Starting phenix.real_space_refine on Wed Sep 17 07:25:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vke_43315/09_2025/8vke_43315.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vke_43315/09_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_43315/09_2025/8vke_43315.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vke_43315/09_2025/8vke_43315.map" model { file = "/net/cci-nas-00/data/ceres_data/8vke_43315/09_2025/8vke_43315.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vke_43315/09_2025/8vke_43315.cif" } resolution = 3.1 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 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 1.59, per 1000 atoms: 0.24 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: 0.50 Conformation dependent library (CDL) restraints added in 337.0 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 0.27 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: 1.04 Time building geometry restraints manager: 0.69 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: 0.00 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: 25.120 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: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.590 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.160 ------------------------------------------------------------------------------- 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 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: -0.05 (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 ARG 0.004 0.000 ARG C 346 TYR 0.018 0.001 TYR L 49 PHE 0.013 0.001 PHE R 392 TRP 0.007 0.001 TRP H 47 HIS 0.001 0.000 HIS C 505 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 6816) covalent geometry : angle 0.59123 ( 9270) SS BOND : bond 0.00373 ( 12) SS BOND : angle 1.40294 ( 24) hydrogen bonds : bond 0.19375 ( 224) hydrogen bonds : angle 9.21471 ( 558) link_NAG-ASN : bond 0.00119 ( 2) link_NAG-ASN : angle 0.91710 ( 6) *********************** 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 : 0.247 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: 0.0858 time to fit residues: 12.3821 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 : 0.281 ------------------------------------------------------------------------------- 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 49 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.0270 chunk 74 optimal weight: 0.9990 overall best weight: 0.7038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 52 ASN R 487 ASN C 448 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.134936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.108822 restraints weight = 8389.778| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 1.96 r_work: 0.3102 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.0944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 6830 Z= 0.203 Angle : 0.592 7.661 9300 Z= 0.320 Chirality : 0.047 0.170 1022 Planarity : 0.005 0.051 1192 Dihedral : 5.898 53.105 980 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.45 % Allowed : 13.18 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.35 (0.27), residues: 838 helix: -3.89 (0.43), residues: 54 sheet: 0.84 (0.32), residues: 278 loop : -0.40 (0.25), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 403 TYR 0.025 0.002 TYR L 49 PHE 0.012 0.001 PHE R 392 TRP 0.011 0.002 TRP H 47 HIS 0.002 0.001 HIS B 34 Details of bonding type rmsd covalent geometry : bond 0.00478 ( 6816) covalent geometry : angle 0.58811 ( 9270) SS BOND : bond 0.00326 ( 12) SS BOND : angle 1.26447 ( 24) hydrogen bonds : bond 0.03693 ( 224) hydrogen bonds : angle 6.64562 ( 558) link_NAG-ASN : bond 0.00038 ( 2) link_NAG-ASN : angle 1.28270 ( 6) *********************** 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 119 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 101 time to evaluate : 0.212 Fit side-chains REVERT: L 69 THR cc_start: 0.9056 (t) cc_final: 0.8566 (m) REVERT: L 78 LEU cc_start: 0.7976 (tp) cc_final: 0.7625 (mt) REVERT: A 56 GLU cc_start: 0.8623 (mp0) cc_final: 0.8404 (mt-10) outliers start: 18 outliers final: 11 residues processed: 112 average time/residue: 0.0902 time to fit residues: 13.2304 Evaluate side-chains 109 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 98 time to evaluate : 0.263 ------------------------------------------------------------------------------- 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 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 36 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 4 optimal weight: 0.0060 chunk 24 optimal weight: 0.9990 chunk 79 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 37 optimal weight: 0.0770 chunk 0 optimal weight: 2.9990 overall best weight: 0.4954 ------------------------------------------------------------------------------- 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 = 0.3599 r_free = 0.3599 target = 0.136844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.108003 restraints weight = 8111.372| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 1.95 r_work: 0.3041 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.1201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 6830 Z= 0.157 Angle : 0.542 8.473 9300 Z= 0.292 Chirality : 0.045 0.172 1022 Planarity : 0.004 0.040 1192 Dihedral : 5.640 53.032 978 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.17 % Allowed : 15.22 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.45 (0.27), residues: 838 helix: -3.82 (0.45), residues: 54 sheet: 0.78 (0.32), residues: 278 loop : -0.49 (0.25), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 466 TYR 0.018 0.002 TYR L 49 PHE 0.008 0.001 PHE B 91 TRP 0.009 0.001 TRP H 47 HIS 0.002 0.001 HIS B 34 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 6816) covalent geometry : angle 0.53764 ( 9270) SS BOND : bond 0.00302 ( 12) SS BOND : angle 1.43236 ( 24) hydrogen bonds : bond 0.03212 ( 224) hydrogen bonds : angle 6.22675 ( 558) link_NAG-ASN : bond 0.00124 ( 2) link_NAG-ASN : angle 1.14779 ( 6) *********************** 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: 16 poor density : 105 time to evaluate : 0.243 Fit side-chains REVERT: L 69 THR cc_start: 0.9076 (t) cc_final: 0.8513 (m) REVERT: L 78 LEU cc_start: 0.7823 (tp) cc_final: 0.7457 (mt) REVERT: R 466 ARG cc_start: 0.8340 (ptm-80) cc_final: 0.8038 (ptt180) REVERT: A 56 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.8218 (mt-10) outliers start: 16 outliers final: 12 residues processed: 112 average time/residue: 0.0915 time to fit residues: 13.3848 Evaluate side-chains 115 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 102 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 R residue 415 THR Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 56 GLU 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 7 optimal weight: 4.9990 chunk 75 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 64 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.133636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.104579 restraints weight = 8236.336| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 1.97 r_work: 0.3005 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 6830 Z= 0.229 Angle : 0.590 6.474 9300 Z= 0.319 Chirality : 0.047 0.173 1022 Planarity : 0.005 0.045 1192 Dihedral : 5.841 52.675 978 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 3.53 % Allowed : 14.54 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.72 (0.27), residues: 838 helix: -3.73 (0.50), residues: 50 sheet: 0.61 (0.31), residues: 278 loop : -0.75 (0.24), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 346 TYR 0.024 0.002 TYR B 49 PHE 0.011 0.002 PHE B 91 TRP 0.013 0.002 TRP H 47 HIS 0.002 0.001 HIS R 505 Details of bonding type rmsd covalent geometry : bond 0.00545 ( 6816) covalent geometry : angle 0.58688 ( 9270) SS BOND : bond 0.00412 ( 12) SS BOND : angle 1.27175 ( 24) hydrogen bonds : bond 0.03165 ( 224) hydrogen bonds : angle 6.11503 ( 558) link_NAG-ASN : bond 0.00079 ( 2) link_NAG-ASN : angle 1.29980 ( 6) *********************** 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 132 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 106 time to evaluate : 0.245 Fit side-chains REVERT: H 76 SER cc_start: 0.8423 (m) cc_final: 0.8044 (p) REVERT: L 69 THR cc_start: 0.9205 (t) cc_final: 0.8748 (m) REVERT: L 78 LEU cc_start: 0.7919 (tp) cc_final: 0.7548 (mt) REVERT: R 442 ASP cc_start: 0.8976 (m-30) cc_final: 0.8507 (m-30) REVERT: A 56 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.7950 (mp0) REVERT: C 501 TYR cc_start: 0.8672 (OUTLIER) cc_final: 