Starting phenix.real_space_refine on Tue Mar 3 12:20:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wqz_32716/03_2026/7wqz_32716.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wqz_32716/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7wqz_32716/03_2026/7wqz_32716.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wqz_32716/03_2026/7wqz_32716.map" model { file = "/net/cci-nas-00/data/ceres_data/7wqz_32716/03_2026/7wqz_32716.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wqz_32716/03_2026/7wqz_32716.cif" } 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-5986/lib/python3.9/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 dihedrals: 15 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 dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 1.14, per 1000 atoms: 0.29 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: 0.30 Conformation dependent library (CDL) restraints added in 151.0 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: 0.14 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: 0.63 Time building geometry restraints manager: 0.40 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: 2395 17.14 - 34.28: 105 34.28 - 51.42: 27 51.42 - 68.56: 9 68.56 - 85.70: 3 Dihedral angle restraints: 2539 sinusoidal: 1127 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 2536 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: 1.640 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: 0.060 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 5.800 Find NCS groups from input model: 0.020 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 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 : 10.730 85.701 1611 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 covalent geometry : bond 0.00290 ( 4070) covalent geometry : angle 0.54421 ( 5541) SS BOND : bond 0.00190 ( 8) SS BOND : angle 0.51469 ( 16) hydrogen bonds : bond 0.25401 ( 66) hydrogen bonds : angle 11.75284 ( 171) link_NAG-ASN : bond 0.00179 ( 9) link_NAG-ASN : angle 1.29990 ( 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 : 0.146 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: 0.0682 time to fit residues: 9.2209 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 : 0.149 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4084 r_free = 0.4084 target = 0.108748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.080106 restraints weight = 10499.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.083245 restraints weight = 5888.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.085356 restraints weight = 4133.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.086652 restraints weight = 3273.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.087761 restraints weight = 2812.711| |-----------------------------------------------------------------------------| r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 4087 Z= 0.150 Angle : 0.844 22.143 5584 Z= 0.375 Chirality : 0.061 0.934 628 Planarity : 0.004 0.034 720 Dihedral : 7.910 58.457 717 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.57 % Favored : 89.43 % Rotamer: Outliers : 2.84 % Allowed : 15.64 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.92 (0.33), residues: 492 helix: -2.10 (0.65), residues: 37 sheet: -2.56 (0.50), residues: 91 loop : -2.89 (0.28), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 624 TYR 0.013 0.002 TYR A 596 PHE 0.030 0.002 PHE B1017 TRP 0.018 0.001 TRP B 915 HIS 0.004 0.001 HIS A 665 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 4070) covalent geometry : angle 0.74589 ( 5541) SS BOND : bond 0.00477 ( 8) SS BOND : angle 2.33698 ( 16) hydrogen bonds : bond 0.04048 ( 66) hydrogen bonds : angle 7.72688 ( 171) link_NAG-ASN : bond 0.00590 ( 9) link_NAG-ASN : angle 5.46168 ( 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 : 0.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 611 ARG cc_start: 0.8441 (ttt-90) cc_final: 0.7819 (ttp80) REVERT: A 679 ARG cc_start: 0.8247 (mtt-85) cc_final: 0.7780 (ptp-110) REVERT: A 723 SER cc_start: 0.8986 (m) cc_final: 0.8645 (p) REVERT: B 785 ILE cc_start: 0.8930 (mp) cc_final: 0.8593 (tt) REVERT: B 860 ASP cc_start: 0.8448 (p0) cc_final: 0.8192 (p0) REVERT: B 873 LYS cc_start: 0.8108 (mmtt) cc_final: 0.7879 (mmmt) REVERT: B 879 MET cc_start: 0.7778 (OUTLIER) cc_final: 0.7290 (mtp) outliers start: 12 outliers final: 5 residues processed: 57 average time/residue: 0.0678 time to fit residues: 4.8249 Evaluate side-chains 46 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 40 time to evaluate : 0.124 ------------------------------------------------------------------------------- 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: 4.9990 chunk 26 optimal weight: 8.9990 chunk 38 optimal weight: 0.0670 chunk 14 optimal weight: 7.9990 chunk 18 optimal weight: 0.8980 chunk 22 optimal weight: 8.9990 chunk 32 optimal weight: 7.9990 chunk 20 optimal weight: 8.9990 chunk 30 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 overall best weight: 1.3922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.104672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.074296 restraints weight = 10606.