Starting phenix.real_space_refine on Fri Oct 10 18:03:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jez_36204/10_2025/8jez_36204_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jez_36204/10_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 { model { file = "/net/cci-nas-00/data/ceres_data/8jez_36204/10_2025/8jez_36204_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jez_36204/10_2025/8jez_36204_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jez_36204/10_2025/8jez_36204.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jez_36204/10_2025/8jez_36204.map" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: {'GLU:plan': 2, 'PHE:plan': 1} 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: {'LBN:plan-3': 1, 'PLM:plan-1': 1} Unresolved non-hydrogen planarities: 4 Restraints were copied for chains: C, D Time building chain proxies: 2.90, per 1000 atoms: 0.35 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: 0.78 Conformation dependent library (CDL) restraints added in 303.6 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.18 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: 1.07 Time building geometry restraints manager: 0.95 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: 0.02 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: 0.120 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: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.450 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.980 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.023 0.003 ARG C 344 TYR 0.039 0.010 TYR C 227 PHE 0.049 0.010 PHE A 502 TRP 0.063 0.010 TRP A 127 HIS 0.012 0.006 HIS C 147 Details of bonding type rmsd covalent geometry : bond 0.01573 ( 8496) covalent geometry : angle 1.78592 (11600) hydrogen bonds : bond 0.18386 ( 518) hydrogen bonds : angle 6.82562 ( 1494) link_BETA1-4 : bond 0.27457 ( 2) link_BETA1-4 : angle 14.66948 ( 6) link_NAG-ASN : bond 0.09566 ( 2) link_NAG-ASN : angle 22.85647 ( 6) *********************** 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 : 0.298 Fit side-chains REVERT: A 78 MET cc_start: 0.8632 (tmt) cc_final: 0.8375 (ttp) 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: 0.8080 (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: 0.5628 (mp0) REVERT: A 545 ASP cc_start: 0.7131 (m-30) cc_final: 0.6910 (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: 0.5103 (m-80) REVERT: A 565 CYS cc_start: 0.6931 (m) cc_final: 0.6132 (t) REVERT: C 78 MET cc_start: 0.8632 (tmt) cc_final: 0.8376 (ttp) REVERT: C 181 ASN cc_start: 0.8571 (m-40) cc_final: 0.8350 (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: 0.8081 (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: 0.5101 (m-80) REVERT: C 565 CYS cc_start: 0.6931 (m) cc_final: 0.6131 (t) outliers start: 4 outliers final: 0 residues processed: 150 average time/residue: 0.5413 time to fit residues: 86.6179 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 : 0.249 ------------------------------------------------------------------------------- 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 49 optimal weight: 0.0170 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 0.3980 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 4.9990 overall best weight: 1.2822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 ASN A 287 GLN A 377 ASN C 181 ASN C 287 GLN C 377 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.144287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.120541 restraints weight = 8656.992| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 1.34 r_work: 0.3203 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.1621 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= 0.144 Angle : 0.668 7.394 11612 Z= 0.322 Chirality : 0.044 0.235 1432 Planarity : 0.005 0.035 1354 Dihedral : 15.330 130.710 1954 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.67 % Allowed : 9.52 % Favored : 88.