0.8118 (m-10) outliers start: 26 outliers final: 19 residues processed: 121 average time/residue: 0.0880 time to fit residues: 14.0126 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 : 0.250 ------------------------------------------------------------------------------- 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 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 56 GLU 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 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 55 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 2 optimal weight: 0.0470 chunk 17 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 overall best weight: 0.7282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 448 ASN A 97 ASN C 370 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.134182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.104880 restraints weight = 8286.032| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 1.98 r_work: 0.3012 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 6830 Z= 0.206 Angle : 0.562 5.580 9300 Z= 0.303 Chirality : 0.046 0.171 1022 Planarity : 0.004 0.037 1192 Dihedral : 5.790 52.566 978 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.80 % Allowed : 14.67 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.84 (0.27), residues: 838 helix: -3.88 (0.47), residues: 50 sheet: 0.50 (0.31), residues: 278 loop : -0.82 (0.24), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 346 TYR 0.021 0.002 TYR L 49 PHE 0.009 0.001 PHE L 91 TRP 0.012 0.002 TRP H 47 HIS 0.002 0.001 HIS R 505 Details of bonding type rmsd covalent geometry : bond 0.00489 ( 6816) covalent geometry : angle 0.55886 ( 9270) SS BOND : bond 0.00420 ( 12) SS BOND : angle 1.15422 ( 24) hydrogen bonds : bond 0.02937 ( 224) hydrogen bonds : angle 6.05215 ( 558) link_NAG-ASN : bond 0.00057 ( 2) link_NAG-ASN : angle 1.28651 ( 6) *********************** 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 137 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 109 time to evaluate : 0.251 Fit side-chains REVERT: H 76 SER cc_start: 0.8412 (m) cc_final: 0.8061 (p) REVERT: L 69 THR cc_start: 0.9208 (t) cc_final: 0.8759 (m) REVERT: L 78 LEU cc_start: 0.7862 (tp) cc_final: 0.7540 (mt) REVERT: R 442 ASP cc_start: 0.8974 (m-30) cc_final: 0.8517 (m-30) REVERT: A 56 GLU cc_start: 0.8613 (OUTLIER) cc_final: 0.8132 (mt-10) REVERT: C 501 TYR cc_start: 0.8676 (OUTLIER) cc_final: 0.8073 (m-10) outliers start: 28 outliers final: 20 residues processed: 126 average time/residue: 0.0918 time to fit residues: 15.0896 Evaluate side-chains 129 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 107 time to evaluate : 0.253 ------------------------------------------------------------------------------- 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 470 THR Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 56 GLU 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 56 optimal weight: 0.9980 chunk 57 optimal weight: 0.1980 chunk 62 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 77 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 61 optimal weight: 0.0970 chunk 71 optimal weight: 0.0040 chunk 69 optimal weight: 0.0670 chunk 18 optimal weight: 0.5980 overall best weight: 0.1928 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.139448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.110696 restraints weight = 8238.712| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 1.97 r_work: 0.3075 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 6830 Z= 0.097 Angle : 0.490 5.980 9300 Z= 0.264 Chirality : 0.043 0.165 1022 Planarity : 0.004 0.032 1192 Dihedral : 5.512 53.082 978 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.99 % Allowed : 15.62 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.68 (0.27), residues: 838 helix: -3.99 (0.43), residues: 54 sheet: 0.74 (0.32), residues: 258 loop : -0.67 (0.24), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 466 TYR 0.012 0.001 TYR R 421 PHE 0.007 0.001 PHE L 91 TRP 0.010 0.001 TRP C 436 HIS 0.001 0.000 HIS B 34 Details of bonding type rmsd covalent geometry : bond 0.00219 ( 6816) covalent geometry : angle 0.48839 ( 9270) SS BOND : bond 0.00314 ( 12) SS BOND : angle 0.86490 ( 24) hydrogen bonds : bond 0.02471 ( 224) hydrogen bonds : angle 5.85265 ( 