Starting phenix.real_space_refine on Wed Jul 1 21:44:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7k45_22660/07_2026/7k45_22660.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k45_22660/07_2026/7k45_22660.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7k45_22660/07_2026/7k45_22660.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k45_22660/07_2026/7k45_22660.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7k45_22660/07_2026/7k45_22660.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7k45_22660/07_2026/7k45_22660.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7k45_22660/07_2026/7k45_22660.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k45_22660/07_2026/7k45_22660.map" } resolution = 3.7 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= 0.015 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 16 5.16 5 C 1960 2.51 5 N 529 2.21 5 O 533 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3038 Number of models: 1 Model: "" Number of chains: 4 Chain: "H" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 849 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 3, 'TRANS': 118} Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "L" Number of atoms: 730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 730 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 96} Chain breaks: 1 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "B" Number of atoms: 1431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1431 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 11, 'TRANS': 182} Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 135 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 4, 'ASP:plan': 5, 'GLN:plan1': 2, 'TYR:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 55 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 0.95, per 1000 atoms: 0.31 Number of scatterers: 3038 At special positions: 0 Unit cell: (70.35, 55.65, 100.8, 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 16 16.00 O 533 8.00 N 529 7.00 C 1960 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.02 Simple disulfide: pdb=" SG CYS H 101 " - pdb=" SG CYS H 106 " distance=2.05 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.10 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 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 BETA1-4 " NAG A 1 " - " NAG A 2 " NAG-ASN " NAG A 1 " - " ASN B 343 " Time building additional restraints: 0.30 Conformation dependent library (CDL) restraints added in 139.4 milliseconds 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 764 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 10 sheets defined 15.3% alpha, 33.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'H' and resid 28 through 31 Processing helix chain 'H' and resid 64 through 66 No H-bonds generated for 'chain 'H' and resid 64 through 66' Processing helix chain 'H' and resid 74 through 76 No H-bonds generated for 'chain 'H' and resid 74 through 76' Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'L' and resid 30 through 32 No H-bonds generated for 'chain 'L' and resid 30 through 32' Processing helix chain 'L' and resid 80 through 84 removed outlier: 3.745A pdb=" N PHE L 84 " --> pdb=" O PRO L 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.815A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 370 removed outlier: 4.227A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.295A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 505 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: 6.052A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 12 Processing sheet with id=AA4, first strand: chain 'H' and resid 101 through 102 Processing sheet with id=AA5, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AA6, first strand: chain 'L' and resid 10 through 11 removed outlier: 6.738A pdb=" N LEU L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N TYR L 50 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 10 through 11 Processing sheet with id=AA8, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AA9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'B' and resid 473 through 474 126 hydrogen bonds defined for protein. 285 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: 0.46 Time building geometry restraints manager: 0.