Starting phenix.real_space_refine on Wed Jul 1 23:27:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7wqz_32716/07_2026/7wqz_32716.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wqz_32716/07_2026/7wqz_32716.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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7wqz_32716/07_2026/7wqz_32716.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7wqz_32716/07_2026/7wqz_32716.cif" model { file = "/net/cci-nas-00/data/ceres_data/7wqz_32716/07_2026/7wqz_32716.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wqz_32716/07_2026/7wqz_32716.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wqz_32716/07_2026/7wqz_32716.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wqz_32716/07_2026/7wqz_32716.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= 0.017 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 29 5.16 5 C 2497 2.51 5 N 676 2.21 5 O 772 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 3974 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2013 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 15, 'TRANS': 245} Chain: "B" Number of atoms: 1835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1835 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 220} Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 0.80, per 1000 atoms: 0.20 Number of scatterers: 3974 At special positions: 0 Unit cell: (62.76, 87.864, 96.232, 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 29 16.00 O 772 8.00 N 676 7.00 C 2497 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 650 " - pdb=" SG CYS A 668 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 677 " distance=2.03 Simple disulfide: pdb=" SG CYS A 716 " - pdb=" SG CYS A 767 " distance=2.03 Simple disulfide: pdb=" SG CYS A 772 " - pdb=" SG CYS B 896 " distance=2.03 Simple disulfide: pdb=" SG CYS B 810 " - pdb=" SG CYS B 826 " distance=2.03 Simple disulfide: pdb=" SG CYS B 910 " - pdb=" SG CYS B 977 " distance=2.03 Simple disulfide: pdb=" SG CYS B 941 " - pdb=" SG CYS B 956 " distance=2.03 Simple disulfide: pdb=" SG CYS B 967 " - pdb=" SG CYS B 995 " 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 A 801 " - " ASN A 534 " " NAG A 802 " - " ASN A 630 " " NAG A 803 " - " ASN A 706 " " NAG A 804 " - " ASN A 725 " " NAG A 805 " - " ASN A 682 " " NAG B1101 " - " ASN B 848 " " NAG B1102 " - " ASN B 887 " " NAG B1103 " - " ASN B 909 " " NAG B1104 " - " ASN B 949 " Time building additional restraints: 0.19 Conformation dependent library (CDL) restraints added in 92.2 milliseconds 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 904 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 10 sheets defined 8.7% alpha, 17.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.07 Creating SS restraints... Processing helix chain 'A' and resid 708 through 719 Processing helix chain 'B' and resid 823 through 828 removed outlier: 4.067A pdb=" N VAL B 827 " --> pdb=" O ALA B 823 " (cutoff:3.500A) Processing helix chain 'B' and resid 833 through 835 No H-bonds generated for 'chain 'B' and resid 833 through 835' Processing helix chain 'B' and resid 937 through 945 Processing helix chain 'B' and resid 1007 through 1009 No H-bonds generated for 'chain 'B' and resid 1007 through 1009' Processing helix chain 'B' and resid 1010 through 1019 removed outlier: 4.096A pdb=" N PHE B1017 " --> pdb=" O TRP B1013 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N HIS B1019 " --> pdb=" O GLN B1015 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 537 through 538 removed outlier: 3.705A pdb=" N PHE A 537 " --> pdb=" O ALA A 629 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA A 629 " --> pdb=" O PHE A 537 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLY A 626 " --> pdb=" O ASP A 572 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASP A 572 " --> pdb=" O GLY A 626 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 553 through 557 removed outlier: 5.927A pdb=" N VAL A 580 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N VAL A 595 " --> pdb=" O VAL A 580 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N ILE A 582 " --> pdb=" O LEU A 593 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 648 through 649 Processing sheet with id=AA4, first strand: chain 'A' and resid 688 through 689 removed outlier: 3.808A pdb=" N GLY A 689 " --> pdb=" O LEU A 765 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LYS A 728 " --> pdb=" O ARG A 764 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 693 through 694 Processing sheet with id=AA6, first strand: chain 'A' and resid 740 through 742 Processing sheet with id=AA7, first strand: chain 'B' and resid 789 through 790 Processing sheet with id=AA8, first strand: chain 'B' and resid 799 through 804 removed outlier: 3.775A pdb=" N CYS B 810 " --> pdb=" O LEU B 802 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N TYR B 804 " --> pdb=" O LEU B 808 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N LEU B 808 " --> pdb=" O TYR B 804 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLU B 861 " --> pdb=" O HIS B 881 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ILE B 859 " --> pdb=" O TRP B 837 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N TRP B 837 " --> pdb=" O ILE B 859 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLY B 801 " --> pdb=" O ILE B 840 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 909 through 911 removed outlier: 3.925A pdb=" N CYS B 910 " --> pdb=" O VAL B 933 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 954 through 957 removed outlier: 3.728A pdb=" N GLY B1002 " --> pdb=" O ALA B 957 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N VAL B1003 " --> pdb=" O SER B 990 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER B 990 " --> pdb=" O VAL B1003 " (cutoff:3.500A) 66 hydrogen bonds defined for protein. 