558) link_NAG-ASN : bond 0.00176 ( 2) link_NAG-ASN : angle 1.05019 ( 6) *********************** 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 130 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 108 time to evaluate : 0.222 Fit side-chains REVERT: L 69 THR cc_start: 0.9096 (t) cc_final: 0.8612 (m) REVERT: L 78 LEU cc_start: 0.7840 (tp) cc_final: 0.7619 (mt) REVERT: R 409 GLN cc_start: 0.9015 (OUTLIER) cc_final: 0.8809 (pt0) REVERT: A 56 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.8209 (mt-10) REVERT: A 58 SER cc_start: 0.8563 (t) cc_final: 0.8335 (m) REVERT: A 82 ASN cc_start: 0.8329 (t0) cc_final: 0.8083 (m-40) REVERT: C 501 TYR cc_start: 0.8522 (OUTLIER) cc_final: 0.7861 (m-10) outliers start: 22 outliers final: 15 residues processed: 123 average time/residue: 0.0942 time to fit residues: 14.8587 Evaluate side-chains 120 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 102 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain L residue 56 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 409 GLN 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 10 VAL Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 108 LEU 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 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 0 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 37 optimal weight: 0.5980 chunk 47 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 80 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.135446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.107269 restraints weight = 8211.467| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 1.87 r_work: 0.3079 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 6830 Z= 0.217 Angle : 0.564 5.503 9300 Z= 0.304 Chirality : 0.046 0.168 1022 Planarity : 0.004 0.036 1192 Dihedral : 5.684 52.611 978 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.80 % Allowed : 15.22 % 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 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: -0.84 (0.26), residues: 838 helix: -4.02 (0.43), residues: 54 sheet: 0.73 (0.33), residues: 248 loop : -0.83 (0.23), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 346 TYR 0.022 0.002 TYR L 49 PHE 0.010 0.001 PHE B 91 TRP 0.011 0.002 TRP H 47 HIS 0.002 0.001 HIS B 34 Details of bonding type rmsd covalent geometry : bond 0.00519 ( 6816) covalent geometry : angle 0.56164 ( 9270) SS BOND : bond 0.00366 ( 12) SS BOND : angle 1.06688 ( 24) hydrogen bonds : bond 0.02818 ( 224) hydrogen bonds : angle 5.97588 ( 558) link_NAG-ASN : bond 0.00114 ( 2) link_NAG-ASN : angle 1.18457 ( 6) *********************** 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 134 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 106 time to evaluate : 0.240 Fit side-chains REVERT: H 64 LYS cc_start: 0.7821 (OUTLIER) cc_final: 0.7542 (tptm) REVERT: L 69 THR cc_start: 0.9149 (t) cc_final: 0.8681 (m) REVERT: L 78 LEU cc_start: 0.7960 (tp) cc_final: 0.7679 (mt) REVERT: R 409 GLN cc_start: 0.9155 (OUTLIER) cc_final: 0.8866 (pt0) REVERT: A 56 GLU cc_start: 0.8643 (OUTLIER) cc_final: 0.8176 (mt-10) REVERT: A 82 ASN cc_start: 0.8417 (t0) cc_final: 0.8217 (m-40) REVERT: C 501 TYR cc_start: 0.8685 (OUTLIER) cc_final: 0.8098 (m-10) outliers start: 28 outliers final: 21 residues processed: 124 average time/residue: 0.0847 time to fit residues: 13.7007 Evaluate side-chains 129 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 104 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 64 LYS 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 95 LEU Chi-restraints excluded: chain R residue 362 VAL Chi-restraints excluded: chain R residue 389 ASP Chi-restraints excluded: chain R residue 409 GLN 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 32 VAL Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain A residue 108 LEU 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 417 ASN Chi-restraints excluded: chain C residue 470 THR 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 31 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 81 optimal weight: 0.3980 chunk 74 optimal weight: 0.4980 chunk 13 optimal weight: 0.0980 chunk 7 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3600 r_free = 0.3600 target = 0.136083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.105066 