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 933 1.33 - 1.47: 940 1.47 - 1.60: 1225 1.60 - 1.73: 2 1.73 - 1.86: 18 Bond restraints: 3118 Sorted by residual: bond pdb=" CB ILE L 2 " pdb=" CG1 ILE L 2 " ideal model delta sigma weight residual 1.530 1.611 -0.081 2.00e-02 2.50e+03 1.65e+01 bond pdb=" C5 NAG A 2 " pdb=" O5 NAG A 2 " ideal model delta sigma weight residual 1.413 1.479 -0.066 2.00e-02 2.50e+03 1.09e+01 bond pdb=" C5 NAG A 1 " pdb=" O5 NAG A 1 " ideal model delta sigma weight residual 1.413 1.474 -0.061 2.00e-02 2.50e+03 9.37e+00 bond pdb=" NE1 TRP H 50 " pdb=" CE2 TRP H 50 " ideal model delta sigma weight residual 1.370 1.337 0.033 1.10e-02 8.26e+03 8.78e+00 bond pdb=" CB ASN B 422 " pdb=" CG ASN B 422 " ideal model delta sigma weight residual 1.516 1.446 0.070 2.50e-02 1.60e+03 7.94e+00 ... (remaining 3113 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 3463 1.63 - 3.26: 641 3.26 - 4.89: 116 4.89 - 6.53: 36 6.53 - 8.16: 11 Bond angle restraints: 4267 Sorted by residual: angle pdb=" C GLY H 8 " pdb=" N PRO H 9 " pdb=" CA PRO H 9 " ideal model delta sigma weight residual 120.03 128.19 -8.16 9.90e-01 1.02e+00 6.79e+01 angle pdb=" C ILE L 59 " pdb=" N PRO L 60 " pdb=" CA PRO L 60 " ideal model delta sigma weight residual 120.21 126.95 -6.74 9.60e-01 1.09e+00 4.93e+01 angle pdb=" C SER B 383 " pdb=" N PRO B 384 " pdb=" CA PRO B 384 " ideal model delta sigma weight residual 119.56 126.42 -6.86 1.02e+00 9.61e-01 4.53e+01 angle pdb=" C ALA B 520 " pdb=" N PRO B 521 " pdb=" CA PRO B 521 " ideal model delta sigma weight residual 119.56 126.33 -6.77 1.02e+00 9.61e-01 4.41e+01 angle pdb=" C GLN B 498 " pdb=" N PRO B 499 " pdb=" CA PRO B 499 " ideal model delta sigma weight residual 119.87 126.70 -6.83 1.04e+00 9.25e-01 4.31e+01 ... (remaining 4262 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.65: 1710 16.65 - 33.30: 55 33.30 - 49.94: 10 49.94 - 66.59: 4 66.59 - 83.24: 1 Dihedral angle restraints: 1780 sinusoidal: 576 harmonic: 1204 Sorted by residual: dihedral pdb=" CB CYS B 391 " pdb=" SG CYS B 391 " pdb=" SG CYS B 525 " pdb=" CB CYS B 525 " ideal model delta sinusoidal sigma weight residual 93.00 121.87 -28.87 1 1.00e+01 1.00e-02 1.19e+01 dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 89 " pdb=" CB CYS L 89 " ideal model delta sinusoidal sigma weight residual 93.00 66.25 26.75 1 1.00e+01 1.00e-02 1.03e+01 dihedral pdb=" C TYR L 92 " pdb=" N TYR L 92 " pdb=" CA TYR L 92 " pdb=" CB TYR L 92 " ideal model delta harmonic sigma weight residual -122.60 -115.16 -7.44 0 2.50e+00 1.60e-01 8.85e+00 ... (remaining 1777 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 306 0.068 - 0.136: 127 0.136 - 0.204: 28 0.204 - 0.272: 5 0.272 - 0.340: 4 Chirality restraints: 470 Sorted by residual: chirality pdb=" C1 NAG A 2 " pdb=" O4 NAG A 1 " pdb=" C2 NAG A 2 " pdb=" O5 NAG A 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.54 0.14 2.00e-02 2.50e+03 4.64e+01 chirality pdb=" C2 NAG A 2 " pdb=" C1 NAG A 2 " pdb=" C3 NAG A 2 " pdb=" N2 NAG A 2 " both_signs ideal model delta sigma weight residual False -2.49 -2.83 0.34 2.00e-01 2.50e+01 2.89e+00 chirality pdb=" C2 NAG A 1 " pdb=" C1 NAG A 1 " pdb=" C3 NAG A 1 " pdb=" N2 NAG A 1 " both_signs ideal model delta sigma weight residual False -2.49 -2.82 0.33 2.00e-01 2.50e+01 2.65e+00 ... (remaining 467 not shown) Planarity restraints: 561 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR L 92 " -0.030 2.00e-02 2.50e+03 1.51e-02 4.56e+00 pdb=" CG TYR L 92 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR L 92 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR L 92 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR L 92 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR L 92 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR L 92 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR L 92 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 50 " 0.027 2.00e-02 2.50e+03 1.34e-02 4.49e+00 pdb=" CG TRP H 50 " -0.017 2.00e-02 2.50e+03 pdb=" CD1 TRP H 50 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TRP H 50 " -0.019 2.00e-02 2.50e+03 pdb=" NE1 TRP H 50 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP H 50 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP H 50 " -0.012 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 50 " 0.008 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 50 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP H 50 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 47 " -0.023 2.00e-02 2.50e+03 1.32e-02 4.34e+00 pdb=" CG TRP H 47 " 0.013 2.00e-02 2.50e+03 pdb=" CD1 TRP H 47 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TRP H 47 " 0.018 2.00e-02 2.50e+03 pdb=" NE1 TRP H 47 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP H 47 " 0.011 2.00e-02 2.50e+03 pdb=" CE3 TRP H 47 " 0.014 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 47 " -0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 47 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP H 47 " -0.017 2.00e-02 2.50e+03 ... (remaining 558 not shown) Histogram of nonbonded interaction distances: 2.57 - 3.03: 1766 3.03 - 3.50: 2712 3.50 - 3.97: 4880 3.97 - 4.43: 5575 4.43 - 4.90: 9162 Nonbonded interactions: 24095 Sorted by model distance: nonbonded pdb=" N LYS B 462 " pdb=" O LYS B 462 " model vdw 2.568 2.496 nonbonded pdb=" N GLU L 80 " pdb=" O GLU L 80 " model vdw 2.592 2.496 nonbonded pdb=" CB GLN H 6 " pdb=" OE1 GLN H 6 " model vdw 2.598 2.752 nonbonded pdb=" N GLY B 502 " pdb=" O GLY B 502 " model vdw 2.601 2.496 nonbonded pdb=" N SER B 373 " pdb=" N PHE B 374 " model vdw 2.605 2.560 ... (remaining 24090 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 group one per residue 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: 10.710 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: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 5.360 Find NCS groups from input model: 0.010 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:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 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 : 0.015 0.092 3127 Z= 0.793 Angle : 1.425 8.157 4287 Z= 0.964 Chirality : 0.079 0.340 470 Planarity : 0.006 0.039 560 Dihedral : 9.478 83.236 995 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 0.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 are not related in a simple way. whole: 0.92 (0.41), residues: 411 helix: -4.00 (0.49), residues: 33 sheet: 1.14 (0.43), residues: 150 loop : 1.17 (0.40), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 67 TYR 0.030 0.004 TYR L 92 PHE 0.013 0.003 PHE H 64 TRP 0.027 0.008 TRP H 50 HIS 0.002 0.001 HIS H 65 Details of bonding type rmsd/Z covalent geometry : bond 0.01446 / 0.79 ( 3118) covalent geometry : angle 1.41601 / 0.96 ( 4267) SS BOND : bond 0.02869 / 2.28 ( 7) SS BOND : angle 2.53855 / 1.45 ( 14) hydrogen bonds : bond 0.15086 / 10.14 ( 116) hydrogen bonds : angle 9.13726 / 6.31 ( 285) link_BETA1-4 : bond 0.06505 / 3.42 ( 1) link_BETA1-4 : angle 4.01691 / 2.09 ( 3) link_NAG-ASN : bond 0.06242 / 3.29 ( 1) link_NAG-ASN : angle 1.79789 / 0.90 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.069 Fit side-chains revert: symmetry clash REVERT: B 369 TYR cc_start: 0.7080 (t80) cc_final: 0.6653 (t80) outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.0606 time to fit residues: 5.9087 Evaluate side-chains 44 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 24 optimal weight: 0.5980 chunk 26 optimal weight: 0.0770 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 0.3980 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 0.0980 chunk 25 optimal weight: 0.1980 chunk 19 optimal weight: 0.3980 chunk 30 optimal weight: 0.6980 chunk 22 optimal weight: 0.0470 chunk 37 optimal weight: 0.0770 overall best weight: 0.0994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 35 GLN B 474 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.106053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.095978 restraints weight = 7341.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.098606 restraints weight = 3998.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.100469 restraints weight = 2535.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.101654 restraints weight = 1746.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.102598 restraints weight = 1302.013| |-----------------------------------------------------------------------------| r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 3127 Z= 0.137 Angle : 0.667 9.615 4287 Z= 0.353 Chirality : 0.047 0.142 470 Planarity : 0.005 0.035 560 Dihedral : 4.892 21.758 460 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 3.64 % Allowed : 12.96 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 are not related in a simple way. whole: 0.67 (0.41), residues: 411 helix: -3.56 (0.68), residues: 27 sheet: 0.74 (0.41), residues: 150 loop : 0.94 (0.40), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L 24 TYR 0.022 0.002 TYR L 92 PHE 0.013 0.002 PHE B 497 TRP 0.008 0.001 TRP B 436 HIS 0.002 0.001 HIS H 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 ( 3118) covalent geometry : angle 0.63780 / 0.34 ( 4267) SS BOND : bond 0.00370 / 0.29 ( 7) SS BOND : angle 3.42969 / 2.45 ( 14) hydrogen bonds : bond 0.03906 / 2.73 ( 116) hydrogen bonds : angle 6.78666 / 4.63 ( 285) link_BETA1-4 : bond 0.00136 / 0.07 ( 1) link_BETA1-4 : angle 1.47115 / 0.61 ( 3) link_NAG-ASN : bond 0.00644 / 0.34 ( 1) link_NAG-ASN : angle 0.72646 / 0.32 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.111 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 37 TYR cc_start: 0.8594 (m-10) cc_final: 0.7971 (m-80) REVERT: B 398 ASP cc_start: 0.8401 (m-30) cc_final: 0.8174 (m-30) outliers start: 9 outliers final: 6 residues processed: 64 average time/residue: 0.0576 time to fit residues: 4.4690 Evaluate side-chains 52 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 35 GLN Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 480 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 0.3980 chunk 10 optimal weight: 0.9980 chunk 38 optimal weight: 0.0870 chunk 8 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 6 GLN ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.099684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.089844 restraints weight = 7320.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.092279 restraints weight = 4275.