Starting phenix.real_space_refine on Sun Apr 27 23:26:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vke_43315/04_2025/8vke_43315.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vke_43315/04_2025/8vke_43315.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vke_43315/04_2025/8vke_43315.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vke_43315/04_2025/8vke_43315.map" model { file = "/net/cci-nas-00/data/ceres_data/8vke_43315/04_2025/8vke_43315.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vke_43315/04_2025/8vke_43315.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 30 5.16 5 C 4218 2.51 5 N 1114 2.21 5 O 1290 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 6652 Number of models: 1 Model: "" Number of chains: 8 Chain: "H" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 991 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "L" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 825 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 7, 'TRANS': 105} Chain: "R" Number of atoms: 1496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1496 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 10, 'TRANS': 175} Chain breaks: 1 Chain: "A" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 991 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "B" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 825 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 7, 'TRANS': 105} Chain: "C" Number of atoms: 1496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1496 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 10, 'TRANS': 175} Chain breaks: 1 Chain: "R" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 9.77, per 1000 atoms: 1.47 Number of scatterers: 6652 At special positions: 0 Unit cell: (81.78, 88.36, 103.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 30 16.00 O 1290 8.00 N 1114 7.00 C 4218 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS R 336 " - pdb=" SG CYS R 361 " distance=2.03 Simple disulfide: pdb=" SG CYS R 379 " - pdb=" SG CYS R 432 " distance=2.03 Simple disulfide: pdb=" SG CYS R 391 " - pdb=" SG CYS R 525 " distance=2.04 Simple disulfide: pdb=" SG CYS R 480 " - pdb=" SG CYS R 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 92 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG C1301 " - " ASN C 343 " " NAG R1301 " - " ASN R 343 " Time building additional restraints: 1.40 Conformation dependent library (CDL) restraints added in 932.8 milliseconds 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1572 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 20 sheets defined 12.2% alpha, 35.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'H' and resid 99 through 100A No H-bonds generated for 'chain 'H' and resid 99 through 100A' Processing helix chain 'L' and resid 27A through 30 Processing helix chain 'R' and resid 338 through 343 Processing helix chain 'R' and resid 349 through 353 removed outlier: 3.616A pdb=" N TRP R 353 " --> pdb=" O VAL R 350 " (cutoff:3.500A) Processing helix chain 'R' and resid 364 through 372 removed outlier: 3.756A pdb=" N LEU R 368 " --> pdb=" O ASP R 364 " (cutoff:3.500A) Processing helix chain 'R' and resid 383 through 387 removed outlier: 3.820A pdb=" N LEU R 387 " --> pdb=" O PRO R 384 " (cutoff:3.500A) Processing helix chain 'R' and resid 404 through 410 removed outlier: 3.687A pdb=" N VAL R 407 " --> pdb=" O GLY R 404 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARG R 408 " --> pdb=" O ASP R 405 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN R 409 " --> pdb=" O GLU R 406 " (cutoff:3.500A) Processing helix chain 'R' and resid 416 through 422 Processing helix chain 'A' and resid 83 through 87 Processing helix chain 'A' and resid 99 through 100A No H-bonds generated for 'chain 'A' and resid 99 through 100A' Processing helix chain 'B' and resid 27A through 30 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.575A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 372 removed outlier: 3.566A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.796A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 408 removed outlier: 3.751A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.981A pdb=" N VAL H 35A" --> pdb=" O ASP H 50 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N ASP H 50 " --> pdb=" O VAL H 35A" (cutoff:3.500A) removed outlier: 6.554A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 12 removed outlier: 4.063A pdb=" N ASN H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ALA H 96 " --> pdb=" O PHE H 100K" (cutoff:3.500A) removed outlier: 4.967A pdb=" N PHE H 100K" --> pdb=" O ALA H 96 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 100C