restraints weight = 8141.010| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 2.22 r_work: 0.3009 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6830 Z= 0.166 Angle : 0.535 4.841 9300 Z= 0.288 Chirality : 0.045 0.169 1022 Planarity : 0.004 0.045 1192 Dihedral : 5.657 52.727 978 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.80 % Allowed : 15.62 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.87 (0.26), residues: 838 helix: -4.06 (0.42), residues: 54 sheet: 0.68 (0.33), residues: 248 loop : -0.83 (0.23), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 71 TYR 0.020 0.002 TYR L 49 PHE 0.008 0.001 PHE L 91 TRP 0.010 0.001 TRP H 47 HIS 0.001 0.001 HIS R 505 Details of bonding type rmsd covalent geometry : bond 0.00394 ( 6816) covalent geometry : angle 0.53307 ( 9270) SS BOND : bond 0.00363 ( 12) SS BOND : angle 0.98720 ( 24) hydrogen bonds : bond 0.02678 ( 224) hydrogen bonds : angle 5.93572 ( 558) link_NAG-ASN : bond 0.00100 ( 2) link_NAG-ASN : angle 1.16269 ( 6) *********************** 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 : 0.248 Fit side-chains REVERT: H 64 LYS cc_start: 0.7541 (OUTLIER) cc_final: 0.7137 (tptm) REVERT: L 69 THR cc_start: 0.8958 (t) cc_final: 0.8493 (m) REVERT: L 78 LEU cc_start: 0.7639 (tp) cc_final: 0.7385 (mt) REVERT: A 56 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.7969 (mt-10) REVERT: A 58 SER cc_start: 0.8609 (t) cc_final: 0.8395 (m) REVERT: A 82 ASN cc_start: 0.8349 (t0) cc_final: 0.8032 (m-40) REVERT: C 501 TYR cc_start: 0.8495 (OUTLIER) cc_final: 0.7725 (m-10) outliers start: 28 outliers final: 19 residues processed: 124 average time/residue: 0.0935 time to fit residues: 15.1679 Evaluate side-chains 124 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 102 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 64 LYS 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 56 GLU 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 390 LEU Chi-restraints excluded: chain C residue 417 ASN 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 22 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 68 optimal weight: 0.9990 chunk 37 optimal weight: 0.4980 chunk 71 optimal weight: 0.5980 chunk 53 optimal weight: 0.0970 chunk 46 optimal weight: 1.9990 chunk 48 optimal weight: 0.3980 chunk 31 optimal weight: 0.9980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.136988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.105803 restraints weight = 8241.733| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 2.25 r_work: 0.3015 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6830 Z= 0.145 Angle : 0.523 5.392 9300 Z= 0.282 Chirality : 0.044 0.168 1022 Planarity : 0.004 0.039 1192 Dihedral : 5.597 52.861 978 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 3.40 % Allowed : 16.03 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.77 (0.27), residues: 838 helix: -3.55 (0.47), residues: 66 sheet: 0.70 (0.33), residues: 248 loop : -0.69 (0.24), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 346 TYR 0.018 0.001 TYR L 49 PHE 0.008 0.001 PHE L 91 TRP 0.008 0.001 TRP H 47 HIS 0.001 0.000 HIS R 505 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 6816) covalent geometry : angle 0.52122 ( 9270) SS BOND : bond 0.00283 ( 12) SS BOND : angle 0.91564 ( 24) hydrogen bonds : bond 0.02603 ( 224) hydrogen bonds : angle 5.89908 ( 558) link_NAG-ASN : bond 0.00117 ( 2) link_NAG-ASN : angle 1.10173 ( 6) *********************** 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 127 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 102 time to evaluate : 0.193 Fit side-chains REVERT: H 64 LYS cc_start: 0.7650 (OUTLIER) cc_final: 0.7254 (tptm) REVERT: L 69 THR cc_start: 0.8936 (t) cc_final: 0.8468 (m) REVERT: L 78 LEU cc_start: 0.7653 (tp) cc_final: 0.7424 (mt) REVERT: A 56 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.7951 (mt-10) REVERT: A 82 ASN cc_start: 0.8360 (t0) cc_final: 0.8064 (m-40) REVERT: C 501 TYR cc_start: 0.8477 (OUTLIER) cc_final: 0.7748 (m-10) outliers start: 25 outliers final: 18 residues processed: 117 average time/residue: 0.0956 time to fit residues: 14.4804 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 : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 64 LYS 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 