171 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: 0.47 Time building geometry restraints manager: 0.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1306 1.34 - 1.46: 928 1.46 - 1.58: 1800 1.58 - 1.70: 0 1.70 - 1.82: 36 Bond restraints: 4070 Sorted by residual: bond pdb=" C1 NAG A 802 " pdb=" O5 NAG A 802 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.45e+00 bond pdb=" C1 NAG B1101 " pdb=" O5 NAG B1101 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.04e+00 bond pdb=" C1 NAG B1104 " pdb=" O5 NAG B1104 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.97e+00 bond pdb=" C1 NAG A 804 " pdb=" O5 NAG A 804 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.96e+00 bond pdb=" C1 NAG B1103 " pdb=" O5 NAG B1103 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.95e+00 ... (remaining 4065 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.96: 5208 0.96 - 1.92: 226 1.92 - 2.88: 86 2.88 - 3.84: 14 3.84 - 4.80: 7 Bond angle restraints: 5541 Sorted by residual: angle pdb=" C TRP A 531 " pdb=" N GLU A 532 " pdb=" CA GLU A 532 " ideal model delta sigma weight residual 120.26 124.06 -3.80 1.34e+00 5.57e-01 8.05e+00 angle pdb=" CA PHE A 631 " pdb=" C PHE A 631 " pdb=" O PHE A 631 " ideal model delta sigma weight residual 120.54 122.94 -2.40 1.04e+00 9.25e-01 5.35e+00 angle pdb=" C GLY A 683 " pdb=" N THR A 684 " pdb=" CA THR A 684 " ideal model delta sigma weight residual 121.54 125.44 -3.90 1.91e+00 2.74e-01 4.17e+00 angle pdb=" N THR A 684 " pdb=" CA THR A 684 " pdb=" C THR A 684 " ideal model delta sigma weight residual 110.80 115.09 -4.29 2.13e+00 2.20e-01 4.06e+00 angle pdb=" N GLY A 689 " pdb=" CA GLY A 689 " pdb=" C GLY A 689 " ideal model delta sigma weight residual 110.46 113.32 -2.86 1.43e+00 4.89e-01 4.01e+00 ... (remaining 5536 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.14: 2222 17.14 - 34.28: 101 34.28 - 51.42: 22 51.42 - 68.56: 2 68.56 - 85.70: 3 Dihedral angle restraints: 2350 sinusoidal: 938 harmonic: 1412 Sorted by residual: dihedral pdb=" CB CYS A 716 " pdb=" SG CYS A 716 " pdb=" SG CYS A 767 " pdb=" CB CYS A 767 " ideal model delta sinusoidal sigma weight residual 93.00 134.90 -41.90 1 1.00e+01 1.00e-02 2.45e+01 dihedral pdb=" N CYS A 772 " pdb=" CA CYS A 772 " pdb=" CB CYS A 772 " pdb=" SG CYS A 772 " ideal model delta sinusoidal sigma weight residual -60.00 -114.57 54.57 3 1.50e+01 4.44e-03 9.29e+00 dihedral pdb=" N ARG A 583 " pdb=" CA ARG A 583 " pdb=" CB ARG A 583 " pdb=" CG ARG A 583 " ideal model delta sinusoidal sigma weight residual -180.00 -125.49 -54.51 3 1.50e+01 4.44e-03 9.29e+00 ... (remaining 2347 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 428 0.035 - 0.069: 122 0.069 - 0.104: 56 0.104 - 0.138: 19 0.138 - 0.173: 3 Chirality restraints: 628 Sorted by residual: chirality pdb=" C2 NAG A 802 " pdb=" C1 NAG A 802 " pdb=" C3 NAG A 802 " pdb=" N2 NAG A 802 " both_signs ideal model delta sigma weight residual False -2.49 -2.32 -0.17 2.00e-01 2.50e+01 7.46e-01 chirality pdb=" C2 NAG A 801 " pdb=" C1 NAG A 801 " pdb=" C3 NAG A 801 " pdb=" N2 NAG A 801 " both_signs ideal model delta sigma weight residual False -2.49 -2.33 -0.16 2.00e-01 2.50e+01 6.73e-01 chirality pdb=" C2 NAG B1101 " pdb=" C1 NAG B1101 " pdb=" C3 NAG B1101 " pdb=" N2 NAG B1101 " both_signs ideal model delta sigma weight residual False -2.49 -2.33 -0.16 2.00e-01 2.50e+01 6.60e-01 ... (remaining 625 not shown) Planarity restraints: 729 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 526 " 0.015 5.00e-02 4.00e+02 2.28e-02 8.35e-01 pdb=" N PRO A 527 " -0.040 5.00e-02 4.00e+02 pdb=" CA PRO A 527 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 527 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 997 " 0.014 5.00e-02 4.00e+02 2.08e-02 6.93e-01 pdb=" N PRO B 998 " -0.036 5.00e-02 4.00e+02 pdb=" CA PRO B 998 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO B 998 " 0.012 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 728 " -0.013 5.00e-02 4.00e+02 2.02e-02 6.51e-01 pdb=" N PRO A 729 " 0.035 5.00e-02 4.00e+02 pdb=" CA PRO A 729 " -0.010 5.00e-02 4.00e+02 pdb=" CD PRO A 729 " -0.011 5.00e-02 4.00e+02 ... (remaining 726 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 1017 2.80 - 3.32: 3732 3.32 - 3.85: 6498 3.85 - 4.37: 7286 4.37 - 4.90: 12362 Nonbonded interactions: 30895 Sorted by model distance: nonbonded pdb=" OG1 THR B 917 " pdb=" O GLN B 968 " model vdw 2.272 3.040 nonbonded pdb=" OG1 THR A 632 " pdb=" O7 NAG A 802 " model vdw 2.296 3.040 nonbonded pdb=" OD1 ASP A 584 " pdb=" OG1 THR A 609 " model vdw 2.315 3.040 nonbonded pdb=" O SER A 723 " pdb=" ND2 ASN A 768 " model vdw 2.344 3.120 nonbonded pdb=" NH2 ARG B 908 " pdb=" OE1 GLU B 979 " model vdw 2.354 3.120 ... (remaining 30890 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: 1.