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.077008 restraints weight = 6172.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.078879 restraints weight = 4465.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.080133 restraints weight = 3622.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.080895 restraints weight = 3151.304| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.3419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 4087 Z= 0.202 Angle : 0.803 13.699 5584 Z= 0.379 Chirality : 0.057 0.753 628 Planarity : 0.004 0.031 720 Dihedral : 7.652 57.105 717 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.41 % Favored : 86.59 % Rotamer: Outliers : 4.74 % Allowed : 15.64 % Favored : 79.62 % 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: -3.55 (0.35), residues: 492 helix: -1.43 (0.72), residues: 38 sheet: -2.46 (0.46), residues: 104 loop : -2.61 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 583 TYR 0.009 0.002 TYR B 828 PHE 0.024 0.002 PHE A 568 TRP 0.011 0.002 TRP A 707 HIS 0.004 0.001 HIS A 700 Details of bonding type rmsd covalent geometry : bond 0.00449 ( 4070) covalent geometry : angle 0.74730 ( 5541) SS BOND : bond 0.00478 ( 8) SS BOND : angle 3.12199 ( 16) hydrogen bonds : bond 0.04029 ( 66) hydrogen bonds : angle 7.32032 ( 171) link_NAG-ASN : bond 0.00219 ( 9) link_NAG-ASN : angle 3.59367 ( 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 72 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 52 time to evaluate : 0.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 575 ASN cc_start: 0.7965 (m-40) cc_final: 0.7608 (p0) REVERT: A 723 SER cc_start: 0.9027 (m) cc_final: 0.8776 (p) REVERT: B 785 ILE cc_start: 0.8827 (mp) cc_final: 0.8427 (tt) REVERT: B 873 LYS cc_start: 0.8451 (mmtt) cc_final: 0.7920 (mmmt) REVERT: B 891 TYR cc_start: 0.8206 (m-80) cc_final: 0.7985 (m-80) REVERT: B 976 MET cc_start: 0.8413 (OUTLIER) cc_final: 0.7894 (ptp) REVERT: B 983 TRP cc_start: 0.8689 (m100) cc_final: 0.8311 (m100) outliers start: 20 outliers final: 12 residues processed: 69 average time/residue: 0.0750 time to fit residues: 6.4858 Evaluate side-chains 46 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 33 time to evaluate : 0.153 ------------------------------------------------------------------------------- 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 695 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 956 CYS 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: 2.9990 chunk 14 optimal weight: 7.9990 chunk 37 optimal weight: 5.9990 chunk 39 optimal weight: 0.0060 chunk 2 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 21 optimal weight: 9.9990 chunk 38 optimal weight: 0.9990 overall best weight: 1.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 759 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.103420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.074005 restraints weight = 10440.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.076500 restraints weight = 6217.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.078178 restraints weight = 4545.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.079402 restraints weight = 3730.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.080130 restraints weight = 3261.235| |-----------------------------------------------------------------------------| r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.3874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4087 Z= 0.171 Angle : 0.774 10.960 5584 Z= 0.368 Chirality : 0.054 0.562 628 Planarity : 0.004 0.028 720 Dihedral : 7.643 57.829 717 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.43 % Favored : 85.57 % Rotamer: Outliers : 4.27 % Allowed : 17.06 % Favored : 78.67 % 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 (0.36), residues: 492 helix: -1.23 (0.77), residues: 38 sheet: -2.15 (0.51), residues: 88 loop : -2.58 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 679 TYR 0.014 0.002 TYR B 959 PHE 0.015 0.002 PHE A 568 TRP 0.014 0.002 TRP A 699 HIS 0.003 0.001 HIS A 700 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 4070) covalent geometry : angle 0.73204 ( 5541) SS BOND : bond 0.00403 ( 8) SS BOND : angle 3.18422 ( 16) hydrogen bonds : bond 0.03150 ( 66) hydrogen bonds : angle 6.45490 ( 171) link_NAG-ASN : bond 0.00104 ( 9) link_NAG-ASN : angle 2.81812 ( 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 61 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 43 time to evaluate : 0.