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.90 (0.26), residues: 1014 helix: 1.57 (0.19), residues: 694 sheet: None (None), residues: 0 loop : 0.79 (0.37), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 555 TYR 0.009 0.001 TYR A 402 PHE 0.016 0.002 PHE A 558 TRP 0.009 0.001 TRP C 41 HIS 0.002 0.001 HIS C 354 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 8496) covalent geometry : angle 0.65836 (11600) hydrogen bonds : bond 0.05608 ( 518) hydrogen bonds : angle 4.85703 ( 1494) link_BETA1-4 : bond 0.00628 ( 2) link_BETA1-4 : angle 1.92975 ( 6) link_NAG-ASN : bond 0.00186 ( 2) link_NAG-ASN : angle 4.72568 ( 6) *********************** 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 150 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 136 time to evaluate : 0.222 Fit side-chains REVERT: A 32 LEU cc_start: 0.7347 (OUTLIER) cc_final: 0.7026 (tp) REVERT: A 78 MET cc_start: 0.8478 (tmt) cc_final: 0.8239 (ttp) REVERT: A 255 PHE cc_start: 0.7853 (OUTLIER) cc_final: 0.7624 (p90) REVERT: A 262 MET cc_start: 0.7943 (mmm) cc_final: 0.7529 (mpt) REVERT: A 269 TYR cc_start: 0.7843 (t80) cc_final: 0.7633 (t80) REVERT: A 488 GLU cc_start: 0.7576 (tt0) cc_final: 0.6729 (mp0) REVERT: A 545 ASP cc_start: 0.7453 (m-30) cc_final: 0.7162 (m-30) REVERT: A 555 ARG cc_start: 0.7049 (mtm110) cc_final: 0.6117 (mtm180) REVERT: A 561 TYR cc_start: 0.5474 (m-80) cc_final: 0.5005 (m-80) REVERT: C 32 LEU cc_start: 0.7347 (OUTLIER) cc_final: 0.7031 (tp) REVERT: C 78 MET cc_start: 0.8465 (tmt) cc_final: 0.8232 (ttp) REVERT: C 255 PHE cc_start: 0.7851 (OUTLIER) cc_final: 0.7619 (p90) REVERT: C 262 MET cc_start: 0.7941 (mmm) cc_final: 0.7529 (mpt) REVERT: C 269 TYR cc_start: 0.7842 (t80) cc_final: 0.7631 (t80) REVERT: C 488 GLU cc_start: 0.7567 (tt0) cc_final: 0.6715 (mp0) REVERT: C 545 ASP cc_start: 0.7462 (m-30) cc_final: 0.7171 (m-30) REVERT: C 555 ARG cc_start: 0.7037 (mtm110) cc_final: 0.6107 (mtm180) REVERT: C 561 TYR cc_start: 0.5491 (m-80) cc_final: 0.5022 (m-80) outliers start: 14 outliers final: 2 residues processed: 140 average time/residue: 0.5562 time to fit residues: 82.9801 Evaluate side-chains 120 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 114 time to evaluate : 0.323 ------------------------------------------------------------------------------- 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 94 optimal weight: 10.0000 chunk 42 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 26 optimal weight: 0.0470 chunk 88 optimal weight: 9.9990 chunk 100 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 21 optimal weight: 8.9990 chunk 77 optimal weight: 0.3980 chunk 56 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 overall best weight: 1.2884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 GLN A 377 ASN C 287 GLN C 377 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.147096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.124852 restraints weight = 8747.652| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 1.28 r_work: 0.3264 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.2109 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= 0.130 Angle : 0.607 7.524 11612 Z= 0.291 Chirality : 0.044 0.379 1432 Planarity : 0.004 0.038 1354 Dihedral : 13.756 127.410 1952 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.33 % Allowed : 10.00 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.39 (0.26), residues: 1014 helix: 1.90 (0.19), residues: 692 sheet: None (None), residues: 0 loop : 1.10 (0.38), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 126 TYR 0.009 0.001 TYR C 307 PHE 0.017 0.002 PHE A 558 TRP 0.010 0.001 TRP C 149 HIS 0.001 0.000 HIS C 354 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 8496) covalent geometry : angle 0.60035 (11600) hydrogen bonds : bond 0.04890 ( 518) hydrogen bonds : angle 4.57632 ( 1494) link_BETA1-4 : bond 0.00463 ( 2) link_BETA1-4 : angle 1.56978 ( 6) link_NAG-ASN : bond 0.00044 ( 2) link_NAG-ASN : angle 3.56059 ( 6) *********************** 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 160 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 132 time to evaluate : 0.315 Fit side-chains REVERT: A 32 LEU cc_start: 0.7416 (OUTLIER) cc_final: 0.7118 (tp) REVERT: A 251 ILE cc_start: 0.7044 (tt) cc_final: 0.6481 (tp) REVERT: A 262 MET cc_start: 0.7983 (mmm) cc_final: 0.7461 (mpt) REVERT: A 393 LYS cc_start: 0.7638 (OUTLIER) cc_final: 0.7199 (mppt) REVERT: A 488 GLU cc_start: 0.7619 (tt0) cc_final: 0.6659 (mp0) REVERT: A 561 TYR cc_start: 0.5438 (m-80) cc_final: 0.5007 (m-80) REVERT: C 32 LEU cc_start: 0.7412 (OUTLIER) cc_final: 0.7122 (tp) REVERT: C 251 ILE cc_start: 0.7054 (tt) cc_final: 0.6491 (tp) REVERT: C 262 MET cc_start: 0.7969 (mmm) cc_final: 0.7441 (mpt) REVERT: C 393 LYS cc_start: 0.7652 (OUTLIER) cc_final: 0.7217 (mppt) REVERT: C 488 GLU cc_start: 0.7623 (tt0) cc_final: 0.6655 (mp0) REVERT: C 561 TYR cc_start: 0.5453 (m-80) cc_final: 0.5020 (m-80) outliers start: 28 outliers final: 18 residues processed: 140 average time/residue: 0.4758 time to fit residues: 71.6873 Evaluate side-chains 138 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 116 time to evaluate : 0.302 ------------------------------------------------------------------------------- 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 393 LYS Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 489 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 393 LYS Chi-restraints excluded: chain C residue 465 MET Chi-restraints excluded: chain C residue 489 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 84 optimal weight: 20.0000 chunk 18 optimal weight: 10.0000 chunk 8 optimal weight: 10.0000 chunk 38 optimal weight: 0.9990 chunk 92 optimal weight: 7.9990 chunk 79 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 91 optimal weight: 5.9990 chunk 56 optimal weight: 10.0000 chunk 19 optimal weight: 5.9990 chunk 70 optimal weight: 7.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- 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 = 0.3586 r_free = 0.3586 target = 0.142553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.119679 restraints weight = 8942.487| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.32 r_work: 0.3191 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 8500 Z= 0.193 Angle : 0.690 7.600 11612 Z= 0.334 Chirality : 0.048 0.376 1432 Planarity : 0.005 0.047 1354 Dihedral : 13.855 133.599 1952 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 4.29 % Allowed : 10.24 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.74 (0.26), residues: 1014 helix: 1.43 (0.19), residues: 704 sheet: None (None), residues: 0 loop : 0.75 (0.38), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 555 TYR 0.013 0.002 TYR C 307 PHE 0.017 0.002 PHE A 459 TRP 0.007 0.002 TRP A 527 HIS 0.002 0.001 HIS A 147 Details of bonding type rmsd covalent geometry : bond 0.00457 ( 8496) covalent geometry : angle 0.68616 (11600) hydrogen bonds : bond 0.06081 ( 518) hydrogen bonds : angle 4.80995 ( 1494) link_BETA1-4 : bond 0.00248 ( 2) link_BETA1-4 : angle 1.44107 ( 6) link_NAG-ASN : bond 0.00232 ( 2) link_NAG-ASN : angle 2.85960 ( 6) *********************** 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 152 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 116 time to evaluate : 0.297 Fit side-chains REVERT: A 31 MET cc_start: 0.6874 (tpp) cc_final: 0.6621 (tpt) REVERT: A 250 GLN cc_start: 0.7306 (OUTLIER) cc_final: 0.7010 (mm-40) REVERT: A 255 PHE cc_start: 0.7908 (OUTLIER) cc_final: 0.6381 (p90) REVERT: A 262 MET cc_start: 0.8110 (mmm) cc_final: 0.7519 (mpt) REVERT: A 488 GLU cc_start: 0.7590 (tt0) cc_final: 0.6688 (mp0) REVERT: A 555 ARG cc_start: 0.7080 (mtm110) cc_final: 0.6085 (mtm180) REVERT: C 31 MET cc_start: 0.6898 (tpp) cc_final: 0.6645 (tpt) REVERT: C 250 GLN cc_start: 0.7307 (OUTLIER) cc_final: 0.7012 (mm-40) REVERT: C 255 PHE cc_start: 0.7905 (OUTLIER) cc_final: 0.6379 (p90) REVERT: C 262 MET cc_start: 0.8102 (mmm) cc_final: 0.7508 (mpt) REVERT: C 488 GLU cc_start: 0.7597 (tt0) cc_final: 0.6684 (mp0) REVERT: C 555 ARG cc_start: 0.7080 (mtm110) cc_final: 0.6089 (mtm180) outliers start: 36 outliers final: 20 residues processed: 128 average time/residue: 0.5654 time to fit residues: 77.0617 Evaluate side-chains 126 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 102 time to evaluate : 0.329 ------------------------------------------------------------------------------- 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 388 VAL Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 393 LYS 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 388 VAL Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 393 LYS 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 56 optimal weight: 7.9990 chunk 9 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 chunk 37 optimal weight: 7.9990 chunk 