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.110 Find NCS groups from input model: 0.030 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:0.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 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 0.031 4087 Z= 0.152 Angle : 0.550 4.798 5584 Z= 0.283 Chirality : 0.044 0.173 628 Planarity : 0.003 0.023 720 Dihedral : 10.184 85.701 1422 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.54 % Favored : 91.46 % Rotamer: Outliers : 2.13 % Allowed : 9.00 % Favored : 88.86 % 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 are not related in a simple way. whole: -4.46 (0.30), residues: 492 helix: -2.91 (0.53), residues: 35 sheet: -2.75 (0.52), residues: 82 loop : -3.30 (0.26), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 583 TYR 0.006 0.001 TYR A 546 PHE 0.009 0.001 PHE A 631 TRP 0.003 0.000 TRP A 699 HIS 0.001 0.000 HIS A 700 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.15 ( 4070) covalent geometry : angle 0.54421 / 0.28 ( 5541) SS BOND : bond 0.00190 / 0.09 ( 8) SS BOND : angle 0.51469 / 0.28 ( 16) hydrogen bonds : bond 0.25401 / 15.65 ( 66) hydrogen bonds : angle 11.75284 / 7.74 ( 171) link_NAG-ASN : bond 0.00179 / 0.10 ( 9) link_NAG-ASN : angle 1.29990 / 0.97 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 102 time to evaluate : 0.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 723 SER cc_start: 0.9080 (m) cc_final: 0.8680 (p) REVERT: B 785 ILE cc_start: 0.8820 (mp) cc_final: 0.8442 (tt) REVERT: B 804 TYR cc_start: 0.8712 (t80) cc_final: 0.8140 (t80) REVERT: B 828 TYR cc_start: 0.7966 (t80) cc_final: 0.7756 (t80) REVERT: B 868 TYR cc_start: 0.8963 (t80) cc_final: 0.8752 (t80) REVERT: B 880 MET cc_start: 0.7518 (mtp) cc_final: 0.7317 (mtp) outliers start: 9 outliers final: 0 residues processed: 110 average time/residue: 0.0552 time to fit residues: 7.5056 Evaluate side-chains 47 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 24 optimal weight: 7.9990 chunk 48 optimal weight: 2.9990 chunk 26 optimal weight: 8.9990 chunk 2 optimal weight: 0.0870 chunk 16 optimal weight: 10.0000 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 7.9990 chunk 25 optimal weight: 0.0470 chunk 19 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 overall best weight: 0.5856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 686 ASN A 713 ASN A 717 GLN ** A 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 768 ASN B 790 ASN B 921 GLN B 978 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.113948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.081383 restraints weight = 10472.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.084702 restraints weight = 5875.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.087041 restraints weight = 4128.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.088454 restraints weight = 3281.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.089612 restraints weight = 2821.138| |-----------------------------------------------------------------------------| r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 4087 Z= 0.159 Angle : 0.845 21.913 5584 Z= 0.378 Chirality : 0.061 0.888 628 Planarity : 0.004 0.036 720 Dihedral : 3.805 14.309 528 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.37 % Favored : 89.63 % Rotamer: Outliers : 2.84 % Allowed : 15.88 % Favored : 81.28 % 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 are not related in a simple way. whole: -3.93 (0.33), residues: 492 helix: -2.09 (0.66), residues: 37 sheet: -2.59 (0.50), residues: 91 loop : -2.89 (0.28), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 679 TYR 0.013 0.002 TYR A 596 PHE 0.029 0.002 PHE B1017 TRP 0.017 0.001 TRP B 915 HIS 0.003 0.001 HIS A 665 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.16 ( 4070) covalent geometry : angle 0.74960 / 0.35 ( 5541) SS BOND : bond 0.01051 / 0.53 ( 8) SS BOND : angle 2.70816 / 1.36 ( 16) hydrogen bonds : bond 0.04042 / 2.53 ( 66) hydrogen bonds : angle 7.71937 / 5.07 ( 171) link_NAG-ASN : bond 0.00736 / 0.35 ( 9) link_NAG-ASN : angle 5.27593 / 4.60 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 48 time to evaluate : 0.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 611 ARG cc_start: 0.8374 (ttt-90) cc_final: 0.7870 (ttp80) REVERT: A 679 ARG cc_start: 0.8256 (mtt-85) cc_final: 0.7780 (ptp-110) REVERT: A 723 SER cc_start: 0.8995 (m) cc_final: 0.8655 (p) REVERT: B 785 ILE cc_start: 0.8934 (mp) cc_final: 0.8588 (tt) REVERT: B 860 ASP cc_start: 0.8524 (p0) cc_final: 0.8276 (p0) REVERT: B 873 LYS cc_start: 0.8084 (mmtt) cc_final: 0.7863 (mmmt) REVERT: B 879 MET cc_start: 0.7785 (OUTLIER) cc_final: 0.7257 (mtp) outliers start: 12 outliers final: 5 residues processed: 57 average time/residue: 0.0575 time to fit residues: 4.1671 Evaluate side-chains 47 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 781 ILE Chi-restraints excluded: chain B residue 848 ASN Chi-restraints excluded: chain B residue 879 MET Chi-restraints excluded: chain B residue 918 VAL Chi-restraints excluded: chain B residue 1003 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 37 optimal weight: 3.9990 chunk 26 optimal weight: 7.9990 chunk 38 optimal weight: 6.9990 chunk 14 optimal weight: 8.9990 chunk 18 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 32 optimal weight: 7.9990 chunk 20 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 548 ASN ** A 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 759 GLN B 902 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.101027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.070573 restraints weight = 10730.