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.093928 restraints weight = 2827.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.095074 restraints weight = 2029.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.095863 restraints weight = 1540.028| |-----------------------------------------------------------------------------| r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.3522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.040 3127 Z= 0.298 Angle : 0.738 8.470 4287 Z= 0.398 Chirality : 0.049 0.133 470 Planarity : 0.005 0.037 560 Dihedral : 5.147 25.832 460 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 4.45 % Allowed : 12.96 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 are not related in a simple way. whole: 0.21 (0.39), residues: 411 helix: -3.16 (0.98), residues: 20 sheet: 0.26 (0.39), residues: 152 loop : 0.53 (0.39), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 24 TYR 0.046 0.003 TYR L 92 PHE 0.014 0.002 PHE B 347 TRP 0.016 0.002 TRP L 36 HIS 0.006 0.004 HIS H 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00674 / 0.30 ( 3118) covalent geometry : angle 0.72373 / 0.39 ( 4267) SS BOND : bond 0.00340 / 0.23 ( 7) SS BOND : angle 2.53670 / 1.59 ( 14) hydrogen bonds : bond 0.04358 / 3.09 ( 116) hydrogen bonds : angle 6.51432 / 4.41 ( 285) link_BETA1-4 : bond 0.00570 / 0.30 ( 1) link_BETA1-4 : angle 1.65203 / 0.82 ( 3) link_NAG-ASN : bond 0.00313 / 0.16 ( 1) link_NAG-ASN : angle 0.88253 / 0.41 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 47 time to evaluate : 0.115 Fit side-chains revert: symmetry clash REVERT: H 90 ASP cc_start: 0.7681 (m-30) cc_final: 0.7275 (m-30) REVERT: L 74 LEU cc_start: 0.8700 (tt) cc_final: 0.8497 (tt) REVERT: B 369 TYR cc_start: 0.7043 (t80) cc_final: 0.6746 (t80) outliers start: 11 outliers final: 9 residues processed: 55 average time/residue: 0.0832 time to fit residues: 5.3968 Evaluate side-chains 52 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 43 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 92 TYR Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 480 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 0.9990 chunk 22 optimal weight: 0.0020 chunk 9 optimal weight: 0.0970 chunk 2 optimal weight: 0.9980 chunk 0 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 chunk 24 optimal weight: 0.5980 chunk 23 optimal weight: 0.0770 chunk 1 optimal weight: 0.6980 chunk 21 optimal weight: 0.0980 chunk 33 optimal weight: 0.1980 overall best weight: 0.0944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 35 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.101323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.091604 restraints weight = 7207.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.094151 restraints weight = 4047.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.095871 restraints weight = 2607.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.097078 restraints weight = 1826.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.097828 restraints weight = 1361.428| |-----------------------------------------------------------------------------| r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.3852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3127 Z= 0.122 Angle : 0.629 8.083 4287 Z= 0.334 Chirality : 0.047 0.160 470 Planarity : 0.004 0.034 560 Dihedral : 4.613 24.554 460 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.64 % Allowed : 15.38 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 are not related in a simple way. whole: 0.22 (0.39), residues: 411 helix: -2.88 (1.08), residues: 20 sheet: 0.21 (0.39), residues: 148 loop : 0.54 (0.38), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L 55 TYR 0.028 0.001 TYR L 92 PHE 0.020 0.001 PHE B 392 TRP 0.010 0.001 TRP L 98 HIS 0.001 0.001 HIS H 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 ( 3118) covalent geometry : angle 0.61383 / 0.33 ( 4267) SS BOND : bond 0.00250 / 0.14 ( 7) SS BOND : angle 2.45861 / 2.03 ( 14) hydrogen bonds : bond 0.03525 / 2.53 ( 116) hydrogen bonds : angle 6.11749 / 4.10 ( 285) link_BETA1-4 : bond 0.00479 / 0.25 ( 1) link_BETA1-4 : angle 1.14024 / 0.52 ( 3) link_NAG-ASN : bond 0.00255 / 0.13 ( 1) link_NAG-ASN : angle 0.46780 / 0.21 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 0.112 Fit side-chains revert: symmetry clash REVERT: H 90 ASP cc_start: 0.7470 (m-30) cc_final: 0.7160 (m-30) REVERT: B 369 TYR cc_start: 0.7031 (t80) cc_final: 0.6596 (t80) outliers start: 9 outliers final: 9 residues processed: 55 average time/residue: 0.0839 time to fit residues: 5.4316 Evaluate side-chains 50 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 41 time to evaluate : 0.