through 100E Processing sheet with id=AA5, first strand: chain 'L' and resid 9 through 13 removed outlier: 6.322A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 9 through 13 Processing sheet with id=AA7, first strand: chain 'L' and resid 19 through 24 Processing sheet with id=AA8, first strand: chain 'R' and resid 391 through 392 removed outlier: 3.861A pdb=" N PHE R 392 " --> pdb=" O VAL R 524 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL R 524 " --> pdb=" O PHE R 392 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'R' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'R' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 3 through 6 Processing sheet with id=AB3, first strand: chain 'A' and resid 10 through 12 removed outlier: 6.915A pdb=" N VAL A 35A" --> pdb=" O ASP A 50 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ASP A 50 " --> pdb=" O VAL A 35A" (cutoff:3.500A) removed outlier: 6.570A pdb=" N TRP A 36 " --> pdb=" O LEU A 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 10 through 12 removed outlier: 4.054A pdb=" N ASN A 102 " --> pdb=" O ARG A 94 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ALA A 96 " --> pdb=" O PHE A 100K" (cutoff:3.500A) removed outlier: 4.993A pdb=" N PHE A 100K" --> pdb=" O ALA A 96 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 100C through 100E Processing sheet with id=AB6, first strand: chain 'B' and resid 9 through 13 removed outlier: 6.330A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 9 through 13 Processing sheet with id=AB8, first strand: chain 'B' and resid 19 through 24 Processing sheet with id=AB9, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.766A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AC2, first strand: chain 'C' and resid 473 through 474 248 hydrogen bonds defined for protein. 558 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.26 Time building geometry restraints manager: 1.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2123 1.35 - 1.48: 1885 1.48 - 1.60: 2772 1.60 - 1.72: 0 1.72 - 1.85: 36 Bond restraints: 6816 Sorted by residual: bond pdb=" N VAL B 11 " pdb=" CA VAL B 11 " ideal model delta sigma weight residual 1.456 1.495 -0.040 1.11e-02 8.12e+03 1.28e+01 bond pdb=" C GLN B 6 " pdb=" N PRO B 7 " ideal model delta sigma weight residual 1.329 1.363 -0.034 1.18e-02 7.18e+03 8.35e+00 bond pdb=" N SER B 9 " pdb=" CA SER B 9 " ideal model delta sigma weight residual 1.456 1.486 -0.030 1.23e-02 6.61e+03 5.97e+00 bond pdb=" N CYS R 480 " pdb=" CA CYS R 480 " ideal model delta sigma weight residual 1.456 1.486 -0.029 1.21e-02 6.83e+03 5.84e+00 bond pdb=" N LYS R 478 " pdb=" CA LYS R 478 " ideal model delta sigma weight residual 1.454 1.485 -0.030 1.45e-02 4.76e+03 4.34e+00 ... (remaining 6811 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 8977 1.49 - 2.98: 260 2.98 - 4.47: 31 4.47 - 5.95: 1 5.95 - 7.44: 1 Bond angle restraints: 9270 Sorted by residual: angle pdb=" CA VAL B 11 " pdb=" C VAL B 11 " pdb=" O VAL B 11 " ideal model delta sigma weight residual 121.67 118.17 3.50 1.05e+00 9.07e-01 1.11e+01 angle pdb=" CA CYS R 391 " pdb=" CB CYS R 391 " pdb=" SG CYS R 391 " ideal model delta sigma weight residual 114.40 121.84 -7.44 2.30e+00 1.89e-01 1.05e+01 angle pdb=" CA SER B 9 " pdb=" C SER B 9 " pdb=" O SER B 9 " ideal model delta sigma weight residual 121.23 118.05 3.18 1.07e+00 8.73e-01 8.85e+00 angle pdb=" N PRO B 7 " pdb=" CA PRO B 7 " pdb=" C PRO B 7 " ideal model delta sigma weight residual 110.70 107.15 3.55 1.22e+00 6.72e-01 8.48e+00 angle pdb=" O GLN B 6 " pdb=" C GLN B 6 " pdb=" N PRO B 7 " ideal model delta sigma weight residual 121.55 119.38 2.17 7.80e-01 1.64e+00 7.76e+00 ... (remaining 9265 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.11: 3642 17.11 - 34.22: 308 34.22 - 51.33: 79 51.33 - 68.45: 16 68.45 - 85.56: 11 Dihedral angle restraints: 4056 sinusoidal: 1588 harmonic: 2468 Sorted by residual: dihedral pdb=" CB CYS R 480 " pdb=" SG CYS R 480 " pdb=" SG CYS R 488 " pdb=" CB CYS R 488 " ideal model delta sinusoidal sigma weight residual 93.00 168.41 -75.41 1 1.00e+01 1.00e-02 7.18e+01 dihedral pdb=" CB CYS C 480 " pdb=" SG CYS C 480 " pdb=" SG CYS C 488 " pdb=" CB CYS C 488 " ideal model delta sinusoidal sigma weight residual 93.00 161.94 -68.94 1 1.00e+01 1.00e-02 6.15e+01 dihedral pdb=" CB CYS C 336 " pdb=" SG CYS C 336 " pdb=" SG CYS C 361 " pdb=" CB CYS C 361 " ideal model delta sinusoidal sigma weight residual -86.00 -38.05 -47.95 1 1.00e+01 1.00e-02 3.17e+01 ... (remaining 4053 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 693 0.037 - 0.074: 217 0.074 - 0.111: 78 0.111 - 0.148: 31 0.148 - 0.185: 3 Chirality restraints: 1022 Sorted by residual: chirality pdb=" CA VAL B 11 " pdb=" N VAL B 11 " pdb=" C VAL B 11 " pdb=" CB VAL B 11 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.18 2.00e-01 2.50e+01 8.52e-01 chirality pdb=" CA ILE B 48 " pdb=" N ILE B 48 " pdb=" C ILE B 48 " pdb=" CB ILE B 48 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.50e-01 chirality pdb=" CA ASN B 52 " pdb=" N ASN B 52 " pdb=" C ASN B 52 " pdb=" CB ASN B 52 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.89e-01 ... (remaining 1019 not shown) Planarity restraints: 1194 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS C 478 " -0.052 5.00e-02 4.00e+02 7.77e-02 9.66e+00 pdb=" N PRO C 479 " 0.134 5.00e-02 4.00e+02 pdb=" CA PRO C 479 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO C 479 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 372 " 0.020 5.00e-02 4.00e+02 3.02e-02 1.46e+00 pdb=" N PRO C 373 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO C 373 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 373 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 362 " 0.006 2.00e-02 2.50e+03 1.17e-02 1.37e+00 pdb=" C VAL C 362 " -0.020 2.00e-02 2.50e+03 pdb=" O VAL C 362 " 0.008 2.00e-02 2.50e+03 pdb=" N ALA C 363 " 0.007 2.00e-02 2.50e+03 ... (remaining 1191 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 111 2.66 - 3.22: 5977 3.22 - 3.78: 10000 3.78 - 4.34: 14631 4.34 - 4.90: 24437 Nonbonded interactions: 55156 Sorted by model distance: nonbonded pdb=" O SER C 366 " pdb=" ND2 ASN C 370 " model vdw 2.103 3.120 nonbonded pdb=" O PHE R 486 " pdb=" ND2 ASN C 450 " model vdw 2.240 3.120 nonbonded pdb=" O TRP R 353 " pdb=" NH1 ARG R 466 " model vdw 2.275 3.120 nonbonded pdb=" NH1 ARG H 71 " pdb=" OG1 THR H 73 " model vdw 2.281 3.120 nonbonded pdb=" N GLN H 105 " pdb=" OE1 GLN H 105 " model vdw 2.294 3.120 ... (remaining 55151 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'H' } ncs_group { reference = chain 'B' selection = chain 'L' } ncs_group { reference = chain 'C' selection = chain 'R' } 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: 134.480 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 27.020 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 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:3.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 165.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 6830 Z= 0.179 Angle : 0.595 7.443 9300 Z= 0.351 Chirality : 0.045 0.185 1022 Planarity : 0.004 0.078 1192 Dihedral : 14.192 85.558 2448 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.14 % Allowed : 13.86 % Favored : 86.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.28), residues: 838 helix: -3.52 (0.46), residues: 64 sheet: 1.18 (0.33), residues: 276 loop : -0.22 (0.25), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 47 HIS 0.001 0.000 HIS C 505 PHE 0.013 0.001 PHE R 392 TYR 0.018 0.001 TYR L 49 ARG 0.004 0.000 ARG C 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00119 ( 2) link_NAG-ASN : angle 0.91710 ( 6) hydrogen bonds : bond 0.19375 ( 224) hydrogen bonds : angle 9.21471 ( 558) SS BOND : bond 0.00373 ( 12) SS BOND : angle 1.40294 ( 24) covalent geometry : bond 0.00349 ( 6816) covalent geometry : angle 0.59123 ( 9270) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 109 time to evaluate : 0.756 Fit side-chains REVERT: L 17 GLN cc_start: 0.7476 (mm-40) cc_final: 0.7062 (tt0) REVERT: L 78 LEU cc_start: 0.7864 (tp) cc_final: 0.7593 (mt) REVERT: R 466 ARG cc_start: 0.8088 (ptm160) cc_final: 0.7887 (ptt180) outliers start: 1 outliers final: 1 residues processed: 109 average time/residue: 0.2857 time to fit residues: 42.0972 Evaluate side-chains 105 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 104 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 427 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 69 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 64 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 39 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 487 ASN C 448 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.134639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.108746 restraints weight = 8271.227| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 1.96 r_work: 0.3100 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.0982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 6830 Z= 0.206 Angle : 0.591 7.612 9300 Z= 0.319 Chirality : 0.047 0.175 1022 Planarity : 0.005 0.051 1192 Dihedral : 5.923 53.138 980 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.31 % Allowed : 13.18 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.27), residues: 838 helix: -3.88 (0.44), residues: 54 sheet: 0.94 (0.32), residues: 274 loop : -0.42 (0.25), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 47 HIS 0.002 0.001 HIS B 34 PHE 0.012 0.001 PHE R 392 TYR 0.026 0.002 TYR L 49 ARG 0.003 0.000 ARG C 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00132 ( 2) link_NAG-ASN : angle 1.32051 ( 6) hydrogen bonds : bond 0.03959 ( 224) hydrogen bonds : angle 6.60607 ( 558) SS BOND : bond 0.00334 ( 12) SS BOND : angle 1.30199 ( 24) covalent geometry : bond 0.00486 ( 6816) covalent geometry : angle 0.58730 ( 9270) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 101 time to evaluate : 0.799 Fit side-chains REVERT: H 77 GLN cc_start: 0.8192 (OUTLIER) cc_final: 0.7990 (pt0) REVERT: L 17 GLN cc_start: 0.7298 (mm-40) cc_final: 0.7060 (tt0) REVERT: L 69 THR cc_start: 0.9062 (t) cc_final: 0.8517 (m) REVERT: L 78 LEU cc_start: 0.7958 (tp) cc_final: 0.7607 (mt) outliers start: 17 outliers final: 10 residues processed: 111 average time/residue: 0.2644 time to fit residues: 39.0400 Evaluate side-chains 107 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 96 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 77 GLN Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain L residue 95 LEU Chi-restraints excluded: chain R residue 362 VAL Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 470 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 39 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 79 optimal weight: 0.5980 chunk 7 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 53 optimal weight: 0.0970 chunk 69 optimal weight: 0.6980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 370 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.135443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.106348 restraints weight = 8233.694| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 1.97 r_work: 0.3031 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6830 Z= 0.188 Angle : 0.563 7.583 9300 Z= 0.304 Chirality : 0.046 0.171 1022 Planarity : 0.005 0.048 1192 Dihedral : 5.738 52.846 978 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.31 % Allowed : 14.67 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.27), residues: 838 helix: -3.77 (0.46), residues: 50 sheet: 0.74 (0.31), residues: 278 loop : -0.63 (0.24), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.002 0.001 HIS B 34 PHE 0.010 0.001 PHE B 91 TYR 0.021 0.002 TYR L 49 ARG 0.004 0.000 ARG R 466 Details of bonding type rmsd link_NAG-ASN : bond 0.00115 ( 2) link_NAG-ASN : angle 1.18567 ( 6) hydrogen bonds : bond 0.03301 ( 224) hydrogen bonds : angle 6.19058 ( 558) SS BOND : bond 0.00365 ( 12) SS BOND : angle 1.36469 ( 24) covalent geometry : bond 0.00442 ( 6816) covalent geometry : angle 0.55885 ( 9270) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 104 time to evaluate : 0.684 Fit side-chains REVERT: L 17 GLN cc_start: 0.7293 (mm-40) cc_final: 0.6937 (tt0) REVERT: L 69 THR cc_start: 0.9118 (t) cc_final: 0.8639 (m) REVERT: L 78 LEU cc_start: 0.7860 (tp) cc_final: 0.7509 (mt) REVERT: A 56 GLU cc_start: 0.8760 (mt-10) cc_final: 0.8558 (mt-10) REVERT: C 501 TYR cc_start: 0.8652 (OUTLIER) cc_final: 0.8351 (m-10) outliers start: 17 outliers final: 13 residues processed: 113 average time/residue: 0.1906 time to fit residues: 28.4259 Evaluate side-chains 115 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 101 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 95 LEU Chi-restraints excluded: chain R residue 362 VAL Chi-restraints excluded: chain R residue 470 THR Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 501 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 24 optimal weight: 0.8980 chunk 71 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 22 optimal weight: 0.9980 chunk 38 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 448 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.133541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.104394 restraints weight = 8273.152| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 1.97 r_work: 0.3008 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 6830 Z= 0.237 Angle : 0.588 6.354 9300 Z= 0.317 Chirality : 0.047 0.171 1022 Planarity : 0.005 0.044 1192 Dihedral : 5.833 52.592 978 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.53 % Allowed : 14.40 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.27), residues: 838 helix: -3.83 (0.47), residues: 50 sheet: 0.58 (0.31), residues: 278 loop : -0.77 (0.24), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 47 HIS 0.002 0.001 HIS R 505 PHE 0.011 0.002 PHE B 91 TYR 0.023 0.002 TYR B 49 ARG 0.003 0.000 ARG C 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00062 ( 2) link_NAG-ASN : angle 1.32448 ( 6) hydrogen bonds : bond 