61 optimal weight: 6.9990 chunk 54 optimal weight: 4.9990 chunk 7 optimal weight: 0.8980 chunk 95 optimal weight: 7.9990 chunk 100 optimal weight: 9.9990 chunk 87 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- 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 = 0.3612 r_free = 0.3612 target = 0.144678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.122366 restraints weight = 8822.267| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 1.31 r_work: 0.3227 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.2298 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= 0.143 Angle : 0.609 7.294 11612 Z= 0.297 Chirality : 0.045 0.354 1432 Planarity : 0.005 0.046 1354 Dihedral : 13.267 132.575 1952 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 3.33 % Allowed : 12.14 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.98 (0.26), residues: 1014 helix: 1.53 (0.19), residues: 710 sheet: None (None), residues: 0 loop : 1.06 (0.39), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 126 TYR 0.009 0.002 TYR A 42 PHE 0.015 0.002 PHE C 325 TRP 0.010 0.001 TRP C 149 HIS 0.001 0.001 HIS A 354 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 8496) covalent geometry : angle 0.60670 (11600) hydrogen bonds : bond 0.05183 ( 518) hydrogen bonds : angle 4.61648 ( 1494) link_BETA1-4 : bond 0.00355 ( 2) link_BETA1-4 : angle 1.28117 ( 6) link_NAG-ASN : bond 0.00045 ( 2) link_NAG-ASN : angle 2.28980 ( 6) *********************** 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 144 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 116 time to evaluate : 0.321 Fit side-chains REVERT: A 31 MET cc_start: 0.6782 (tpp) cc_final: 0.6529 (tpt) REVERT: A 32 LEU cc_start: 0.7408 (OUTLIER) cc_final: 0.7060 (tp) REVERT: A 250 GLN cc_start: 0.7213 (OUTLIER) cc_final: 0.6960 (mm-40) REVERT: A 262 MET cc_start: 0.8089 (mmm) cc_final: 0.7520 (mpt) REVERT: A 393 LYS cc_start: 0.7683 (OUTLIER) cc_final: 0.7231 (mppt) REVERT: A 488 GLU cc_start: 0.7577 (tt0) cc_final: 0.6680 (mp0) REVERT: A 550 MET cc_start: 0.7219 (tpt) cc_final: 0.6696 (mmt) REVERT: A 555 ARG cc_start: 0.7014 (mtm110) cc_final: 0.6024 (mtm180) REVERT: C 31 MET cc_start: 0.6795 (tpp) cc_final: 0.6541 (tpt) REVERT: C 32 LEU cc_start: 0.7414 (OUTLIER) cc_final: 0.7067 (tp) REVERT: C 250 GLN cc_start: 0.7210 (OUTLIER) cc_final: 0.6956 (mm-40) REVERT: C 262 MET cc_start: 0.8090 (mmm) cc_final: 0.7518 (mpt) REVERT: C 393 LYS cc_start: 0.7691 (OUTLIER) cc_final: 0.7239 (mppt) REVERT: C 488 GLU cc_start: 0.7584 (tt0) cc_final: 0.6687 (mp0) REVERT: C 550 MET cc_start: 0.7234 (tpt) cc_final: 0.6715 (mmt) REVERT: C 555 ARG cc_start: 0.7015 (mtm110) cc_final: 0.6025 (mtm180) outliers start: 28 outliers final: 16 residues processed: 126 average time/residue: 0.5890 time to fit residues: 78.9617 Evaluate side-chains 134 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 112 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU 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 393 LYS Chi-restraints excluded: chain A residue 435 LEU 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 275 ASP Chi-restraints excluded: chain C residue 381 SER Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 393 LYS 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 92 optimal weight: 7.9990 chunk 19 optimal weight: 7.9990 chunk 13 optimal weight: 10.0000 chunk 46 optimal weight: 8.9990 chunk 16 optimal weight: 1.9990 chunk 2 optimal weight: 9.9990 chunk 85 optimal weight: 5.9990 chunk 93 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 = 0.3613 r_free = 0.3613 target = 0.144519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.122386 restraints weight = 8829.164| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 1.30 r_work: 0.3229 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.2374 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= 0.139 Angle : 0.604 7.240 11612 Z= 0.295 Chirality : 0.044 0.314 1432 Planarity : 0.005 0.045 1354 Dihedral : 13.038 134.475 1952 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.33 % Allowed : 12.86 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.06 (0.27), residues: 1014 helix: 1.57 (0.19), residues: 708 sheet: None (None), residues: 0 loop : 1.14 (0.40), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 126 TYR 0.010 0.002 TYR C 42 PHE 0.014 0.002 PHE A 558 TRP 0.009 0.001 TRP C 149 HIS 0.002 0.000 HIS C 354 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 8496) covalent geometry : angle 0.60166 (11600) hydrogen bonds : bond 0.05107 ( 518) hydrogen bonds : angle 4.60678 ( 1494) link_BETA1-4 : bond 0.00399 ( 2) link_BETA1-4 : angle 1.16574 ( 6) link_NAG-ASN : bond 0.00050 ( 2) link_NAG-ASN : angle 2.17872 ( 6) *********************** 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 140 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 112 time to evaluate : 0.325 Fit side-chains REVERT: A 250 GLN cc_start: 0.7303 (OUTLIER) cc_final: 0.7059 (mm-40) REVERT: A 255 PHE cc_start: 0.7805 (OUTLIER) cc_final: 0.6248 (p90) REVERT: A 262 MET cc_start: 0.8146 (mmm) cc_final: 0.7577 (mpt) REVERT: A 393 LYS cc_start: 0.7672 (OUTLIER) cc_final: 0.7204 (mppt) REVERT: A 488 GLU cc_start: 0.7592 (tt0) cc_final: 0.6695 (mp0) REVERT: A 555 ARG cc_start: 0.7006 (mtm110) cc_final: 0.6083 (mtm180) REVERT: C 250 GLN cc_start: 0.7309 (OUTLIER) cc_final: 0.7063 (mm-40) REVERT: C 255 PHE cc_start: 0.7803 (OUTLIER) cc_final: 0.6240 (p90) REVERT: C 262 MET cc_start: 0.8143 (mmm) cc_final: 0.7569 (mpt) REVERT: C 393 LYS cc_start: 0.7679 (OUTLIER) cc_final: 0.7213 (mppt) REVERT: C 488 GLU cc_start: 0.7602 (tt0) cc_final: 0.6695 (mp0) REVERT: C 555 ARG cc_start: 0.6994 (mtm110) cc_final: 0.6072 (mtm180) outliers start: 28 outliers final: 18 residues processed: 124 average time/residue: 0.5903 time to fit residues: 77.8520 Evaluate side-chains 132 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 108 time to evaluate : 0.231 ------------------------------------------------------------------------------- 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 393 LYS 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 388 VAL Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 393 LYS 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 71 optimal weight: 0.0170 chunk 48 optimal weight: 3.9990 chunk 6 optimal weight: 7.9990 chunk 82 optimal weight: 9.9990 chunk 14 optimal weight: 9.9990 chunk 57 optimal weight: 1.9990 chunk 58 optimal weight: 8.9990 chunk 46 optimal weight: 7.9990 chunk 75 optimal weight: 4.9990 chunk 4 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 overall best weight: 2.6026 ------------------------------------------------------------------------------- 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 = 0.3601 r_free = 0.3601 target = 0.143631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.121334 restraints weight = 8905.942| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 1.32 r_work: 0.3212 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.2413 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= 0.151 Angle : 0.615 7.471 11612 Z= 0.301 Chirality : 0.044 0.278 1432 Planarity : 0.005 0.045 1354 Dihedral : 12.994 137.071 1952 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.86 % Allowed : 13.10 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.99 (0.26), residues: 1014 helix: 1.53 (0.19), residues: 708 sheet: None (None), residues: 0 loop : 1.10 (0.40), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 126 TYR 0.011 0.002 TYR A 42 PHE 0.013 0.002 PHE A 361 TRP 0.009 0.001 TRP A 149 HIS 0.001 0.000 HIS A 354 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 8496) covalent geometry : angle 0.61238 (11600) hydrogen bonds : bond 0.05349 ( 518) hydrogen bonds : angle 4.62683 ( 1494) link_BETA1-4 : bond 0.00259 ( 2) link_BETA1-4 : angle 1.15316 ( 6) link_NAG-ASN : bond 0.00037 ( 2) link_NAG-ASN : angle 2.20480 ( 6) *********************** 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 137 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 113 time to evaluate : 0.218 Fit side-chains REVERT: A 250 GLN cc_start: 0.7315 (OUTLIER) cc_final: 0.7053 (mm-40) REVERT: A 255 PHE cc_start: 0.7850 (OUTLIER) cc_final: 0.6322 (p90) REVERT: A 262 MET cc_start: 0.8136 (mmm) cc_final: 0.7559 (mpt) REVERT: A 393 LYS cc_start: 0.7723 (OUTLIER) cc_final: 0.7258 (mppt) REVERT: A 488 GLU cc_start: 0.7559 (tt0) cc_final: 0.6722 (mp0) REVERT: A 555 ARG cc_start: 0.6976 (mtm110) cc_final: 0.6031 (mtm180) REVERT: C 250 GLN