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 575 ASN cc_start: 0.7976 (m-40) cc_final: 0.7623 (p0) REVERT: A 723 SER cc_start: 0.9104 (m) cc_final: 0.8786 (p) REVERT: B 785 ILE cc_start: 0.8659 (mp) cc_final: 0.8331 (tt) REVERT: B 873 LYS cc_start: 0.8467 (mmtt) cc_final: 0.7992 (mmmt) REVERT: B 976 MET cc_start: 0.8235 (OUTLIER) cc_final: 0.7970 (ptp) outliers start: 18 outliers final: 11 residues processed: 59 average time/residue: 0.0733 time to fit residues: 5.5035 Evaluate side-chains 46 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 34 time to evaluate : 0.145 ------------------------------------------------------------------------------- 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 695 ILE Chi-restraints excluded: chain A residue 730 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 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: 0.0670 chunk 46 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 30 optimal weight: 0.0980 chunk 8 optimal weight: 1.9990 chunk 21 optimal weight: 10.0000 chunk 23 optimal weight: 2.9990 overall best weight: 0.5920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3949 r_free = 0.3949 target = 0.103113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.071874 restraints weight = 10450.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.074609 restraints weight = 6221.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.076481 restraints weight = 4551.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.077619 restraints weight = 3729.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.078218 restraints weight = 3288.521| |-----------------------------------------------------------------------------| r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.3972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4087 Z= 0.128 Angle : 0.744 10.252 5584 Z= 0.350 Chirality : 0.052 0.469 628 Planarity : 0.003 0.027 720 Dihedral : 7.436 58.064 717 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.99 % Favored : 88.01 % Rotamer: Outliers : 4.50 % Allowed : 16.35 % Favored : 79.15 % 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: -3.24 (0.36), residues: 492 helix: -0.90 (0.83), residues: 38 sheet: -2.05 (0.52), residues: 88 loop : -2.51 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 679 TYR 0.013 0.001 TYR B 993 PHE 0.009 0.001 PHE B1017 TRP 0.010 0.001 TRP A 699 HIS 0.002 0.001 HIS A 665 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 4070) covalent geometry : angle 0.70902 ( 5541) SS BOND : bond 0.00355 ( 8) SS BOND : angle 2.92997 ( 16) hydrogen bonds : bond 0.02746 ( 66) hydrogen bonds : angle 6.02311 ( 171) link_NAG-ASN : bond 0.00191 ( 9) link_NAG-ASN : angle 2.46908 ( 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 61 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 42 time to evaluate : 0.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 575 ASN cc_start: 0.7991 (m-40) cc_final: 0.7642 (p0) REVERT: A 723 SER cc_start: 0.9079 (m) cc_final: 0.8775 (p) REVERT: B 785 ILE cc_start: 0.8637 (mp) cc_final: 0.8388 (tt) REVERT: B 873 LYS cc_start: 0.8437 (mmtt) cc_final: 0.7923 (mmmt) REVERT: B 965 ASP cc_start: 0.7588 (OUTLIER) cc_final: 0.7300 (m-30) REVERT: B 976 MET cc_start: 0.8225 (OUTLIER) cc_final: 0.7593 (pmm) outliers start: 19 outliers final: 13 residues processed: 58 average time/residue: 0.0712 time to fit residues: 5.2014 Evaluate side-chains 50 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 35 time to evaluate : 0.121 ------------------------------------------------------------------------------- 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 695 ILE Chi-restraints excluded: chain A residue 730 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 Chi-restraints excluded: chain B residue 976 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 38 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 21 optimal weight: 10.0000 chunk 13 optimal weight: 9.9990 chunk 35 optimal weight: 4.9990 chunk 17 optimal weight: 0.0270 chunk 23 optimal weight: 5.9990 chunk 32 optimal weight: 10.0000 chunk 20 optimal weight: 0.5980 chunk 36 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 overall best weight: 2.5244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 902 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.102883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.072539 restraints weight = 10708.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.075028 restraints weight = 6603.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.076737 restraints weight = 4916.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.077893 restraints weight = 4066.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.078589 restraints weight = 3584.808| |-----------------------------------------------------------------------------| r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.4764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 4087 Z= 0.307 Angle : 0.865 10.092 5584 Z= 0.423 Chirality : 0.054 0.447 628 Planarity : 0.004 0.040 720 Dihedral : 8.016 56.869 717 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 20.