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 24 VAL Chi-restraints excluded: chain A residue 56 GLU 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 417 ASN 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 78 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 57 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 chunk 50 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 34 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3581 r_free = 0.3581 target = 0.134315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.102662 restraints weight = 8152.996| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 2.29 r_work: 0.2989 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 6830 Z= 0.194 Angle : 0.554 5.153 9300 Z= 0.298 Chirality : 0.045 0.169 1022 Planarity : 0.004 0.036 1192 Dihedral : 5.681 52.691 978 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.26 % Allowed : 16.30 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.85 (0.27), residues: 838 helix: -3.55 (0.46), residues: 66 sheet: 0.67 (0.33), residues: 248 loop : -0.77 (0.24), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 346 TYR 0.021 0.002 TYR L 49 PHE 0.009 0.001 PHE B 91 TRP 0.010 0.001 TRP H 47 HIS 0.001 0.001 HIS R 505 Details of bonding type rmsd covalent geometry : bond 0.00461 ( 6816) covalent geometry : angle 0.55200 ( 9270) SS BOND : bond 0.00320 ( 12) SS BOND : angle 0.98909 ( 24) hydrogen bonds : bond 0.02751 ( 224) hydrogen bonds : angle 5.96264 ( 558) link_NAG-ASN : bond 0.00097 ( 2) link_NAG-ASN : angle 1.16398 ( 6) ********************** 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 126 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 102 time to evaluate : 0.261 Fit side-chains REVERT: H 64 LYS cc_start: 0.7631 (OUTLIER) cc_final: 0.7223 (tptm) REVERT: L 69 THR cc_start: 0.8924 (t) cc_final: 0.8467 (m) REVERT: L 78 LEU cc_start: 0.7560 (tp) cc_final: 0.7307 (mt) REVERT: A 56 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.7869 (mt-10) REVERT: A 82 ASN cc_start: 0.8349 (t0) cc_final: 0.8061 (m-40) REVERT: C 501 TYR cc_start: 0.8497 (OUTLIER) cc_final: 0.7708 (m-10) outliers start: 24 outliers final: 20 residues processed: 117 average time/residue: 0.0979 time to fit residues: 14.8792 Evaluate side-chains 124 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 101 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 64 LYS 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 415 THR Chi-restraints excluded: chain R residue 468 ILE Chi-restraints excluded: chain R residue 470 THR Chi-restraints excluded: chain R residue 501 TYR Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 56 GLU 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 417 ASN 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 47 optimal weight: 2.9990 chunk 39 optimal weight: 0.2980 chunk 55 optimal weight: 1.9990 chunk 33 optimal weight: 0.4980 chunk 35 optimal weight: 0.9980 chunk 80 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 chunk 42 optimal weight: 0.4980 chunk 72 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.136036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.105357 restraints weight = 8046.328| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 2.18 r_work: 0.3040 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6830 Z= 0.158 Angle : 0.531 5.133 9300 Z= 0.286 Chirality : 0.044 0.170 1022 Planarity : 0.004 0.033 1192 Dihedral : 5.645 52.821 978 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.67 % Allowed : 16.30 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.87 (0.27), residues: 838 helix: -3.78 (0.41), residues: 66 sheet: 0.65 (0.33), residues: 248 loop : -0.75 (0.24), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 346 TYR 0.020 0.001 TYR L 49 PHE 0.008 0.001 PHE L 91 TRP 0.009 0.001 TRP H 47 HIS 0.001 0.001 HIS R 505 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 6816) covalent geometry : angle 0.52885 ( 9270) SS BOND : bond 0.00301 ( 12) SS BOND : angle 0.93726 ( 24) hydrogen bonds : bond 0.02649 ( 224) hydrogen bonds : angle 5.93200 ( 558) link_NAG-ASN : bond 0.00108 ( 2) link_NAG-ASN : angle 1.12733 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2303.53 seconds wall clock time: 40 minutes 21.49 seconds (2421.49 seconds total)