0.03150 ( 224) hydrogen bonds : angle 6.11545 ( 558) SS BOND : bond 0.00451 ( 12) SS BOND : angle 1.32547 ( 24) covalent geometry : bond 0.00567 ( 6816) covalent geometry : angle 0.58432 ( 9270) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 105 time to evaluate : 0.716 Fit side-chains REVERT: L 17 GLN cc_start: 0.7343 (mm-40) cc_final: 0.6943 (tt0) REVERT: L 69 THR cc_start: 0.9205 (t) cc_final: 0.8751 (m) REVERT: L 78 LEU cc_start: 0.7906 (tp) cc_final: 0.7539 (mt) REVERT: R 442 ASP cc_start: 0.8978 (m-30) cc_final: 0.8503 (m-30) REVERT: A 56 GLU cc_start: 0.8734 (mt-10) cc_final: 0.8419 (mt-10) REVERT: C 370 ASN cc_start: 0.8016 (m-40) cc_final: 0.7796 (m110) REVERT: C 501 TYR cc_start: 0.8710 (OUTLIER) cc_final: 0.8387 (m-10) outliers start: 26 outliers final: 20 residues processed: 121 average time/residue: 0.1909 time to fit residues: 30.7934 Evaluate side-chains 122 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 101 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 97 ASN Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 95 LEU Chi-restraints excluded: chain R residue 362 VAL Chi-restraints excluded: chain R residue 415 THR Chi-restraints excluded: chain R residue 468 ILE Chi-restraints excluded: chain R residue 470 THR Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 501 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 6 optimal weight: 2.9990 chunk 72 optimal weight: 0.4980 chunk 67 optimal weight: 0.6980 chunk 34 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 25 optimal weight: 0.0060 chunk 61 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 57 optimal weight: 0.5980 chunk 39 optimal weight: 0.6980 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.135784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.106580 restraints weight = 8127.236| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 1.97 r_work: 0.3046 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6830 Z= 0.153 Angle : 0.525 6.634 9300 Z= 0.284 Chirality : 0.045 0.170 1022 Planarity : 0.004 0.031 1192 Dihedral : 5.672 52.708 978 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.67 % Allowed : 15.08 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.27), residues: 838 helix: -3.93 (0.44), residues: 54 sheet: 0.53 (0.31), residues: 278 loop : -0.69 (0.24), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.001 0.000 HIS B 34 PHE 0.008 0.001 PHE L 91 TYR 0.018 0.001 TYR L 49 ARG 0.002 0.000 ARG R 466 Details of bonding type rmsd link_NAG-ASN : bond 0.00099 ( 2) link_NAG-ASN : angle 1.17990 ( 6) hydrogen bonds : bond 0.02737 ( 224) hydrogen bonds : angle 5.97052 ( 558) SS BOND : bond 0.00375 ( 12) SS BOND : angle 1.03825 ( 24) covalent geometry : bond 0.00360 ( 6816) covalent geometry : angle 0.52257 ( 9270) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 106 time to evaluate : 0.752 Fit side-chains REVERT: H 76 SER cc_start: 0.8414 (m) cc_final: 0.8046 (p) REVERT: L 17 GLN cc_start: 0.7337 (mm-40) cc_final: 0.6972 (tt0) REVERT: L 69 THR cc_start: 0.9162 (t) cc_final: 0.8696 (m) REVERT: L 78 LEU cc_start: 0.7894 (tp) cc_final: 0.7621 (mt) REVERT: A 56 GLU cc_start: 0.8701 (mt-10) cc_final: 0.8347 (mt-10) REVERT: C 501 TYR cc_start: 0.8643 (OUTLIER) cc_final: 0.8321 (m-10) outliers start: 27 outliers final: 20 residues processed: 124 average time/residue: 0.2007 time to fit residues: 32.6587 Evaluate side-chains 125 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 104 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 97 ASN Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 95 LEU Chi-restraints excluded: chain R residue 362 VAL Chi-restraints excluded: chain R residue 389 ASP Chi-restraints excluded: chain R residue 415 THR Chi-restraints excluded: chain R residue 470 THR Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 501 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 63 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 2 optimal weight: 0.4980 chunk 70 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 79 optimal weight: 0.7980 chunk 58 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 69 optimal weight: 0.0970 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 370 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.134467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.104934 restraints weight = 8121.917| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 2.02 r_work: 0.2998 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6830 Z= 0.186 Angle : 0.550 6.009 9300 Z= 0.296 Chirality : 0.045 0.171 1022 Planarity : 0.004 0.037 1192 Dihedral : 5.692 52.549 978 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.94 % Allowed : 14.81 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.27), residues: 838 helix: -3.92 (0.45), residues: 54 sheet: 0.66 (0.32), residues: 258 loop : -0.82 (0.24), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.001 0.001 HIS R 505 PHE 0.009 0.001 PHE L 91 TYR 0.021 0.002 TYR L 49 ARG 0.003 0.000 ARG H 71 Details of bonding type rmsd link_NAG-ASN : bond 0.00076 ( 2) link_NAG-ASN : angle 1.22387 ( 6) hydrogen bonds : bond 0.02813 ( 224) hydrogen bonds : angle 5.96166 ( 558) SS BOND : bond 0.00272 ( 12) SS BOND : angle 1.14209 ( 24) covalent geometry : bond 0.00442 ( 6816) covalent geometry : angle 0.54661 ( 9270) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 109 time to evaluate : 0.632 Fit side-chains REVERT: H 76 SER cc_start: 0.8334 (m) cc_final: 0.7999 (p) REVERT: L 17 GLN cc_start: 0.7319 (mm-40) cc_final: 0.6910 (tt0) REVERT: L 69 THR cc_start: 0.9151 (t) cc_final: 0.8687 (m) REVERT: L 78 LEU cc_start: 0.7836 (tp) cc_final: 0.7535 (mt) REVERT: A 56 GLU cc_start: 0.8694 (mt-10) cc_final: 0.8265 (mt-10) REVERT: A 82 ASN cc_start: 0.8371 (t0) cc_final: 0.8082 (m-40) REVERT: C 370 ASN cc_start: 0.7827 (m-40) cc_final: 0.7625 (m110) REVERT: C 452 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8726 (mt) REVERT: C 501 TYR cc_start: 0.8676 (OUTLIER) cc_final: 0.8328 (m-10) outliers start: 29 outliers final: 23 residues processed: 127 average time/residue: 0.1967 time to fit residues: 32.6961 Evaluate side-chains 131 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 106 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 97 ASN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 95 LEU Chi-restraints excluded: chain R residue 362 VAL Chi-restraints excluded: chain R residue 389 ASP Chi-restraints excluded: chain R residue 415 THR Chi-restraints excluded: chain R residue 468 ILE Chi-restraints excluded: chain R residue 470 THR Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 501 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 77 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 chunk 35 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 2 optimal weight: 0.0970 chunk 1 optimal weight: 0.0270 overall best weight: 0.3836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.137703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.110755 restraints weight = 8145.656| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 2.04 r_work: 0.3128 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6830 Z= 0.131 Angle : 0.522 4.946 9300 Z= 0.280 Chirality : 0.044 0.168 1022 Planarity : 0.004 0.035 1192 Dihedral : 5.578 52.807 978 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.53 % Allowed : 15.49 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.27), residues: 838 helix: -3.90 (0.45), residues: 54 sheet: 0.75 (0.33), residues: 248 loop : -0.78 (0.23), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 436 HIS 0.001 0.000 HIS B 34 PHE 0.008 0.001 PHE L 91 TYR 0.016 0.001 TYR L 49 ARG 0.004 0.000 ARG H 71 Details of bonding type rmsd link_NAG-ASN : bond 0.00132 ( 2) link_NAG-ASN : angle 1.10777 ( 6) hydrogen bonds : bond 0.02567 ( 224) hydrogen bonds : angle 5.87020 ( 558) SS BOND : bond 0.00288 ( 12) SS BOND : angle 0.94939 ( 24) covalent geometry : bond 0.00306 ( 6816) covalent geometry : angle 0.51969 ( 9270) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 106 time to evaluate : 0.698 Fit side-chains REVERT: H 64 LYS cc_start: 0.7829 (OUTLIER) cc_final: 0.7576 (tptm) REVERT: H 76 SER cc_start: 0.8433 (m) cc_final: 0.8178 (p) REVERT: L 17 GLN cc_start: 0.7393 (mm-40) cc_final: 0.7089 (tt0) REVERT: L 69 THR cc_start: 0.9133 (t) cc_final: 0.8652 (m) REVERT: L 78 LEU cc_start: 0.7944 (tp) cc_final: 0.7720 (mt) REVERT: A 56 GLU cc_start: 0.8628 (mt-10) cc_final: 0.8299 (mt-10) REVERT: C 452 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8698 (mt) REVERT: C 501 TYR cc_start: 0.8613 (OUTLIER) cc_final: 0.8275 (m-10) outliers start: 26 outliers final: 20 residues processed: 124 average time/residue: 0.2006 time to fit residues: 32.3434 Evaluate side-chains 129 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 106 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain H residue 97 ASN Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 95 LEU Chi-restraints excluded: chain R residue 362 VAL Chi-restraints excluded: chain R residue 389 ASP Chi-restraints excluded: chain R residue 415 THR Chi-restraints excluded: chain R residue 470 THR Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 501 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 70 optimal weight: 0.1980 chunk 32 optimal weight: 0.0980 chunk 26 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 