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 35 GLN Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 92 TYR Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 480 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 17 optimal weight: 0.9980 chunk 38 optimal weight: 0.5980 chunk 31 optimal weight: 0.4980 chunk 27 optimal weight: 0.2980 chunk 7 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 16 optimal weight: 0.3980 chunk 12 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 20 optimal weight: 0.3980 chunk 11 optimal weight: 0.9980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 90 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** 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 = 0.3589 r_free = 0.3589 target = 0.097661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.087800 restraints weight = 7371.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.090233 restraints weight = 4235.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.091870 restraints weight = 2769.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.093045 restraints weight = 1979.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.093833 restraints weight = 1503.188| |-----------------------------------------------------------------------------| r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.4196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 3127 Z= 0.238 Angle : 0.672 7.348 4287 Z= 0.356 Chirality : 0.047 0.134 470 Planarity : 0.005 0.054 560 Dihedral : 4.760 22.135 460 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 4.45 % Allowed : 15.38 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 are not related in a simple way. whole: 0.03 (0.41), residues: 411 helix: -2.92 (1.10), residues: 20 sheet: 0.02 (0.39), residues: 156 loop : 0.46 (0.41), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 55 TYR 0.037 0.002 TYR L 92 PHE 0.013 0.002 PHE B 392 TRP 0.013 0.002 TRP L 36 HIS 0.005 0.003 HIS H 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00548 / 0.24 ( 3118) covalent geometry : angle 0.66713 / 0.35 ( 4267) SS BOND : bond 0.00786 / 0.60 ( 7) SS BOND : angle 1.50234 / 0.92 ( 14) hydrogen bonds : bond 0.03994 / 2.90 ( 116) hydrogen bonds : angle 6.05913 / 4.09 ( 285) link_BETA1-4 : bond 0.00634 / 0.33 ( 1) link_BETA1-4 : angle 1.19305 / 0.56 ( 3) link_NAG-ASN : bond 0.00209 / 0.11 ( 1) link_NAG-ASN : angle 0.58226 / 0.28 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 42 time to evaluate : 0.116 Fit side-chains revert: symmetry clash REVERT: H 90 ASP cc_start: 0.7721 (m-30) cc_final: 0.7218 (m-30) REVERT: B 369 TYR cc_start: 0.7146 (t80) cc_final: 0.6615 (t80) outliers start: 11 outliers final: 10 residues processed: 50 average time/residue: 0.0841 time to fit residues: 4.9614 Evaluate side-chains 49 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 39 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 35 GLN Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 92 TYR Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 480 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 37 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 chunk 9 optimal weight: 0.0980 chunk 28 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 2 optimal weight: 0.2980 chunk 27 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 21 optimal weight: 0.5980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 35 GLN ** B 422 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 = 0.3570 r_free = 0.3570 target = 0.096461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.086363 restraints weight = 7382.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.088826 restraints weight = 4305.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.090495 restraints weight = 2850.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.091586 restraints weight = 2049.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.092423 restraints weight = 1584.019| |-----------------------------------------------------------------------------| r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.4567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 3127 Z= 0.244 Angle : 0.678 7.202 4287 Z= 0.359 Chirality : 0.047 0.137 470 Planarity : 0.005 0.041 560 Dihedral : 4.819 19.134 460 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 4.86 % Allowed : 14.57 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 are not related in a simple way. whole: -0.18 (0.41), residues: 411 helix: -3.10 (1.02), residues: 20 sheet: 0.12 (0.40), residues: 152 loop : 0.12 (0.41), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 55 TYR 0.037 0.002 TYR L 92 PHE 0.011 0.002 PHE B 392 TRP 0.015 0.002 TRP L 36 HIS 0.005 0.003 HIS H 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00561 / 0.24 ( 3118) covalent geometry : angle 0.67489 / 0.36 ( 4267) SS BOND : bond 0.00586 / 0.43 ( 7) SS BOND : angle 1.32598 / 0.80 ( 14) hydrogen bonds : bond 0.03997 / 2.88 ( 116) hydrogen bonds : angle 6.14837 / 4.16 ( 285) link_BETA1-4 : bond 0.00515 / 