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.073073 restraints weight = 6368.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.074797 restraints weight = 4689.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.075901 restraints weight = 3850.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.076688 restraints weight = 3392.067| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.3814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 4087 Z= 0.275 Angle : 0.881 13.347 5584 Z= 0.422 Chirality : 0.057 0.646 628 Planarity : 0.005 0.042 720 Dihedral : 5.025 28.140 528 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 17.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.63 % Favored : 85.37 % Rotamer: Outliers : 4.74 % Allowed : 16.82 % Favored : 78.44 % 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 are not related in a simple way. whole: -3.63 (0.35), residues: 492 helix: -1.15 (0.77), residues: 36 sheet: -2.62 (0.47), residues: 105 loop : -2.67 (0.32), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 583 TYR 0.011 0.002 TYR B 828 PHE 0.035 0.003 PHE A 568 TRP 0.015 0.002 TRP A 707 HIS 0.005 0.001 HIS A 700 Details of bonding type rmsd/Z covalent geometry : bond 0.00618 / 0.27 ( 4070) covalent geometry : angle 0.82834 / 0.41 ( 5541) SS BOND : bond 0.01043 / 0.52 ( 8) SS BOND : angle 3.30620 / 1.86 ( 16) hydrogen bonds : bond 0.04577 / 2.84 ( 66) hydrogen bonds : angle 7.68386 / 5.04 ( 171) link_NAG-ASN : bond 0.00407 / 0.26 ( 9) link_NAG-ASN : angle 3.61427 / 2.96 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 50 time to evaluate : 0.123 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 785 ILE cc_start: 0.8657 (mp) cc_final: 0.8326 (tt) REVERT: B 858 LEU cc_start: 0.8659 (tt) cc_final: 0.8303 (tp) REVERT: B 860 ASP cc_start: 0.8690 (p0) cc_final: 0.8484 (p0) REVERT: B 868 TYR cc_start: 0.9207 (t80) cc_final: 0.8141 (t80) REVERT: B 873 LYS cc_start: 0.8637 (mmtt) cc_final: 0.8110 (mmmt) REVERT: B 891 TYR cc_start: 0.8202 (m-80) cc_final: 0.7961 (m-80) REVERT: B 976 MET cc_start: 0.8502 (OUTLIER) cc_final: 0.7936 (ptp) outliers start: 20 outliers final: 10 residues processed: 65 average time/residue: 0.0539 time to fit residues: 4.5295 Evaluate side-chains 42 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 31 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 781 ILE Chi-restraints excluded: chain B residue 838 THR Chi-restraints excluded: chain B residue 848 ASN Chi-restraints excluded: chain B residue 918 VAL Chi-restraints excluded: chain B residue 919 VAL Chi-restraints excluded: chain B residue 965 ASP Chi-restraints excluded: chain B residue 976 MET Chi-restraints excluded: chain B residue 1003 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 46 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 5 optimal weight: 0.0980 chunk 14 optimal weight: 6.9990 chunk 37 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 21 optimal weight: 10.0000 chunk 38 optimal weight: 8.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.097435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.066304 restraints weight = 10463.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.068616 restraints weight = 6640.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.070228 restraints weight = 5026.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.071208 restraints weight = 4205.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.071901 restraints weight = 3748.154| |-----------------------------------------------------------------------------| r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.4365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 4087 Z= 0.247 Angle : 0.847 10.979 5584 Z= 0.407 Chirality : 0.054 0.534 628 Planarity : 0.004 0.043 720 Dihedral : 5.246 26.607 528 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 17.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.06 % Favored : 83.94 % Rotamer: Outliers : 4.50 % Allowed : 17.30 % Favored : 78.20 % 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 are not related in a simple way. whole: -3.62 (0.36), residues: 492 helix: -1.10 (0.78), residues: 36 sheet: -2.83 (0.49), residues: 95 loop : -2.61 (0.32), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 764 TYR 0.012 0.002 TYR B 959 PHE 0.024 0.002 PHE A 568 TRP 0.010 0.002 TRP A 707 HIS 0.005 0.001 HIS A 700 Details of bonding type rmsd/Z covalent geometry : bond 0.00564 / 0.25 ( 4070) covalent geometry : angle 0.80398 / 0.39 ( 5541) SS BOND : bond 0.00417 / 0.23 ( 8) SS BOND : angle 3.47066 / 1.99 ( 16) hydrogen bonds : bond 0.03797 / 2.37 ( 66) hydrogen bonds : angle 6.85730 / 4.43 ( 171) link_NAG-ASN : bond 0.00133 / 0.08 ( 9) link_NAG-ASN : angle 2.94069 / 2.39 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 34 time to evaluate : 0.159 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 765 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8394 (tt) REVERT: B 785 