cc_start: 0.7312 (OUTLIER) cc_final: 0.7049 (mm-40) REVERT: C 255 PHE cc_start: 0.7846 (OUTLIER) cc_final: 0.6313 (p90) REVERT: C 262 MET cc_start: 0.8140 (mmm) cc_final: 0.7558 (mpt) REVERT: C 393 LYS cc_start: 0.7724 (OUTLIER) cc_final: 0.7262 (mppt) REVERT: C 407 MET cc_start: 0.8565 (tpt) cc_final: 0.8257 (tpp) REVERT: C 488 GLU cc_start: 0.7567 (tt0) cc_final: 0.6720 (mp0) REVERT: C 555 ARG cc_start: 0.6970 (mtm110) cc_final: 0.6026 (mtm180) outliers start: 24 outliers final: 18 residues processed: 125 average time/residue: 0.5797 time to fit residues: 77.0434 Evaluate side-chains 128 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 104 time to evaluate : 0.243 ------------------------------------------------------------------------------- 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 393 LYS 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 388 VAL Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 393 LYS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 101 optimal weight: 3.9990 chunk 23 optimal weight: 6.9990 chunk 94 optimal weight: 7.9990 chunk 66 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 76 optimal weight: 6.9990 chunk 59 optimal weight: 0.9990 chunk 39 optimal weight: 5.9990 chunk 65 optimal weight: 0.9980 chunk 25 optimal weight: 6.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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 = 0.3602 r_free = 0.3602 target = 0.143733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.121525 restraints weight = 8794.555| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 1.31 r_work: 0.3222 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.2480 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= 0.146 Angle : 0.602 7.574 11612 Z= 0.297 Chirality : 0.043 0.231 1432 Planarity : 0.005 0.045 1354 Dihedral : 12.880 139.067 1952 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 3.33 % Allowed : 12.86 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.13 (0.26), residues: 1014 helix: 1.65 (0.19), residues: 698 sheet: None (None), residues: 0 loop : 1.14 (0.39), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 126 TYR 0.010 0.002 TYR A 42 PHE 0.013 0.002 PHE C 361 TRP 0.009 0.001 TRP A 149 HIS 0.001 0.000 HIS C 354 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 8496) covalent geometry : angle 0.60037 (11600) hydrogen bonds : bond 0.05217 ( 518) hydrogen bonds : angle 4.59596 ( 1494) link_BETA1-4 : bond 0.00261 ( 2) link_BETA1-4 : angle 1.07194 ( 6) link_NAG-ASN : bond 0.00017 ( 2) link_NAG-ASN : angle 2.07713 ( 6) *********************** 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 140 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 112 time to evaluate : 0.327 Fit side-chains REVERT: A 250 GLN cc_start: 0.7315 (OUTLIER) cc_final: 0.7051 (mm-40) REVERT: A 255 PHE cc_start: 0.7836 (OUTLIER) cc_final: 0.6314 (p90) REVERT: A 262 MET cc_start: 0.8071 (mmm) cc_final: 0.7521 (mpt) REVERT: A 393 LYS cc_start: 0.7712 (OUTLIER) cc_final: 0.7248 (mppt) REVERT: A 407 MET cc_start: 0.8549 (tpt) cc_final: 0.8249 (tpp) REVERT: A 488 GLU cc_start: 0.7561 (tt0) cc_final: 0.6750 (mp0) REVERT: A 550 MET cc_start: 0.7187 (tpt) cc_final: 0.6895 (mmt) REVERT: A 554 LYS cc_start: 0.6234 (mttt) cc_final: 0.6026 (mttt) REVERT: A 555 ARG cc_start: 0.6993 (mtm110) cc_final: 0.6105 (mtm180) REVERT: C 250 GLN cc_start: 0.7308 (OUTLIER) cc_final: 0.7041 (mm-40) REVERT: C 255 PHE cc_start: 0.7834 (OUTLIER) cc_final: 0.6314 (p90) REVERT: C 262 MET cc_start: 0.8082 (mmm) cc_final: 0.7527 (mpt) REVERT: C 393 LYS cc_start: 0.7714 (OUTLIER) cc_final: 0.7251 (mppt) REVERT: C 407 MET cc_start: 0.8552 (tpt) cc_final: 0.8243 (tpp) REVERT: C 488 GLU cc_start: 0.7569 (tt0) cc_final: 0.6747 (mp0) REVERT: C 550 MET cc_start: 0.7196 (tpt) cc_final: 0.6911 (mmt) REVERT: C 554 LYS cc_start: 0.6243 (mttt) cc_final: 0.6035 (mttt) REVERT: C 555 ARG cc_start: 0.6988 (mtm110) cc_final: 0.6102 (mtm180) outliers start: 28 outliers final: 18 residues processed: 126 average time/residue: 0.5817 time to fit residues: 78.1597 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 : 0.316 ------------------------------------------------------------------------------- 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 