69 optimal weight: 0.6980 chunk 71 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 38 optimal weight: 0.3980 chunk 19 optimal weight: 0.1980 chunk 39 optimal weight: 0.9990 overall best weight: 0.3180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 370 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.137423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.107282 restraints weight = 8088.716| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 2.13 r_work: 0.3072 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6830 Z= 0.118 Angle : 0.507 4.638 9300 Z= 0.272 Chirality : 0.044 0.165 1022 Planarity : 0.004 0.032 1192 Dihedral : 5.480 52.933 978 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.80 % Allowed : 15.35 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.27), residues: 838 helix: -3.96 (0.43), residues: 54 sheet: 0.75 (0.33), residues: 248 loop : -0.69 (0.24), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 436 HIS 0.001 0.000 HIS B 34 PHE 0.008 0.001 PHE L 91 TYR 0.015 0.001 TYR L 49 ARG 0.003 0.000 ARG C 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00139 ( 2) link_NAG-ASN : angle 1.06152 ( 6) hydrogen bonds : bond 0.02492 ( 224) hydrogen bonds : angle 5.83362 ( 558) SS BOND : bond 0.00302 ( 12) SS BOND : angle 0.87884 ( 24) covalent geometry : bond 0.00275 ( 6816) covalent geometry : angle 0.50488 ( 9270) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 105 time to evaluate : 0.669 Fit side-chains REVERT: H 64 LYS cc_start: 0.7583 (OUTLIER) cc_final: 0.7222 (tptm) REVERT: L 17 GLN cc_start: 0.7256 (mm-40) cc_final: 0.6756 (tt0) REVERT: L 78 LEU cc_start: 0.7719 (tp) cc_final: 0.7505 (mt) REVERT: A 56 GLU cc_start: 0.8652 (mt-10) cc_final: 0.8150 (mt-10) REVERT: C 452 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8760 (mt) REVERT: C 501 TYR cc_start: 0.8536 (OUTLIER) cc_final: 0.8123 (m-10) outliers start: 28 outliers final: 22 residues processed: 122 average time/residue: 0.2078 time to fit residues: 32.7632 Evaluate side-chains 128 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 103 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain H residue 97 ASN Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 95 LEU Chi-restraints excluded: chain R residue 362 VAL Chi-restraints excluded: chain R residue 389 ASP Chi-restraints excluded: chain R residue 415 THR Chi-restraints excluded: chain R residue 468 ILE Chi-restraints excluded: chain R residue 470 THR Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 501 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 61 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 chunk 29 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 12 optimal weight: 0.0870 chunk 19 optimal weight: 2.9990 chunk 45 optimal weight: 0.0470 overall best weight: 0.4656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 ASN C 370 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.136747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.106521 restraints weight = 8151.963| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 2.14 r_work: 0.3065 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6830 Z= 0.147 Angle : 0.523 4.512 9300 Z= 0.281 Chirality : 0.044 0.167 1022 Planarity : 0.004 0.032 1192 Dihedral : 5.503 52.780 978 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.80 % Allowed : 15.90 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.27), residues: 838 helix: -3.93 (0.44), residues: 54 sheet: 0.73 (0.33), residues: 248 loop : -0.71 (0.24), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 47 HIS 0.001 0.000 HIS B 34 PHE 0.008 0.001 PHE L 91 TYR 0.018 0.001 TYR L 49 ARG 0.004 0.000 ARG C 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00110 ( 2) link_NAG-ASN : angle 1.09668 ( 6) hydrogen bonds : bond 0.02589 ( 224) hydrogen bonds : angle 5.86484 ( 558) SS BOND : bond 0.00297 ( 12) SS BOND : angle 0.88579 ( 24) covalent geometry : bond 0.00347 ( 6816) covalent geometry : angle 0.52116 ( 9270) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 103 time to evaluate : 0.759 Fit side-chains REVERT: H 64 LYS cc_start: 0.7608 (OUTLIER) cc_final: 0.7244 (tptm) REVERT: L 17 GLN cc_start: 0.7277 (mm-40) cc_final: 0.6774 (tt0) REVERT: L 78 LEU cc_start: 0.7754 (tp) cc_final: 0.7528 (mt) REVERT: A 56 GLU cc_start: 0.8646 (mt-10) cc_final: 0.8121 (mt-10) REVERT: C 452 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8741 (mt) REVERT: C 501 TYR cc_start: 0.8572 (OUTLIER) cc_final: 0.8232 (m-10) outliers start: 28 outliers final: 22 residues processed: 121 average time/residue: 0.2029 time to fit residues: 32.1288 Evaluate side-chains 127 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 