ILE cc_start: 0.8582 (mp) cc_final: 0.8228 (tt) REVERT: B 860 ASP cc_start: 0.8646 (p0) cc_final: 0.8442 (p0) REVERT: B 873 LYS cc_start: 0.8559 (mmtt) cc_final: 0.8028 (mmmt) REVERT: B 965 ASP cc_start: 0.7811 (OUTLIER) cc_final: 0.7595 (m-30) outliers start: 19 outliers final: 8 residues processed: 49 average time/residue: 0.0503 time to fit residues: 3.4272 Evaluate side-chains 40 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 30 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 781 ILE Chi-restraints excluded: chain B residue 838 THR Chi-restraints excluded: chain B residue 848 ASN Chi-restraints excluded: chain B residue 919 VAL Chi-restraints excluded: chain B residue 965 ASP Chi-restraints excluded: chain B residue 976 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 42 optimal weight: 0.1980 chunk 46 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 47 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 21 optimal weight: 0.0770 chunk 23 optimal weight: 3.9990 overall best weight: 0.5540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.100370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.068768 restraints weight = 10564.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.071363 restraints weight = 6375.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.073225 restraints weight = 4702.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.074320 restraints weight = 3860.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.075228 restraints weight = 3404.488| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.4302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4087 Z= 0.131 Angle : 0.773 10.164 5584 Z= 0.362 Chirality : 0.052 0.436 628 Planarity : 0.004 0.034 720 Dihedral : 4.964 28.671 528 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.80 % Favored : 87.20 % Rotamer: Outliers : 4.98 % Allowed : 17.06 % Favored : 77.96 % 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 are not related in a simple way. whole: -3.44 (0.36), residues: 492 helix: -1.01 (0.79), residues: 38 sheet: -2.56 (0.46), residues: 106 loop : -2.50 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 764 TYR 0.007 0.001 TYR B 959 PHE 0.010 0.001 PHE B1017 TRP 0.007 0.001 TRP B 915 HIS 0.003 0.001 HIS A 700 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 ( 4070) covalent geometry : angle 0.73626 / 0.35 ( 5541) SS BOND : bond 0.00225 / 0.14 ( 8) SS BOND : angle 3.16772 / 1.78 ( 16) hydrogen bonds : bond 0.02960 / 1.75 ( 66) hydrogen bonds : angle 6.14142 / 3.95 ( 171) link_NAG-ASN : bond 0.00233 / 0.12 ( 9) link_NAG-ASN : angle 2.54602 / 2.11 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 36 time to evaluate : 0.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 765 LEU cc_start: 0.8939 (mt) cc_final: 0.8444 (tt) REVERT: B 785 ILE cc_start: 0.8502 (mp) cc_final: 0.8284 (tt) REVERT: B 873 LYS cc_start: 0.8472 (mmtt) cc_final: 0.7923 (mmmt) REVERT: B 965 ASP cc_start: 0.8170 (OUTLIER) cc_final: 0.7669 (m-30) REVERT: B 983 TRP cc_start: 0.8599 (m100) cc_final: 0.8239 (m100) outliers start: 21 outliers final: 11 residues processed: 55 average time/residue: 0.0478 time to fit residues: 3.4807 Evaluate side-chains 45 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 33 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 781 ILE Chi-restraints excluded: chain B residue 810 CYS Chi-restraints excluded: chain B residue 838 THR Chi-restraints excluded: chain B residue 848 ASN Chi-restraints excluded: chain B residue 918 VAL Chi-restraints excluded: chain B residue 919 VAL Chi-restraints excluded: chain B residue 927 ILE Chi-restraints excluded: chain B residue 943 GLN Chi-restraints excluded: chain B residue 965 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 38 optimal weight: 5.9990 chunk 26 optimal weight: 6.9990 chunk 21 optimal weight: 0.7980 chunk 13 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 32 optimal weight: 8.9990 chunk 20 optimal weight: 2.9990 chunk 36 optimal weight: 6.9990 chunk 28 optimal weight: 6.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 636 HIS ** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 759 GLN B 844 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.108270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.073789 restraints weight = 11091.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.076603 restraints weight = 6629.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.078426 restraints weight = 4922.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.079499 restraints weight = 4098.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.080593 restraints weight = 3657.636| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.5096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.069 4087 Z= 0.350 Angle : 0.915 12.101 5584 Z= 0.447 Chirality : 0.055 0.441 628 Planarity : 0.005 0.037 720 Dihedral : 5.826 28.530 528 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 22.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.70 % Favored : 81.30 % Rotamer: Outliers : 4.03 % Allowed : 18.72 % Favored : 77.