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.09 % Favored : 81.91 % Rotamer: Outliers : 4.27 % Allowed : 16.82 % Favored : 78.91 % 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: -3.48 (0.36), residues: 492 helix: -0.83 (0.82), residues: 38 sheet: -2.68 (0.49), residues: 94 loop : -2.55 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 679 TYR 0.014 0.002 TYR B 959 PHE 0.029 0.003 PHE A 568 TRP 0.017 0.002 TRP A 699 HIS 0.005 0.001 HIS A 665 Details of bonding type rmsd covalent geometry : bond 0.00696 ( 4070) covalent geometry : angle 0.83046 ( 5541) SS BOND : bond 0.00547 ( 8) SS BOND : angle 3.55679 ( 16) hydrogen bonds : bond 0.03749 ( 66) hydrogen bonds : angle 6.72008 ( 171) link_NAG-ASN : bond 0.00190 ( 9) link_NAG-ASN : angle 2.39455 ( 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 53 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 35 time to evaluate : 0.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 564 ILE cc_start: 0.9198 (OUTLIER) cc_final: 0.8882 (mm) REVERT: A 765 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8497 (tt) REVERT: B 785 ILE cc_start: 0.8537 (mp) cc_final: 0.8153 (tt) REVERT: B 873 LYS cc_start: 0.8559 (mmtt) cc_final: 0.8034 (mmmt) REVERT: B 965 ASP cc_start: 0.7937 (OUTLIER) cc_final: 0.7546 (m-30) REVERT: B 983 TRP cc_start: 0.8527 (m100) cc_final: 0.8200 (m100) outliers start: 18 outliers final: 10 residues processed: 49 average time/residue: 0.0505 time to fit residues: 3.2964 Evaluate side-chains 47 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 34 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 695 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 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 Chi-restraints excluded: chain B residue 976 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 26 optimal weight: 6.9990 chunk 4 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 38 optimal weight: 0.0470 chunk 24 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 overall best weight: 1.1682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4020 r_free = 0.4020 target = 0.101375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.073420 restraints weight = 10530.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.076115 restraints weight = 6256.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.077933 restraints weight = 4528.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.079314 restraints weight = 3679.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.080143 restraints weight = 3178.534| |-----------------------------------------------------------------------------| r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.4751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4087 Z= 0.169 Angle : 0.795 10.436 5584 Z= 0.375 Chirality : 0.052 0.454 628 Planarity : 0.003 0.027 720 Dihedral : 7.684 57.698 717 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.82 % Favored : 86.18 % Rotamer: Outliers : 4.50 % Allowed : 16.59 % Favored : 78.91 % 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: -3.30 (0.36), residues: 492 helix: -0.81 (0.82), residues: 38 sheet: -2.46 (0.50), residues: 94 loop : -2.45 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 679 TYR 0.010 0.001 TYR B 959 PHE 0.011 0.001 PHE A 568 TRP 0.017 0.001 TRP A 699 HIS 0.003 0.001 HIS A 700 Details of bonding type rmsd covalent geometry : bond 0.00384 ( 4070) covalent geometry : angle 0.76397 ( 5541) SS BOND : bond 0.00332 ( 8) SS BOND : angle 2.98425 ( 16) hydrogen bonds : bond 0.02928 ( 66) hydrogen bonds : angle 6.06152 ( 171) link_NAG-ASN : bond 0.00219 ( 9) link_NAG-ASN : angle 2.39511 ( 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 55 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 36 time to evaluate : 0.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 765 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8466 (tt) REVERT: B 785 ILE cc_start: 0.8484 (mp) cc_final: 0.8225 (tt) REVERT: B 873 LYS cc_start: 0.8462 (mmtt) cc_final: 0.7968 (mmmt) REVERT: B 915 TRP cc_start: 0.7923 (m-90) cc_final: 0.7598 (m-90) REVERT: B 965 ASP cc_start: 0.8148 (OUTLIER) cc_final: 0.7567 (m-30) outliers start: 19 outliers final: 11 residues processed: 52 average time/residue: 0.0512 time to fit residues: 3.7065 Evaluate side-chains 47 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 34 time to evaluate : 0.129 ------------------------------------------------------------------------------- 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 695 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 918 VAL Chi-restraints excluded: chain B residue 919 VAL Chi-restraints excluded: chain B residue 943 GLN Chi-restraints excluded: chain B residue 965 ASP Chi-restraints excluded: chain B residue 976 MET 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: 3.9990 chunk 11 optimal weight: 0.5980 chunk 31 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 22 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 29 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4038 r_free = 0.4038 target = 0.102373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.073357 restraints weight = 10197.