0.27 ( 1) link_BETA1-4 : angle 1.25557 / 0.63 ( 3) link_NAG-ASN : bond 0.00287 / 0.15 ( 1) link_NAG-ASN : angle 0.36325 / 0.21 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 40 time to evaluate : 0.114 Fit side-chains revert: symmetry clash REVERT: H 90 ASP cc_start: 0.7901 (m-30) cc_final: 0.7346 (m-30) REVERT: L 102 GLN cc_start: 0.8758 (OUTLIER) cc_final: 0.7166 (mp10) REVERT: B 384 PRO cc_start: 0.6962 (Cg_endo) cc_final: 0.6747 (Cg_exo) outliers start: 12 outliers final: 10 residues processed: 49 average time/residue: 0.0779 time to fit residues: 4.5254 Evaluate side-chains 52 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 41 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 35 GLN Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 50 TYR Chi-restraints excluded: chain L residue 92 TYR Chi-restraints excluded: chain L residue 102 GLN Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 415 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 19 optimal weight: 0.0570 chunk 1 optimal weight: 0.9980 chunk 37 optimal weight: 0.1980 chunk 16 optimal weight: 0.3980 chunk 15 optimal weight: 0.2980 chunk 23 optimal weight: 0.0970 chunk 32 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 11 optimal weight: 0.2980 chunk 33 optimal weight: 0.3980 chunk 24 optimal weight: 0.4980 overall best weight: 0.1896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 35 GLN L 90 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.098666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.088724 restraints weight = 7405.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.091216 restraints weight = 4244.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.092912 restraints weight = 2770.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.094086 restraints weight = 1962.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.094849 restraints weight = 1473.089| |-----------------------------------------------------------------------------| r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.4639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3127 Z= 0.136 Angle : 0.604 6.683 4287 Z= 0.317 Chirality : 0.045 0.139 470 Planarity : 0.004 0.040 560 Dihedral : 4.463 17.965 460 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.64 % Allowed : 17.41 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 are not related in a simple way. whole: -0.13 (0.41), residues: 411 helix: -3.02 (1.02), residues: 20 sheet: 0.09 (0.40), residues: 151 loop : 0.20 (0.41), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 55 TYR 0.029 0.002 TYR L 92 PHE 0.021 0.001 PHE B 392 TRP 0.011 0.001 TRP B 436 HIS 0.002 0.001 HIS H 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 ( 3118) covalent geometry : angle 0.60163 / 0.32 ( 4267) SS BOND : bond 0.00453 / 0.32 ( 7) SS BOND : angle 1.07299 / 0.65 ( 14) hydrogen bonds : bond 0.03485 / 2.52 ( 116) hydrogen bonds : angle 6.04806 / 4.06 ( 285) link_BETA1-4 : bond 0.00448 / 0.24 ( 1) link_BETA1-4 : angle 0.96083 / 0.44 ( 3) link_NAG-ASN : bond 0.00273 / 0.14 ( 1) link_NAG-ASN : angle 0.36352 / 0.21 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.071 Fit side-chains revert: symmetry clash REVERT: H 90 ASP cc_start: 0.7839 (m-30) cc_final: 0.7421 (m-30) REVERT: L 102 GLN cc_start: 0.8683 (OUTLIER) cc_final: 0.6856 (mp10) outliers start: 9 outliers final: 7 residues processed: 49 average time/residue: 0.0712 time to fit residues: 4.1373 Evaluate side-chains 46 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 38 time to evaluate : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 35 GLN Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 92 TYR Chi-restraints excluded: chain L residue 102 GLN Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 415 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 4 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 27 optimal weight: 0.0870 chunk 19 optimal weight: 0.3980 chunk 13 optimal weight: 0.1980 chunk 18 optimal weight: 0.3980 chunk 9 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 overall best weight: 0.3358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 35 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.098156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.088307 restraints weight = 7432.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.090666 restraints weight = 4387.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.092241 restraints weight = 2928.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.093315 restraints weight = 2137.