393 LYS 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 388 VAL Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 393 LYS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 43 optimal weight: 5.9990 chunk 48 optimal weight: 9.9990 chunk 5 optimal weight: 10.0000 chunk 92 optimal weight: 3.9990 chunk 41 optimal weight: 6.9990 chunk 63 optimal weight: 5.9990 chunk 99 optimal weight: 9.9990 chunk 23 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- 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 = 0.3570 r_free = 0.3570 target = 0.141855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.118931 restraints weight = 8779.264| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 1.37 r_work: 0.3173 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.2478 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= 0.163 Angle : 0.631 7.819 11612 Z= 0.311 Chirality : 0.044 0.211 1432 Planarity : 0.005 0.046 1354 Dihedral : 12.961 141.025 1952 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 3.21 % Allowed : 13.21 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.99 (0.26), residues: 1014 helix: 1.56 (0.19), residues: 690 sheet: None (None), residues: 0 loop : 1.03 (0.39), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 126 TYR 0.011 0.002 TYR A 307 PHE 0.014 0.002 PHE A 325 TRP 0.008 0.001 TRP A 149 HIS 0.001 0.001 HIS A 147 Details of bonding type rmsd covalent geometry : bond 0.00374 ( 8496) covalent geometry : angle 0.62903 (11600) hydrogen bonds : bond 0.05563 ( 518) hydrogen bonds : angle 4.68989 ( 1494) link_BETA1-4 : bond 0.00152 ( 2) link_BETA1-4 : angle 1.14637 ( 6) link_NAG-ASN : bond 0.00112 ( 2) link_NAG-ASN : angle 2.24258 ( 6) *********************** 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 134 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 107 time to evaluate : 0.299 Fit side-chains REVERT: A 250 GLN cc_start: 0.7240 (OUTLIER) cc_final: 0.6715 (mm-40) REVERT: A 255 PHE cc_start: 0.7865 (OUTLIER) cc_final: 0.6352 (p90) REVERT: A 262 MET cc_start: 0.8168 (mmm) cc_final: 0.7598 (mpt) REVERT: A 393 LYS cc_start: 0.7748 (OUTLIER) cc_final: 0.7334 (mppt) REVERT: A 407 MET cc_start: 0.8549 (tpt) cc_final: 0.8204 (tpp) REVERT: A 488 GLU cc_start: 0.7568 (tt0) cc_final: 0.6738 (mp0) REVERT: A 550 MET cc_start: 0.7197 (tpt) cc_final: 0.6844 (mmt) REVERT: C 250 GLN cc_start: 0.7235 (OUTLIER) cc_final: 0.6706 (mm-40) REVERT: C 255 PHE cc_start: 0.7862 (OUTLIER) cc_final: 0.6344 (p90) REVERT: C 262 MET cc_start: 0.8174 (mmm) cc_final: 0.7601 (mpt) REVERT: C 393 LYS cc_start: 0.7752 (OUTLIER) cc_final: 0.7343 (mppt) REVERT: C 488 GLU cc_start: 0.7567 (tt0) cc_final: 0.6745 (mp0) REVERT: C 550 MET cc_start: 0.7201 (tpt) cc_final: 0.6846 (mmt) outliers start: 27 outliers final: 16 residues processed: 122 average time/residue: 0.6015 time to fit residues: 78.2005 Evaluate side-chains 124 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 102 time to evaluate : 0.307 ------------------------------------------------------------------------------- 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 388 VAL Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 393 LYS 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 388 VAL Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 393 LYS 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 24 optimal weight: 9.9990 chunk 30 optimal weight: 0.7980 chunk 73 optimal weight: 0.9990 chunk 5 optimal weight: 10.0000 chunk 91 optimal weight: 6.9990 chunk 98 optimal weight: 0.6980 chunk 20 optimal weight: 7.9990 chunk 90 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 52 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 = 0.3602 r_free = 0.3602 target = 0.144572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.121886 restraints weight = 8773.580| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 1.36 r_work: 0.3218 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.2655 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= 0.127 Angle : 0.588 7.371 11612 Z= 0.291 Chirality : 0.042 0.185 1432 Planarity : 0.005 0.043 1354 Dihedral : 12.689 138.755 1952 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.86 % Allowed : 13.93 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.19 (0.27), residues: 1014 helix: 1.68 (0.19), residues: 704 sheet: None (None), residues: 0 loop : 1.18 (0.40), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 555 TYR 0.013 0.001 TYR C 402 PHE 0.015 0.002 PHE C 325 TRP 0.011 0.001 TRP A 149 HIS 0.002 0.000 HIS A 354 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 8496) covalent geometry : angle 0.58608 (11600) hydrogen bonds : bond 0.04739 ( 518) hydrogen bonds : angle 4.53964 ( 1494) link_BETA1-4 : bond 0.00317 ( 2) link_BETA1-4 : angle 0.95983 ( 6) link_NAG-ASN : bond 0.00192 ( 2) link_NAG-ASN : angle 1.80262 ( 6) ********************** 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 131 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 107 time to evaluate : 0.306 Fit side-chains REVERT: A 76 GLN cc_start: 0.8155 (tt0) cc_final: 0.7953 (mt0) REVERT: A 250 GLN cc_start: 0.7209 (OUTLIER) cc_final: 0.6734 (mm-40) REVERT: A 255 PHE cc_start: 0.7790 (OUTLIER) cc_final: 0.6260 (p90) REVERT: A 262 MET cc_start: 0.8093 (mmm) cc_final: 0.7537 (mpt) REVERT: A 393 LYS cc_start: 0.7669 (OUTLIER) cc_final: 0.7150 (mppt) REVERT: A 407 MET cc_start: 0.8529 (tpt) cc_final: 0.8212 (tpp) REVERT: A 488 GLU cc_start: 0.7569 (tt0) cc_final: 0.6767 (mp0) REVERT: A 555 ARG cc_start: 0.7041 (mtm110) cc_final: 0.5963 (mtm110) REVERT: C 250 GLN cc_start: 0.7192 (OUTLIER) cc_final: 0.6713 (mm-40) REVERT: C 255 PHE cc_start: 0.7789 (OUTLIER) cc_final: 0.6257 (p90) REVERT: C 262 MET cc_start: 0.8111 (mmm) cc_final: 0.7547 (mpt) REVERT: C 393 LYS cc_start: 0.7673 (OUTLIER) cc_final: 0.7157 (mppt) REVERT: C 407 MET cc_start: 0.8498 (tpt) cc_final: 0.8167 (tpp) REVERT: C 488 GLU cc_start: 0.7568 (tt0) cc_final: 0.6773 (mp0) REVERT: C 555 ARG cc_start: 0.7038 (mtm110) cc_final: 0.5951 (mtm110) outliers start: 24 outliers final: 14 residues processed: 121 average time/residue: 0.6336 time to fit residues: 81.3082 Evaluate side-chains 120 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 100 time to evaluate : 0.372 ------------------------------------------------------------------------------- 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 388 VAL Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 393 LYS 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 381 SER Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 392 THR Chi-restraints excluded: chain C residue 393 LYS Chi-restraints excluded: chain C residue 435 LEU 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 78 optimal weight: 8.9990 chunk 94 optimal weight: 0.6980 chunk 29 optimal weight: 10.0000 chunk 12 optimal weight: 8.9990 chunk 65 optimal weight: 9.9990 chunk 13 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 7 optimal weight: 6.9990 chunk 51 optimal weight: 20.0000 chunk 19 optimal weight: 8.9990 chunk 90 optimal weight: 2.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- 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 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 = 0.3572 r_free = 0.3572 target = 0.142082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.119120 restraints weight = 8795.578| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 1.38 r_work: 0.3176 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8500 Z= 0.161 Angle : 0.636 7.689 11612 Z= 0.314 Chirality : 0.044 0.182 1432 Planarity : 0.005 0.053 1354 Dihedral : 12.867 141.830 1952 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.74 % Allowed : 13.93 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.99 (0.27), residues: 1014 helix: 1.54 (0.19), residues: 700 sheet: None (None), residues: 0 loop : 1.07 (0.40), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 555 TYR 0.020 0.002 TYR C 402 PHE 0.015 0.002 PHE A 325 TRP 0.008 0.001 TRP C 149 HIS 0.001 0.001 HIS C 354 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 8496) covalent geometry : angle 0.63426 (11600) hydrogen bonds : bond 0.05443 ( 518) hydrogen bonds : angle 4.66097 ( 1494) link_BETA1-4 : bond 0.00159 ( 2) link_BETA1-4 : angle 1.14889 ( 6) link_NAG-ASN : bond 0.00092 ( 2) link_NAG-ASN : angle 2.12230 ( 6) =============================================================================== Job complete usr+sys time: 2731.42 seconds wall clock time: 47 minutes 22.40 seconds (2842.40 seconds total)