Starting phenix.real_space_refine on Wed Jun 4 20:40:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wqz_32716/06_2025/7wqz_32716.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wqz_32716/06_2025/7wqz_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_32716/06_2025/7wqz_32716.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wqz_32716/06_2025/7wqz_32716.map" model { file = "/net/cci-nas-00/data/ceres_data/7wqz_32716/06_2025/7wqz_32716.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wqz_32716/06_2025/7wqz_32716.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.017 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-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 3.30, per 1000 atoms: 0.83 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: 0.98 Conformation dependent library (CDL) restraints added in 495.2 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: 0.42 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: 0.96 Time building geometry restraints manager: 1.15 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: 2.940 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.150 Find NCS groups from input model: 0.050 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.220 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.003 0.000 TRP A 699 HIS 0.001 0.000 HIS A 700 PHE 0.009 0.001 PHE A 631 TYR 0.006 0.001 TYR A 546 ARG 0.001 0.000 ARG A 583 Details of bonding type rmsd link_NAG-ASN : bond 0.00179 ( 9) link_NAG-ASN : angle 1.29990 ( 27) hydrogen bonds : bond 0.25401 ( 66) hydrogen bonds : angle 11.75284 ( 171) SS BOND : bond 0.00190 ( 8) SS BOND : angle 0.51469 ( 16) covalent geometry : bond 0.00290 ( 4070) covalent geometry : angle 0.54421 ( 5541) *********************** 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 : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash 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: 0.8682 (p) REVERT: B 785 ILE cc_start: 0.8820 (mp) cc_final: 0.8440 (tt) outliers start: 9 outliers final: 0 residues processed: 110 average time/residue: 0.1738 time to fit residues: 23.1210 Evaluate side-chains 48 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 41 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 12 optimal weight: 7.9990 chunk 25 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 38 optimal weight: 5.9990 chunk 14 optimal weight: 9.9990 chunk 23 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 44 optimal weight: 0.9980 overall best weight: 2.5986 ------------------------------------------------------------------------------- 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 686 ASN ** A 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 717 GLN ** A 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 902 GLN B 921 GLN B 978 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.099879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.068660 restraints weight = 10390.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.071033 restraints weight = 6316.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.072513 restraints weight = 4733.836| |-----------------------------------------------------------------------------| r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.3430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 4087 Z= 0.327 Angle : 0.956 23.796 5584 Z= 0.449 Chirality : 0.062 0.883 628 Planarity : 0.005 0.050 720 Dihedral : 8.373 59.917 717 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 19.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.65 % Favored : 84.35 % Rotamer: Outliers : 3.08 % Allowed : 16.11 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.98 (0.34), residues: 492 helix: -1.97 (0.66), residues: 38 sheet: -2.84 (0.46), residues: 101 loop : -2.86 (0.31), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 915 HIS 0.005 0.002 HIS A 700 PHE 0.037 0.003 PHE A 568 TYR 0.012 0.003 TYR B 993 ARG 0.007 0.001 ARG B 940 Details of bonding type rmsd link_NAG-ASN : bond 0.00619 ( 9) link_NAG-ASN : angle 5.60051 ( 27) hydrogen bonds : bond 0.04626 ( 66) hydrogen bonds : angle 8.28467 ( 171) SS BOND : bond 0.00557 ( 8) SS BOND : angle 2.80234 ( 16) covalent geometry : bond 0.00740 ( 4070) covalent geometry : angle 0.86301 ( 5541) *********************** 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 59 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 46 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 723 SER cc_start: 0.9031 (m) cc_final: 0.8825 (p) REVERT: B 785 ILE cc_start: 0.8766 (mp) cc_final: 0.8347 (tt) REVERT: B 873 LYS cc_start: 0.8582 (mmtt) cc_final: 0.8067 (mmmt) outliers start: 13 outliers final: 8 residues processed: 57 average time/residue: 0.2025 time to fit residues: 14.4430 Evaluate side-chains 44 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 36 time to evaluate : 0.458 ------------------------------------------------------------------------------- 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 781 ILE 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 1003 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 19 optimal weight: 0.9980 chunk 15 optimal weight: 6.9990 chunk 8 optimal weight: 1.9990 chunk 40 optimal weight: 0.3980 chunk 5 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 6 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 710 GLN ** 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 = 0.3934 r_free = 0.3934 target = 0.102005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.071088 restraints weight = 10284.