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.094123 restraints weight = 1654.375| |-----------------------------------------------------------------------------| r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.4856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3127 Z= 0.190 Angle : 0.636 7.464 4287 Z= 0.336 Chirality : 0.046 0.138 470 Planarity : 0.005 0.040 560 Dihedral : 4.501 17.311 460 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 5.26 % Allowed : 16.60 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 are not related in a simple way. whole: -0.13 (0.41), residues: 411 helix: -3.06 (1.03), residues: 20 sheet: 0.14 (0.40), residues: 150 loop : 0.16 (0.41), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L 55 TYR 0.031 0.002 TYR L 92 PHE 0.016 0.002 PHE B 392 TRP 0.012 0.001 TRP B 436 HIS 0.003 0.002 HIS H 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.19 ( 3118) covalent geometry : angle 0.63467 / 0.34 ( 4267) SS BOND : bond 0.00489 / 0.36 ( 7) SS BOND : angle 1.00328 / 0.59 ( 14) hydrogen bonds : bond 0.03585 / 2.59 ( 116) hydrogen bonds : angle 6.05023 / 4.07 ( 285) link_BETA1-4 : bond 0.00354 / 0.19 ( 1) link_BETA1-4 : angle 1.00817 / 0.49 ( 3) link_NAG-ASN : bond 0.00243 / 0.13 ( 1) link_NAG-ASN : angle 0.42998 / 0.25 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 39 time to evaluate : 0.168 Fit side-chains revert: symmetry clash REVERT: H 90 ASP cc_start: 0.7861 (m-30) cc_final: 0.7430 (m-30) REVERT: L 102 GLN cc_start: 0.8678 (OUTLIER) cc_final: 0.6941 (mp10) outliers start: 13 outliers final: 10 residues processed: 50 average time/residue: 0.0571 time to fit residues: 3.5241 Evaluate side-chains 49 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 38 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 35 GLN Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 92 TYR Chi-restraints excluded: chain L residue 102 GLN Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 415 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 0.0670 chunk 32 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 20 optimal weight: 0.2980 chunk 34 optimal weight: 0.9990 chunk 31 optimal weight: 0.4980 chunk 37 optimal weight: 0.0670 chunk 21 optimal weight: 0.0870 chunk 12 optimal weight: 0.3980 chunk 1 optimal weight: 0.9980 overall best weight: 0.1834 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 35 GLN ** B 422 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 = 0.3618 r_free = 0.3618 target = 0.099393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.089138 restraints weight = 7380.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.091625 restraints weight = 4230.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.093325 restraints weight = 2771.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.094428 restraints weight = 1987.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.095272 restraints weight = 1528.817| |-----------------------------------------------------------------------------| r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.4897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3127 Z= 0.133 Angle : 0.604 7.543 4287 Z= 0.317 Chirality : 0.045 0.140 470 Planarity : 0.005 0.039 560 Dihedral : 4.306 16.638 460 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 5.26 % Allowed : 17.00 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 are not related in a simple way. whole: -0.05 (0.42), residues: 411 helix: -3.03 (1.02), residues: 20 sheet: 0.11 (0.41), residues: 153 loop : 0.30 (0.42), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 78 TYR 0.027 0.001 TYR L 92 PHE 0.016 0.001 PHE B 392 TRP 0.012 0.001 TRP B 436 HIS 0.002 0.001 HIS H 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 ( 3118) covalent geometry : angle 0.60261 / 0.32 ( 4267) SS BOND : bond 0.00413 / 0.29 ( 7) SS BOND : angle 0.88771 / 0.55 ( 14) hydrogen bonds : bond 0.03338 / 2.41 ( 116) hydrogen bonds : angle 6.02283 / 4.04 ( 285) link_BETA1-4 : bond 0.00387 / 0.20 ( 1) link_BETA1-4 : angle 0.87758 / 0.39 ( 3) link_NAG-ASN : bond 0.00229 / 0.12 ( 1) link_NAG-ASN : angle 0.42070 / 0.24 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 38 time to evaluate : 0.113 Fit side-chains revert: symmetry clash REVERT: H 90 ASP cc_start: 0.7903 (m-30) cc_final: 0.7439 (m-30) REVERT: L 102 GLN cc_start: 0.8673 (OUTLIER) cc_final: 0.6782 (mp10) outliers start: 13 outliers final: 10 residues processed: 49 average time/residue: 0.0651 time to fit residues: 3.8578 Evaluate side-chains 48 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 37 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 35 GLN Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 92 TYR Chi-restraints excluded: chain L residue 102 GLN Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 415 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 13 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 31 optimal weight: 0.2980 chunk 35 optimal weight: 0.2980 chunk 5 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 4 optimal weight: 0.0770 chunk 14 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 15 optimal weight: 0.4980 chunk 23 optimal weight: 0.3980 overall best weight: 0.3138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 35 GLN ** B 422 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 = 0.3597 r_free = 0.3597 target = 0.098304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.088118 restraints weight = 7340.