OUTLIER) cc_final: 0.6969 (mm-40) REVERT: C 262 MET cc_start: 0.8036 (mmm) cc_final: 0.7483 (mpt) REVERT: C 488 GLU cc_start: 0.7593 (tt0) cc_final: 0.6710 (mp0) REVERT: C 550 MET cc_start: 0.7297 (tpt) cc_final: 0.6855 (mmt) REVERT: C 554 LYS cc_start: 0.6280 (mtpt) cc_final: 0.6032 (mttt) outliers start: 30 outliers final: 18 residues processed: 126 average time/residue: 1.0450 time to fit residues: 141.1502 Evaluate side-chains 128 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 108 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 250 GLN Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 275 ASP Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 250 GLN Chi-restraints excluded: chain C residue 255 PHE Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 275 ASP Chi-restraints excluded: chain C residue 381 SER Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 567 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 17 optimal weight: 8.9990 chunk 74 optimal weight: 9.9990 chunk 13 optimal weight: 10.0000 chunk 68 optimal weight: 9.9990 chunk 62 optimal weight: 7.9990 chunk 29 optimal weight: 9.9990 chunk 37 optimal weight: 9.9990 chunk 36 optimal weight: 5.9990 chunk 63 optimal weight: 0.7980 chunk 26 optimal weight: 0.0970 chunk 80 optimal weight: 9.9990 overall best weight: 4.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN A 76 GLN A 287 GLN C 50 GLN C 76 GLN C 150 HIS C 287 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.139820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.116701 restraints weight = 8732.944| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 1.37 r_work: 0.3142 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 8500 Z= 0.212 Angle : 0.709 8.046 11612 Z= 0.344 Chirality : 0.048 0.327 1432 Planarity : 0.006 0.050 1354 Dihedral : 13.609 138.377 1952 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 3.33 % Allowed : 12.50 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.55 (0.26), residues: 1014 helix: 1.28 (0.19), residues: 696 sheet: None (None), residues: 0 loop : 0.70 (0.39), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP C 527 HIS 0.002 0.001 HIS A 354 PHE 0.017 0.002 PHE C 459 TYR 0.013 0.002 TYR C 307 ARG 0.010 0.001 ARG A 555 Details of bonding type rmsd link_NAG-ASN : bond 0.00350 ( 2) link_NAG-ASN : angle 2.65075 ( 6) link_BETA1-4 : bond 0.00181 ( 2) link_BETA1-4 : angle 1.31391 ( 6) hydrogen bonds : bond 0.06302 ( 518) hydrogen bonds : angle 4.88763 ( 1494) covalent geometry : bond 0.00502 ( 8496) covalent geometry : angle 0.70636 (11600) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 110 time to evaluate : 0.809 Fit side-chains REVERT: A 32 LEU cc_start: 0.7500 (OUTLIER) cc_final: 0.7132 (tp) REVERT: A 250 GLN cc_start: 0.7295 (OUTLIER) cc_final: 0.6966 (mm-40) REVERT: A 255 PHE cc_start: 0.7887 (OUTLIER) cc_final: 0.6417 (p90) REVERT: A 262 MET cc_start: 0.8188 (mmm) cc_final: 0.7567 (mpt) REVERT: A 407 MET cc_start: 0.8559 (tpt) cc_final: 0.8226 (tpp) REVERT: A 488 GLU cc_start: 0.7526 (tt0) cc_final: 0.6672 (mp0) REVERT: A 555 ARG cc_start: 0.7032 (mtm110) cc_final: 0.5984 (mtm180) REVERT: C 32 LEU cc_start: 0.7485 (OUTLIER) cc_final: 0.7115 (tp) REVERT: C 250 GLN cc_start: 0.7295 (OUTLIER) cc_final: 0.6967 (mm-40) REVERT: C 255 PHE cc_start: 0.7883 (OUTLIER) cc_final: 0.6409 (p90) REVERT: C 262 MET cc_start: 0.8181 (mmm) cc_final: 0.7556 (mpt) REVERT: C 407 MET cc_start: 0.8545 (tpt) cc_final: 0.8210 (tpp) REVERT: C 488 GLU cc_start: 0.7535 (tt0) cc_final: 0.6676 (mp0) REVERT: C 555 ARG cc_start: 0.7026 (mtm110) cc_final: 0.5979 (mtm180) outliers start: 28 outliers final: 15 residues processed: 128 average time/residue: 1.0561 time to fit residues: 144.6083 Evaluate side-chains 119 