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.076137 restraints weight = 6063.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.078275 restraints weight = 4394.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.079558 restraints weight = 3531.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.080317 restraints weight = 3060.638| |-----------------------------------------------------------------------------| r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.4732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4087 Z= 0.131 Angle : 0.764 10.148 5584 Z= 0.359 Chirality : 0.051 0.408 628 Planarity : 0.004 0.028 720 Dihedral : 7.462 57.978 717 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.82 % Favored : 86.18 % Rotamer: Outliers : 4.03 % Allowed : 17.06 % Favored : 78.91 % 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: -3.15 (0.36), residues: 492 helix: -0.73 (0.85), residues: 38 sheet: -2.32 (0.50), residues: 96 loop : -2.34 (0.32), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 679 TYR 0.008 0.001 TYR B 959 PHE 0.013 0.001 PHE B 884 TRP 0.008 0.001 TRP A 699 HIS 0.002 0.001 HIS B 881 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 4070) covalent geometry : angle 0.73662 ( 5541) SS BOND : bond 0.00293 ( 8) SS BOND : angle 2.71317 ( 16) hydrogen bonds : bond 0.02850 ( 66) hydrogen bonds : angle 5.78018 ( 171) link_NAG-ASN : bond 0.00214 ( 9) link_NAG-ASN : angle 2.26468 ( 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 57 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 40 time to evaluate : 0.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 765 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8391 (tt) REVERT: B 873 LYS cc_start: 0.8388 (mmtt) cc_final: 0.7899 (mmmt) REVERT: B 915 TRP cc_start: 0.7886 (m-90) cc_final: 0.7560 (m-90) REVERT: B 965 ASP cc_start: 0.8228 (OUTLIER) cc_final: 0.7599 (m-30) outliers start: 17 outliers final: 12 residues processed: 54 average time/residue: 0.0624 time to fit residues: 4.4375 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 : 0.144 ------------------------------------------------------------------------------- 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 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 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 Chi-restraints excluded: chain B residue 976 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 44 optimal weight: 6.9990 chunk 21 optimal weight: 0.9990 chunk 38 optimal weight: 0.4980 chunk 7 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 41 optimal weight: 0.7980 chunk 16 optimal weight: 9.9990 chunk 42 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 6 optimal weight: 0.0870 overall best weight: 0.6560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4049 r_free = 0.4049 target = 0.102905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.073618 restraints weight = 10371.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.076485 restraints weight = 6108.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.078461 restraints weight = 4418.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.079790 restraints weight = 3575.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.080781 restraints weight = 3094.198| |-----------------------------------------------------------------------------| r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.4781 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= 0.134 Angle : 0.748 9.934 5584 Z= 0.354 Chirality : 0.050 0.379 628 Planarity : 0.004 0.030 720 Dihedral : 7.385 57.961 717 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.41 % Favored : 86.59 % Rotamer: Outliers : 3.32 % Allowed : 18.25 % Favored : 78.44 % 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: -3.03 (0.37), residues: 492 helix: -0.60 (0.87), residues: 38 sheet: -2.13 (0.51), residues: 97 loop : -2.30 (0.32), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 583 TYR 0.008 0.001 TYR B 804 PHE 0.013 0.001 PHE B 991 TRP 0.012 0.001 TRP B 915 HIS 0.002 0.001 HIS A 665 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 4070) covalent geometry : angle 0.72154 ( 5541) SS BOND : bond 0.00293 ( 8) SS BOND : angle 2.62905 ( 16) hydrogen bonds : bond 0.02789 ( 66) hydrogen bonds : angle 5.67313 ( 171) link_NAG-ASN : bond 0.00197 ( 9) link_NAG-ASN : angle 2.18689 ( 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 52 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 38 time to evaluate : 0.