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.090577 restraints weight = 4190.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.092250 restraints weight = 2760.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.093378 restraints weight = 1985.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.094213 restraints weight = 1524.811| |-----------------------------------------------------------------------------| r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.4993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3127 Z= 0.179 Angle : 0.644 7.516 4287 Z= 0.337 Chirality : 0.046 0.137 470 Planarity : 0.005 0.039 560 Dihedral : 4.365 15.961 460 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 4.45 % Allowed : 17.81 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 are not related in a simple way. whole: -0.09 (0.42), residues: 411 helix: -3.03 (1.04), residues: 20 sheet: 0.06 (0.41), residues: 154 loop : 0.28 (0.42), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L 78 TYR 0.030 0.002 TYR L 92 PHE 0.014 0.001 PHE B 392 TRP 0.012 0.001 TRP B 436 HIS 0.003 0.002 HIS H 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.18 ( 3118) covalent geometry : angle 0.64248 / 0.34 ( 4267) SS BOND : bond 0.00462 / 0.33 ( 7) SS BOND : angle 0.93908 / 0.55 ( 14) hydrogen bonds : bond 0.03550 / 2.57 ( 116) hydrogen bonds : angle 6.03450 / 4.06 ( 285) link_BETA1-4 : bond 0.00406 / 0.21 ( 1) link_BETA1-4 : angle 0.90958 / 0.42 ( 3) link_NAG-ASN : bond 0.00205 / 0.11 ( 1) link_NAG-ASN : angle 0.49094 / 0.28 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 40 time to evaluate : 0.091 Fit side-chains revert: symmetry clash REVERT: H 90 ASP cc_start: 0.7965 (m-30) cc_final: 0.7468 (m-30) REVERT: L 102 GLN cc_start: 0.8693 (OUTLIER) cc_final: 0.6868 (mp10) outliers start: 11 outliers final: 10 residues processed: 49 average time/residue: 0.0746 time to fit residues: 4.3093 Evaluate side-chains 51 residues out of total 356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 40 time to evaluate : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 35 GLN Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 92 TYR Chi-restraints excluded: chain L residue 102 GLN Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 415 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 18 optimal weight: 0.2980 chunk 16 optimal weight: 0.3980 chunk 23 optimal weight: 0.3980 chunk 5 optimal weight: 0.9990 chunk 13 optimal weight: 0.0970 chunk 3 optimal weight: 0.8980 chunk 29 optimal weight: 0.0970 chunk 14 optimal weight: 0.7980 chunk 38 optimal weight: 0.2980 chunk 0 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 overall best weight: 0.2376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 35 GLN ** B 422 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 = 0.3612 r_free = 0.3612 target = 0.099091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.089340 restraints weight = 7324.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.091662 restraints weight = 4318.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.093254 restraints weight = 2878.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.094295 restraints weight = 2088.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.095107 restraints weight = 1622.372| |-----------------------------------------------------------------------------| r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.5031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3127 Z= 0.150 Angle : 0.624 7.381 4287 Z= 0.325 Chirality : 0.045 0.138 470 Planarity : 0.005 0.039 560 Dihedral : 4.293 15.642 460 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 5.26 % Allowed : 17.00 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 are not related in a simple way. whole: -0.04 (0.42), residues: 411 helix: -3.05 (1.03), residues: 20 sheet: 0.12 (0.41), residues: 155 loop : 0.29 (0.42), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 78 TYR 0.028 0.002 TYR L 92 PHE 0.014 0.001 PHE B 392 TRP 0.011 0.001 TRP B 436 HIS 0.002 0.002 HIS H 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 ( 3118) covalent geometry : angle 0.62306 / 0.33 ( 4267) SS BOND : bond 0.00422 / 0.30 ( 7) SS BOND : angle 0.90340 / 0.54 ( 14) hydrogen bonds : bond 0.03445 / 2.49 ( 116) hydrogen bonds : angle 6.07559 / 4.08 ( 285) link_BETA1-4 : bond 0.00418 / 0.22 ( 1) link_BETA1-4 : angle 0.87074 / 0.38 ( 3) link_NAG-ASN : bond 0.00213 / 0.11 ( 1) link_NAG-ASN : angle 0.50194 / 0.28 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 882.62 seconds wall clock time: 15 minutes 54.55 seconds (954.55 seconds total)