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 98 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 250 GLN Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 250 GLN Chi-restraints excluded: chain C residue 255 PHE Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 381 SER Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 567 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 2 optimal weight: 8.9990 chunk 85 optimal weight: 8.9990 chunk 43 optimal weight: 5.9990 chunk 24 optimal weight: 0.0470 chunk 82 optimal weight: 1.9990 chunk 101 optimal weight: 7.9990 chunk 28 optimal weight: 2.9990 chunk 88 optimal weight: 0.0670 chunk 54 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 70 optimal weight: 8.9990 overall best weight: 1.4222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN A 150 HIS A 287 GLN C 50 GLN C 150 HIS C 287 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.145625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.123632 restraints weight = 8780.339| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 1.30 r_work: 0.3246 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8500 Z= 0.128 Angle : 0.583 7.441 11612 Z= 0.286 Chirality : 0.042 0.263 1432 Planarity : 0.005 0.044 1354 Dihedral : 12.917 135.132 1952 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.86 % Allowed : 13.57 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 2.10 (0.27), residues: 1014 helix: 1.59 (0.19), residues: 706 sheet: None (None), residues: 0 loop : 1.18 (0.40), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 149 HIS 0.002 0.000 HIS A 354 PHE 0.015 0.002 PHE A 361 TYR 0.008 0.001 TYR C 42 ARG 0.007 0.001 ARG C 555 Details of bonding type rmsd link_NAG-ASN : bond 0.00228 ( 2) link_NAG-ASN : angle 1.93367 ( 6) link_BETA1-4 : bond 0.00390 ( 2) link_BETA1-4 : angle 0.99576 ( 6) hydrogen bonds : bond 0.04826 ( 518) hydrogen bonds : angle 4.54606 ( 1494) covalent geometry : bond 0.00274 ( 8496) covalent geometry : angle 0.58128 (11600) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 122 time to evaluate : 0.862 Fit side-chains REVERT: A 250 GLN cc_start: 0.7316 (OUTLIER) cc_final: 0.7081 (mm-40) REVERT: A 255 PHE cc_start: 0.7769 (OUTLIER) cc_final: 0.6178 (p90) REVERT: A 262 MET cc_start: 0.8066 (mmm) cc_final: 0.7491 (mpt) REVERT: A 488 GLU cc_start: 0.7562 (tt0) cc_final: 0.6727 (mp0) REVERT: A 550 MET cc_start: 0.7108 (tpt) cc_final: 0.6807 (mmt) REVERT: A 554 LYS cc_start: 0.6263 (mtpt) cc_final: 0.6031 (mttt) REVERT: A 555 ARG cc_start: 0.7027 (mtm110) cc_final: 0.6047 (mtm180) REVERT: C 250 GLN cc_start: 0.7301 (OUTLIER) cc_final: 0.7062 (mm-40) REVERT: C 255 PHE cc_start: 0.7766 (OUTLIER) cc_final: 0.6176 (p90) REVERT: C 262 MET cc_start: 0.8077 (mmm) cc_final: 0.7499 (mpt) REVERT: C 488 GLU cc_start: 0.7565 (tt0) cc_final: 0.6724 (mp0) REVERT: C 550 MET cc_start: 0.7116 (tpt) cc_final: 0.6818 (mmt) REVERT: C 554 LYS cc_start: 0.6273 (mtpt) cc_final: 0.6044 (mttt) REVERT: C 555 ARG cc_start: 0.7027 (mtm110) cc_final: 0.6052 (mtm180) outliers start: 24 outliers final: 12 residues processed: 136 average time/residue: 1.1069 time to fit residues: 161.4595 Evaluate side-chains 126 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 110 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 250 GLN Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 275 ASP Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 250 GLN Chi-restraints excluded: chain C residue 255 PHE Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 275 ASP Chi-restraints excluded: chain C residue 381 SER Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 489 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 85 optimal weight: 5.9990 chunk 49 optimal weight: 20.0000 chunk 38 