102 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain H residue 97 ASN Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 95 LEU Chi-restraints excluded: chain R residue 362 VAL Chi-restraints excluded: chain R residue 389 ASP Chi-restraints excluded: chain R residue 468 ILE Chi-restraints excluded: chain R residue 470 THR Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 501 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 79 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 80 optimal weight: 0.0270 chunk 52 optimal weight: 0.3980 chunk 5 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 chunk 51 optimal weight: 0.4980 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 77 GLN A 97 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.136860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.105748 restraints weight = 8251.287| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 2.28 r_work: 0.3004 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.122 6830 Z= 0.242 Angle : 1.114 59.185 9300 Z= 0.694 Chirality : 0.045 0.256 1022 Planarity : 0.006 0.122 1192 Dihedral : 5.534 52.778 978 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.67 % Allowed : 16.17 % Favored : 80.16 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.27), residues: 838 helix: -4.00 (0.44), residues: 54 sheet: 0.72 (0.33), residues: 248 loop : -0.71 (0.24), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 47 HIS 0.001 0.000 HIS B 34 PHE 0.008 0.001 PHE L 91 TYR 0.018 0.001 TYR L 49 ARG 0.003 0.000 ARG C 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00111 ( 2) link_NAG-ASN : angle 1.09636 ( 6) hydrogen bonds : bond 0.02851 ( 224) hydrogen bonds : angle 5.88740 ( 558) SS BOND : bond 0.00310 ( 12) SS BOND : angle 0.95626 ( 24) covalent geometry : bond 0.00492 ( 6816) covalent geometry : angle 1.11423 ( 9270) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1676 Ramachandran restraints generated. 838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 102 time to evaluate : 1.051 Fit side-chains REVERT: H 64 LYS cc_start: 0.7530 (OUTLIER) cc_final: 0.7133 (tptm) REVERT: L 17 GLN cc_start: 0.7195 (mm-40) cc_final: 0.6648 (tt0) REVERT: L 78 LEU cc_start: 0.7648 (tp) cc_final: 0.7420 (mt) REVERT: A 56 GLU cc_start: 0.8617 (mt-10) cc_final: 0.8039 (mt-10) REVERT: C 452 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8724 (mt) REVERT: C 501 TYR cc_start: 0.8524 (OUTLIER) cc_final: 0.8157 (m-10) outliers start: 27 outliers final: 23 residues processed: 119 average time/residue: 0.2089 time to fit residues: 32.2577 Evaluate side-chains 128 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 102 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain H residue 97 ASN Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 95 LEU Chi-restraints excluded: chain R residue 362 VAL Chi-restraints excluded: chain R residue 389 ASP Chi-restraints excluded: chain R residue 415 THR Chi-restraints excluded: chain R residue 468 ILE Chi-restraints excluded: chain R residue 470 THR Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 501 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 68 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 28 optimal weight: 0.4980 chunk 26 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 80 optimal weight: 0.0980 chunk 54 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 97 ASN ** C 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.137383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.107106 restraints weight = 8147.234| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 2.14 r_work: 0.3051 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.122 6830 Z= 0.242 Angle : 1.114 59.185 9300 Z= 0.694 Chirality : 0.045 0.256 1022 Planarity : 0.006 0.122 1192 Dihedral : 5.534 52.778 978 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.53 % Allowed : 16.30 % Favored : 80.16 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.27), residues: 838 helix: -4.00 (0.44), residues: 54 sheet: 0.72 (0.33), residues: 248 loop : -0.71 (0.24), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 47 HIS 0.001 0.000 HIS B 34 PHE 0.008 0.001 PHE L 91 TYR 0.018 0.001 TYR L 49 ARG 0.003 0.000 ARG C 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00111 ( 2) link_NAG-ASN : angle 1.09636 ( 6) hydrogen bonds : bond 0.02851 ( 224) hydrogen bonds : angle 5.88740 ( 558) SS BOND : bond 0.00538 ( 12) SS BOND : angle 0.99166 ( 24) covalent geometry : bond 0.00492 ( 6816) covalent geometry : angle 1.11423 ( 9270) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5520.51 seconds wall clock time: 97 minutes 37.02 seconds (5857.02 seconds total)