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 765 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8381 (tt) REVERT: B 873 LYS cc_start: 0.8350 (mmtt) cc_final: 0.7898 (mmmt) REVERT: B 965 ASP cc_start: 0.8190 (OUTLIER) cc_final: 0.7585 (m-30) outliers start: 14 outliers final: 10 residues processed: 49 average time/residue: 0.0568 time to fit residues: 3.6142 Evaluate side-chains 47 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 35 time to evaluate : 0.089 ------------------------------------------------------------------------------- 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 738 PHE Chi-restraints excluded: chain A residue 748 HIS 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 848 ASN Chi-restraints excluded: chain B residue 918 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 47 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 41 optimal weight: 7.9990 chunk 26 optimal weight: 0.6980 chunk 32 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 31 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4048 r_free = 0.4048 target = 0.102636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.073411 restraints weight = 10193.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.076268 restraints weight = 6021.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.078219 restraints weight = 4368.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.079422 restraints weight = 3543.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.080385 restraints weight = 3097.741| |-----------------------------------------------------------------------------| r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.4934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4087 Z= 0.167 Angle : 0.790 10.161 5584 Z= 0.378 Chirality : 0.051 0.370 628 Planarity : 0.004 0.028 720 Dihedral : 7.428 57.756 717 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.84 % Favored : 85.16 % Rotamer: Outliers : 3.32 % Allowed : 19.43 % Favored : 77.25 % 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: -2.96 (0.36), residues: 492 helix: -0.57 (0.86), residues: 38 sheet: -1.63 (0.54), residues: 90 loop : -2.39 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 583 TYR 0.008 0.001 TYR B 959 PHE 0.012 0.001 PHE A 568 TRP 0.050 0.002 TRP B 915 HIS 0.003 0.001 HIS A 665 Details of bonding type rmsd covalent geometry : bond 0.00390 ( 4070) covalent geometry : angle 0.76177 ( 5541) SS BOND : bond 0.00300 ( 8) SS BOND : angle 2.94058 ( 16) hydrogen bonds : bond 0.02747 ( 66) hydrogen bonds : angle 5.76960 ( 171) link_NAG-ASN : bond 0.00167 ( 9) link_NAG-ASN : angle 2.16887 ( 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 46 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 32 time to evaluate : 0.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 873 LYS cc_start: 0.8378 (mmtt) cc_final: 0.7913 (mmmt) REVERT: B 965 ASP cc_start: 0.8399 (OUTLIER) cc_final: 0.7718 (m-30) outliers start: 14 outliers final: 12 residues processed: 44 average time/residue: 0.0519 time to fit residues: 3.1622 Evaluate side-chains 45 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 32 time to evaluate : 0.154 ------------------------------------------------------------------------------- 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 738 PHE Chi-restraints excluded: chain A residue 748 HIS 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 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: 0.9980 chunk 18 optimal weight: 0.9980 chunk 14 optimal weight: 7.9990 chunk 46 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4141 r_free = 0.4141 target = 0.116183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.083396 restraints weight = 10556.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.086326 restraints weight = 6222.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.088359 restraints weight = 4520.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.089795 restraints weight = 3668.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.090612 restraints weight = 3184.690| |-----------------------------------------------------------------------------| r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.4985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4087 Z= 0.151 Angle : 0.772 9.955 5584 Z= 0.366 Chirality : 0.051 0.366 628 Planarity : 0.004 0.027 720 Dihedral : 7.429 57.696 717 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.02 % Favored : 85.98 % Rotamer: Outliers : 3.55 % Allowed : 18.72 % Favored : 77.73 % 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: -2.91 (0.37), residues: 492 helix: -0.53 (0.86), residues: 38 sheet: -1.57 (0.55), residues: 90 loop : -2.37 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 583 TYR 0.008 0.001 TYR B 959 PHE 0.010 0.001 PHE A 568 TRP 0.038 0.002 TRP B 915 HIS 0.003 0.001 HIS A 647 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 4070) covalent geometry : angle 0.74427 ( 5541) SS BOND : bond 0.00281 ( 8) SS BOND : angle 2.85774 ( 16) hydrogen bonds : bond 0.02723 ( 66) hydrogen bonds : angle 5.72187 ( 171) link_NAG-ASN : bond 0.00184 ( 9) link_NAG-ASN : angle 2.19339 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 997.69 seconds wall clock time: 17 minutes 46.75 seconds (1066.75 seconds total)