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 47 optimal weight: 0.0570 chunk 30 optimal weight: 3.9990 chunk 5 optimal weight: 8.9990 chunk 50 optimal weight: 5.9990 chunk 1 optimal weight: 9.9990 chunk 91 optimal weight: 6.9990 overall best weight: 1.9704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN A 150 HIS A 287 GLN C 50 GLN C 150 HIS C 287 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.142964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.120288 restraints weight = 8821.964| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 1.37 r_work: 0.3198 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8500 Z= 0.138 Angle : 0.599 7.491 11612 Z= 0.294 Chirality : 0.043 0.235 1432 Planarity : 0.005 0.045 1354 Dihedral : 12.852 138.172 1952 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.98 % Allowed : 14.17 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 2.10 (0.27), residues: 1014 helix: 1.60 (0.19), residues: 708 sheet: None (None), residues: 0 loop : 1.16 (0.40), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 149 HIS 0.002 0.001 HIS A 147 PHE 0.013 0.002 PHE A 361 TYR 0.009 0.002 TYR C 42 ARG 0.007 0.001 ARG A 555 Details of bonding type rmsd link_NAG-ASN : bond 0.00013 ( 2) link_NAG-ASN : angle 2.05604 ( 6) link_BETA1-4 : bond 0.00270 ( 2) link_BETA1-4 : angle 1.05422 ( 6) hydrogen bonds : bond 0.05065 ( 518) hydrogen bonds : angle 4.56695 ( 1494) covalent geometry : bond 0.00303 ( 8496) covalent geometry : angle 0.59650 (11600) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 110 time to evaluate : 0.817 Fit side-chains REVERT: A 250 GLN cc_start: 0.7271 (OUTLIER) cc_final: 0.6772 (mm-40) REVERT: A 255 PHE cc_start: 0.7792 (OUTLIER) cc_final: 0.6236 (p90) REVERT: A 262 MET cc_start: 0.8121 (mmm) cc_final: 0.7551 (mpt) REVERT: A 488 GLU cc_start: 0.7517 (tt0) cc_final: 0.6700 (mp0) REVERT: A 555 ARG cc_start: 0.7039 (mtm110) cc_final: 0.6556 (ptt90) REVERT: C 250 GLN cc_start: 0.7250 (OUTLIER) cc_final: 0.6746 (mm-40) REVERT: C 255 PHE cc_start: 0.7796 (OUTLIER) cc_final: 0.6240 (p90) REVERT: C 262 MET cc_start: 0.8134 (mmm) cc_final: 0.7560 (mpt) REVERT: C 488 GLU cc_start: 0.7512 (tt0) cc_final: 0.6708 (mp0) REVERT: C 555 ARG cc_start: 0.7024 (mtm110) cc_final: 0.6549 (ptt90) outliers start: 25 outliers final: 16 residues processed: 123 average time/residue: 1.1452 time to fit residues: 150.3871 Evaluate side-chains 140 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 120 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 250 GLN Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 275 ASP Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 250 GLN Chi-restraints excluded: chain C residue 255 PHE Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 275 ASP Chi-restraints excluded: chain C residue 381 SER Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 567 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 70 optimal weight: 6.9990 chunk 59 optimal weight: 6.9990 chunk 56 optimal weight: 10.0000 chunk 62 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 73 optimal weight: 9.9990 chunk 101 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 chunk 96 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 chunk 76 optimal weight: 10.0000 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN A 150 HIS A 287 GLN C 50 GLN C 287 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.140889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.118107 restraints weight = 8916.555| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 1.37 r_work: 0.3165 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8500 Z= 0.172 Angle : 0.648 7.945 11612 Z= 0.318 Chirality : 0.045 0.218 1432 Planarity : 0.005 0.046 1354 Dihedral : 13.050 140.665 1952 