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -3.54 (0.36), residues: 492 helix: -0.72 (0.83), residues: 36 sheet: -2.88 (0.49), residues: 89 loop : -2.58 (0.32), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 679 TYR 0.012 0.002 TYR B 959 PHE 0.023 0.003 PHE A 568 TRP 0.018 0.003 TRP A 699 HIS 0.006 0.002 HIS A 665 Details of bonding type rmsd/Z covalent geometry : bond 0.00793 / 0.35 ( 4070) covalent geometry : angle 0.88094 / 0.44 ( 5541) SS BOND : bond 0.00533 / 0.26 ( 8) SS BOND : angle 3.52559 / 2.00 ( 16) hydrogen bonds : bond 0.04109 / 2.59 ( 66) hydrogen bonds : angle 7.09149 / 4.58 ( 171) link_NAG-ASN : bond 0.00178 / 0.11 ( 9) link_NAG-ASN : angle 2.54396 / 1.94 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 34 time to evaluate : 0.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 873 LYS cc_start: 0.8557 (mmtt) cc_final: 0.8009 (mmmt) REVERT: B 965 ASP cc_start: 0.7948 (OUTLIER) cc_final: 0.7588 (m-30) outliers start: 17 outliers final: 11 residues processed: 46 average time/residue: 0.0645 time to fit residues: 3.8924 Evaluate side-chains 42 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 30 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 612 MET Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 781 ILE Chi-restraints excluded: chain B residue 810 CYS Chi-restraints excluded: chain B residue 838 THR Chi-restraints excluded: chain B residue 848 ASN Chi-restraints excluded: chain B residue 919 VAL Chi-restraints excluded: chain B residue 927 ILE Chi-restraints excluded: chain B residue 943 GLN Chi-restraints excluded: chain B residue 965 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 26 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 649 GLN ** A 660 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 = 0.4063 r_free = 0.4063 target = 0.110205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.075868 restraints weight = 11070.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.078882 restraints weight = 6449.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.081019 restraints weight = 4674.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.082283 restraints weight = 3805.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.083291 restraints weight = 3349.451| |-----------------------------------------------------------------------------| r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.5128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 4087 Z= 0.226 Angle : 0.841 12.569 5584 Z= 0.403 Chirality : 0.053 0.436 628 Planarity : 0.004 0.043 720 Dihedral : 5.573 27.478 528 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 18.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.87 % Favored : 83.13 % Rotamer: Outliers : 4.74 % Allowed : 19.43 % Favored : 75.83 % 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 are not related in a simple way. whole: -3.47 (0.37), residues: 492 helix: -0.64 (0.84), residues: 36 sheet: -2.90 (0.46), residues: 103 loop : -2.46 (0.33), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 679 TYR 0.011 0.001 TYR B 959 PHE 0.013 0.002 PHE A 568 TRP 0.014 0.002 TRP A 699 HIS 0.004 0.001 HIS A 665 Details of bonding type rmsd/Z covalent geometry : bond 0.00510 / 0.23 ( 4070) covalent geometry : angle 0.80711 / 0.39 ( 5541) SS BOND : bond 0.00417 / 0.20 ( 8) SS BOND : angle 3.33006 / 1.88 ( 16) hydrogen bonds : bond 0.03371 / 2.09 ( 66) hydrogen bonds : angle 6.59521 / 4.25 ( 171) link_NAG-ASN : bond 0.00189 / 0.11 ( 9) link_NAG-ASN : angle 2.46501 / 1.94 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 34 time to evaluate : 0.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 785 ILE cc_start: 0.8405 (mp) cc_final: 0.8093 (tt) REVERT: B 845 MET cc_start: 0.8261 (tpt) cc_final: 0.7947 (tpp) REVERT: B 873 LYS cc_start: 0.8593 (mmtt) cc_final: 0.8124 (mmmt) REVERT: B 965 ASP cc_start: 0.8225 (OUTLIER) cc_final: 0.7692 (m-30) REVERT: B 983 TRP cc_start: 0.8680 (m100) cc_final: 0.8400 (m100) outliers start: 20 outliers final: 13 residues processed: 50 average time/residue: 0.0602 time to fit residues: 4.0120 Evaluate side-chains 45 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 31 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 612 MET Chi-restraints excluded: chain A residue 631 PHE Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 738 PHE Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 781 ILE Chi-restraints excluded: chain B residue 810 CYS Chi-restraints excluded: chain B residue 838 THR Chi-restraints excluded: chain B residue 848 ASN Chi-restraints excluded: chain B residue 880 MET Chi-restraints excluded: chain B residue 919 VAL Chi-restraints excluded: chain B residue 943 GLN Chi-restraints excluded: chain B residue 965 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 0 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 2 optimal weight: 4.9990 chunk 29 optimal weight: 0.5980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.107658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.073836 restraints weight = 10802.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.076812 restraints weight = 6510.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.078868 restraints weight = 4745.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.080186 restraints weight = 3869.