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.62 % Allowed : 14.76 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.90 (0.26), residues: 1014 helix: 1.51 (0.19), residues: 688 sheet: None (None), residues: 0 loop : 0.96 (0.39), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 149 HIS 0.002 0.001 HIS A 150 PHE 0.015 0.002 PHE C 459 TYR 0.012 0.002 TYR A 340 ARG 0.006 0.001 ARG A 555 Details of bonding type rmsd link_NAG-ASN : bond 0.00160 ( 2) link_NAG-ASN : angle 2.32621 ( 6) link_BETA1-4 : bond 0.00130 ( 2) link_BETA1-4 : angle 1.16943 ( 6) hydrogen bonds : bond 0.05735 ( 518) hydrogen bonds : angle 4.72171 ( 1494) covalent geometry : bond 0.00397 ( 8496) covalent geometry : angle 0.64539 (11600) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 117 time to evaluate : 0.855 Fit side-chains REVERT: A 250 GLN cc_start: 0.7251 (OUTLIER) cc_final: 0.6714 (mm-40) REVERT: A 255 PHE cc_start: 0.7885 (OUTLIER) cc_final: 0.6375 (p90) REVERT: A 262 MET cc_start: 0.8180 (mmm) cc_final: 0.7576 (mpt) REVERT: A 407 MET cc_start: 0.8546 (tpt) cc_final: 0.8219 (tpp) REVERT: A 488 GLU cc_start: 0.7507 (tt0) cc_final: 0.6703 (mp0) REVERT: A 550 MET cc_start: 0.7190 (tpt) cc_final: 0.6828 (mmt) REVERT: A 554 LYS cc_start: 0.6292 (mttt) cc_final: 0.6057 (mttt) REVERT: A 555 ARG cc_start: 0.7037 (mtm110) cc_final: 0.6540 (tmm160) REVERT: C 250 GLN cc_start: 0.7241 (OUTLIER) cc_final: 0.6699 (mm-40) REVERT: C 255 PHE cc_start: 0.7887 (OUTLIER) cc_final: 0.6368 (p90) REVERT: C 262 MET cc_start: 0.8191 (mmm) cc_final: 0.7586 (mpt) REVERT: C 407 MET cc_start: 0.8528 (tpt) cc_final: 0.8198 (tpp) REVERT: C 488 GLU cc_start: 0.7504 (tt0) cc_final: 0.6700 (mp0) REVERT: C 550 MET cc_start: 0.7192 (tpt) cc_final: 0.6823 (mmt) REVERT: C 554 LYS cc_start: 0.6290 (mttt) cc_final: 0.6055 (mttt) REVERT: C 555 ARG cc_start: 0.7030 (mtm110) cc_final: 0.6531 (tmm160) outliers start: 22 outliers final: 16 residues processed: 131 average time/residue: 1.2578 time to fit residues: 175.3145 Evaluate side-chains 126 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 106 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 250 GLN Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 275 ASP Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 250 GLN Chi-restraints excluded: chain C residue 255 PHE Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 275 ASP Chi-restraints excluded: chain C residue 381 SER Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 567 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 27 optimal weight: 7.9990 chunk 47 optimal weight: 0.1980 chunk 87 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 24 optimal weight: 10.0000 chunk 75 optimal weight: 2.9990 chunk 30 optimal weight: 7.9990 chunk 32 optimal weight: 8.9990 chunk 70 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 60 optimal weight: 6.9990 overall best weight: 2.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN A 76 GLN A 287 GLN C 50 GLN C 76 GLN C 287 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.142380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.119554 restraints weight = 8815.636| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.37 r_work: 0.3186 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8500 Z= 0.143 Angle : 0.606 7.634 11612 Z= 0.299 Chirality : 0.043 0.196 1432 Planarity : 0.005 0.044 1354 Dihedral : 12.883 139.247 1952 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.86 % Allowed : 14.52 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.95 (0.26), residues: 1014 helix: 1.49 (0.19), residues: 708 sheet: None (None), residues: 0 loop : 1.09 (0.40), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 149 HIS 0.001 0.001 HIS C 354 PHE 0.013 0.002 PHE A 361 TYR 0.010 0.002 TYR A 402 ARG 0.006 0.001 ARG C 555 Details of bonding type rmsd link_NAG-ASN : bond 0.00057 ( 2) link_NAG-ASN : angle 2.02824 ( 6) link_BETA1-4 : bond 0.00243 ( 2) link_BETA1-4 : angle 1.04059 ( 6) hydrogen bonds : bond 0.05174 ( 518) hydrogen bonds : angle 4.61817 ( 1494) covalent geometry : bond 0.00321 ( 8496) covalent geometry : angle 0.60377 (11600) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 110 time to evaluate : 0.878 Fit side-chains REVERT: A 250 GLN cc_start: 0.7236 (OUTLIER) cc_final: 0.6729 (mm-40) REVERT: A 255 PHE cc_start: 0.7827 (OUTLIER) cc_final: 0.6310 (p90) REVERT: A 262 MET cc_start: 0.8102 (mmm) cc_final: 0.7531 (mpt) REVERT: A 407 MET cc_start: 0.8526 (tpt) cc_final: 0.8191 (tpp) REVERT: A 488 GLU cc_start: 0.7555 (tt0) cc_final: 0.6739 (mp0) REVERT: A 550 MET cc_start: 0.7199 (tpt) cc_final: 0.6848 (mmt) REVERT: A 554 LYS cc_start: 0.6332 (mttt) cc_final: 0.6103 (mttt) REVERT: A 555 ARG cc_start: 0.6999 (mtm110) cc_final: 0.6532 (ptt90) REVERT: C 250 GLN cc_start: 0.7225 (OUTLIER) cc_final: 0.6712 (mm-40) REVERT: C 255 PHE cc_start: 0.7831 (OUTLIER) cc_final: 0.6311 (p90) REVERT: C 262 MET cc_start: 0.8112 (mmm) cc_final: 0.7538 (mpt) REVERT: C 407 MET cc_start: 0.8519 (tpt) cc_final: 0.8184 (tpp) REVERT: C 488 GLU cc_start: 0.7552 (tt0) cc_final: 0.6738 (mp0) REVERT: C 550 MET cc_start: 0.7200 (tpt) cc_final: 0.6842 (mmt) REVERT: C 554 LYS cc_start: 0.6332 (mttt) cc_final: 0.6104 (mttt) REVERT: C 555 ARG cc_start: 0.6988 (mtm110) cc_final: 0.6526 (ptt90) outliers start: 24 outliers final: 14 residues processed: 126 average time/residue: 1.0962 time to fit residues: 147.7219 Evaluate side-chains 120 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 102 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 250 GLN Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 250 GLN Chi-restraints excluded: chain C residue 255 PHE Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 381 SER Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 567 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 16 optimal weight: 0.9990 chunk 87 optimal weight: 9.9990 chunk 83 optimal weight: 6.9990 chunk 36 optimal weight: 9.9990 chunk 1 optimal weight: 0.9980 chunk 39 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 19 optimal weight: 10.0000 chunk 50 optimal weight: 3.9990 chunk 67 optimal weight: 7.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN A 287 GLN C 50 GLN C 287 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.141955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.119077 restraints weight = 8863.968| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 1.38 r_work: 0.3177 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8500 Z= 0.152 Angle : 0.620 7.710 11612 Z= 0.307 Chirality : 0.044 0.186 1432 Planarity : 0.005 0.043 1354 Dihedral : 12.915 140.473 1952 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.26 % Allowed : 15.36 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.99 (0.26), residues: 1014 helix: 1.53 (0.19), residues: 698 sheet: None (None), residues: 0 loop : 1.12 (0.39), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 149 HIS 0.001 0.000 HIS C 354 PHE 0.013 0.002 PHE A 325 TYR 0.010 0.002 TYR C 307 ARG 0.006 0.001 ARG C 555 Details of bonding type rmsd link_NAG-ASN : bond 0.00037 ( 2) link_NAG-ASN : angle 2.13489 ( 6) link_BETA1-4 : bond 0.00193 ( 2) link_BETA1-4 : angle 1.12347 ( 6) hydrogen bonds : bond 0.05378 ( 518) hydrogen bonds : angle 4.64708 ( 1494) covalent geometry : bond 0.00344 ( 8496) covalent geometry : angle 0.61818 (11600) =============================================================================== Job complete usr+sys time: 5310.79 seconds wall clock time: 92 minutes 14.73 seconds (5534.73 seconds total)