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.081124 restraints weight = 3365.809| |-----------------------------------------------------------------------------| r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.5042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4087 Z= 0.146 Angle : 0.798 11.857 5584 Z= 0.376 Chirality : 0.051 0.372 628 Planarity : 0.004 0.036 720 Dihedral : 5.187 26.834 528 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.63 % Favored : 85.37 % Rotamer: Outliers : 3.32 % Allowed : 20.62 % Favored : 76.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -3.33 (0.37), residues: 492 helix: -0.79 (0.81), residues: 38 sheet: -2.58 (0.47), residues: 108 loop : -2.40 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 679 TYR 0.009 0.001 TYR B 959 PHE 0.010 0.001 PHE B 991 TRP 0.012 0.001 TRP A 699 HIS 0.003 0.001 HIS A 700 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 ( 4070) covalent geometry : angle 0.76684 / 0.37 ( 5541) SS BOND : bond 0.00298 / 0.17 ( 8) SS BOND : angle 3.08016 / 1.74 ( 16) hydrogen bonds : bond 0.03066 / 1.85 ( 66) hydrogen bonds : angle 6.17693 / 3.92 ( 171) link_NAG-ASN : bond 0.00242 / 0.12 ( 9) link_NAG-ASN : angle 2.31207 / 1.89 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 38 time to evaluate : 0.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 785 ILE cc_start: 0.8502 (mp) cc_final: 0.8227 (tt) REVERT: B 845 MET cc_start: 0.8227 (tpt) cc_final: 0.7925 (tpp) REVERT: B 873 LYS cc_start: 0.8465 (mmtt) cc_final: 0.8018 (mmmt) REVERT: B 915 TRP cc_start: 0.7986 (m-90) cc_final: 0.7680 (m-90) REVERT: B 965 ASP cc_start: 0.8219 (OUTLIER) cc_final: 0.7679 (m-30) REVERT: B 983 TRP cc_start: 0.8610 (m100) cc_final: 0.8283 (m100) outliers start: 14 outliers final: 11 residues processed: 51 average time/residue: 0.0505 time to fit residues: 3.3330 Evaluate side-chains 45 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 33 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 631 PHE Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 738 PHE Chi-restraints excluded: chain A residue 781 ILE Chi-restraints excluded: chain B residue 810 CYS Chi-restraints excluded: chain B residue 838 THR Chi-restraints excluded: chain B residue 848 ASN Chi-restraints excluded: chain B residue 919 VAL Chi-restraints excluded: chain B residue 927 ILE Chi-restraints excluded: chain B residue 943 GLN Chi-restraints excluded: chain B residue 965 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 44 optimal weight: 7.9990 chunk 21 optimal weight: 0.7980 chunk 38 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 16 optimal weight: 9.9990 chunk 42 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 chunk 18 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.096892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.068764 restraints weight = 10678.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.071350 restraints weight = 6431.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.073157 restraints weight = 4672.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.074405 restraints weight = 3789.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.074989 restraints weight = 3288.356| |-----------------------------------------------------------------------------| r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.5355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 4087 Z= 0.262 Angle : 0.862 12.144 5584 Z= 0.414 Chirality : 0.053 0.392 628 Planarity : 0.004 0.037 720 Dihedral : 5.600 27.161 528 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 18.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.09 % Favored : 81.91 % Rotamer: Outliers : 3.79 % Allowed : 20.38 % Favored : 75.83 % 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 are not related in a simple way. whole: -3.38 (0.37), residues: 492 helix: -0.89 (0.81), residues: 38 sheet: -2.61 (0.49), residues: 104 loop : -2.44 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG B 871 TYR 0.011 0.002 TYR B 959 PHE 0.015 0.002 PHE A 568 TRP 0.011 0.002 TRP A 531 HIS 0.004 0.001 HIS A 665 Details of bonding type rmsd/Z covalent geometry : bond 0.00601 / 0.26 ( 4070) covalent geometry : angle 0.83111 / 0.40 ( 5541) SS BOND : bond 0.00373 / 0.19 ( 8) SS BOND : angle 3.26541 / 1.87 ( 16) hydrogen bonds : bond 0.03551 / 2.27 ( 66) hydrogen bonds : angle 6.71329 / 4.31 ( 171) link_NAG-ASN : bond 0.00150 / 0.10 ( 9) link_NAG-ASN : angle 2.39056 / 1.85 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 32 time to evaluate : 0.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 845 MET cc_start: 0.8054 (tpt) cc_final: 0.7729 (tpp) REVERT: B 873 LYS cc_start: 0.8571 (mmtt) cc_final: 0.8153 (mmmt) REVERT: B 915 TRP cc_start: 0.7990 (m-90) cc_final: 0.7618 (m-90) REVERT: B 965 ASP cc_start: 0.8167 (OUTLIER) cc_final: 0.7768 (m-30) outliers start: 16 outliers final: 13 residues processed: 45 average time/residue: 0.0611 time to fit residues: 3.6516 Evaluate side-chains 44 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 30 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 612 MET Chi-restraints excluded: chain A residue 631 PHE Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 738 PHE Chi-restraints excluded: chain A residue 781 ILE Chi-restraints excluded: chain B residue 810 CYS Chi-restraints excluded: chain B residue 838 THR Chi-restraints excluded: chain B residue 848 ASN Chi-restraints excluded: chain B residue 918 VAL Chi-restraints excluded: chain B residue 919 VAL Chi-restraints excluded: chain B residue 927 ILE Chi-restraints excluded: chain B residue 943 GLN Chi-restraints excluded: chain B residue 965 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 47 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 11 optimal weight: 0.1980 chunk 8 optimal weight: 0.8980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.107822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.074181 restraints weight = 10723.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.077137 restraints weight = 6456.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.079246 restraints weight = 4709.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.080636 restraints weight = 3805.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.081415 restraints weight = 3308.895| |-----------------------------------------------------------------------------| r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.5213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 4087 Z= 0.146 Angle : 0.813 11.919 5584 Z= 0.384 Chirality : 0.051 0.353 628 Planarity : 0.004 0.036 720 Dihedral : 5.222 29.148 528 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.63 % Favored : 85.37 % Rotamer: Outliers : 3.32 % Allowed : 20.62 % Favored : 76.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -3.20 (0.37), residues: 492 helix: -0.76 (0.83), residues: 38 sheet: -2.40 (0.53), residues: 91 loop : -2.38 (0.33), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 583 TYR 0.009 0.001 TYR B 959 PHE 0.006 0.001 PHE A 568 TRP 0.010 0.001 TRP B 915 HIS 0.003 0.001 HIS A 647 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 ( 4070) covalent geometry : angle 0.78080 / 0.37 ( 5541) SS BOND : bond 0.00308 / 0.17 ( 8) SS BOND : angle 3.25929 / 1.84 ( 16) hydrogen bonds : bond 0.03011 / 1.82 ( 66) hydrogen bonds : angle 6.01752 / 3.79 ( 171) link_NAG-ASN : bond 0.00292 / 0.16 ( 9) link_NAG-ASN : angle 2.28906 / 1.89 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 35 time to evaluate : 0.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 845 MET cc_start: 0.8141 (tpt) cc_final: 0.7769 (tpp) REVERT: B 873 LYS cc_start: 0.8422 (mmtt) cc_final: 0.7915 (mmmt) REVERT: B 915 TRP cc_start: 0.8170 (m-90) cc_final: 0.7870 (m-90) REVERT: B 965 ASP cc_start: 0.8191 (OUTLIER) cc_final: 0.7687 (m-30) REVERT: B 983 TRP cc_start: 0.8574 (m100) cc_final: 0.8196 (m100) outliers start: 14 outliers final: 13 residues processed: 48 average time/residue: 0.0579 time to fit residues: 3.6933 Evaluate side-chains 48 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 34 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 631 PHE Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 738 PHE Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 781 ILE Chi-restraints excluded: chain B residue 810 CYS Chi-restraints excluded: chain B residue 838 THR Chi-restraints excluded: chain B residue 848 ASN Chi-restraints excluded: chain B residue 918 VAL Chi-restraints excluded: chain B residue 919 VAL Chi-restraints excluded: chain B residue 927 ILE Chi-restraints excluded: chain B residue 943 GLN Chi-restraints excluded: chain B residue 965 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 42 optimal weight: 0.0370 chunk 18 optimal weight: 0.8980 chunk 14 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 23 optimal weight: 0.0020 chunk 31 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 overall best weight: 0.5466 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 660 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.109218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.075793 restraints weight = 10762.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.078946 restraints weight = 6293.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.081153 restraints weight = 4496.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.082432 restraints weight = 3592.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.083521 restraints weight = 3131.375| |-----------------------------------------------------------------------------| r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.5174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4087 Z= 0.135 Angle : 0.788 10.798 5584 Z= 0.371 Chirality : 0.050 0.309 628 Planarity : 0.004 0.033 720 Dihedral : 5.047 30.370 528 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.62 % Favored : 86.38 % Rotamer: Outliers : 4.50 % Allowed : 19.43 % Favored : 76.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -3.06 (0.37), residues: 492 helix: -0.68 (0.84), residues: 38 sheet: -1.85 (0.53), residues: 90 loop : -2.41 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 624 TYR 0.007 0.001 TYR B 959 PHE 0.006 0.001 PHE A 568 TRP 0.010 0.001 TRP B 915 HIS 0.003 0.001 HIS A 647 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 ( 4070) covalent geometry : angle 0.75924 / 0.36 ( 5541) SS BOND : bond 0.00342 / 0.17 ( 8) SS BOND : angle 3.00896 / 1.71 ( 16) hydrogen bonds : bond 0.02839 / 1.70 ( 66) hydrogen bonds : angle 5.82035 / 3.65 ( 171) link_NAG-ASN : bond 0.00200 / 0.11 ( 9) link_NAG-ASN : angle 2.16267 / 1.80 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 950.96 seconds wall clock time: 17 minutes 2.92 seconds (1022.92 seconds total)