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.073663 restraints weight = 6186.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.075365 restraints weight = 4563.669| |-----------------------------------------------------------------------------| r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.3507 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= 0.137 Angle : 0.755 15.864 5584 Z= 0.350 Chirality : 0.056 0.754 628 Planarity : 0.003 0.024 720 Dihedral : 7.892 58.056 717 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.18 % Favored : 88.82 % Rotamer: Outliers : 3.79 % Allowed : 17.06 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.50 (0.35), residues: 492 helix: -1.60 (0.71), residues: 38 sheet: -2.04 (0.49), residues: 98 loop : -2.69 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 915 HIS 0.003 0.001 HIS A 700 PHE 0.019 0.002 PHE B 991 TYR 0.010 0.001 TYR B 993 ARG 0.004 0.001 ARG A 764 Details of bonding type rmsd link_NAG-ASN : bond 0.00208 ( 9) link_NAG-ASN : angle 3.88922 ( 27) hydrogen bonds : bond 0.03196 ( 66) hydrogen bonds : angle 6.98255 ( 171) SS BOND : bond 0.00650 ( 8) SS BOND : angle 2.07135 ( 16) covalent geometry : bond 0.00303 ( 4070) covalent geometry : angle 0.69912 ( 5541) *********************** 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 64 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 48 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 723 SER cc_start: 0.9026 (m) cc_final: 0.8712 (p) REVERT: B 785 ILE cc_start: 0.8787 (mp) cc_final: 0.8447 (tt) REVERT: B 860 ASP cc_start: 0.8659 (p0) cc_final: 0.8454 (p0) REVERT: B 873 LYS cc_start: 0.8439 (mmtt) cc_final: 0.7970 (mmmt) REVERT: B 891 TYR cc_start: 0.8180 (m-80) cc_final: 0.7956 (m-80) REVERT: B 965 ASP cc_start: 0.7629 (OUTLIER) cc_final: 0.7050 (m-30) outliers start: 16 outliers final: 7 residues processed: 62 average time/residue: 0.2497 time to fit residues: 18.9369 Evaluate side-chains 43 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 35 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 809 LEU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 3 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 42 optimal weight: 6.9990 chunk 25 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 chunk 26 optimal weight: 6.9990 chunk 45 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 ** B 790 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 = 0.3942 r_free = 0.3942 target = 0.103511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.073403 restraints weight = 10655.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.075904 restraints weight = 6393.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.077440 restraints weight = 4698.828| |-----------------------------------------------------------------------------| r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.3880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 4087 Z= 0.164 Angle : 0.733 12.368 5584 Z= 0.344 Chirality : 0.053 0.604 628 Planarity : 0.004 0.026 720 Dihedral : 7.832 57.642 717 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.84 % Favored : 85.16 % Rotamer: Outliers : 4.27 % Allowed : 16.35 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.31 (0.36), residues: 492 helix: -1.29 (0.80), residues: 36 sheet: -1.89 (0.50), residues: 100 loop : -2.58 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 699 HIS 0.004 0.001 HIS A 700 PHE 0.014 0.002 PHE B 991 TYR 0.010 0.001 TYR B 959 ARG 0.004 0.001 ARG A 679 Details of bonding type rmsd link_NAG-ASN : bond 0.00119 ( 9) link_NAG-ASN : angle 3.12728 ( 27) hydrogen bonds : bond 0.03397 ( 66) hydrogen bonds : angle 6.65955 ( 171) SS BOND : bond 0.00369 ( 8) SS BOND : angle 1.77337 ( 16) covalent geometry : bond 0.00374 ( 4070) covalent geometry : angle 0.69599 ( 5541) *********************** 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 59 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 41 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 604 ASP cc_start: 0.7824 (m-30) cc_final: 0.7590 (m-30) REVERT: B 785 ILE cc_start: 0.8610 (mp) cc_final: 0.8339 (tt) REVERT: B 860 ASP cc_start: 0.8705 (p0) cc_final: 0.8453 (p0) REVERT: B 873 LYS cc_start: 0.8412 (mmtt) cc_final: 0.7909 (mmmt) outliers start: 18 outliers final: 13 residues processed: 56 average time/residue: 0.1819 time to fit residues: 12.5775 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 : 0.417 ------------------------------------------------------------------------------- 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 730 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 809 LEU 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 30 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 chunk 14 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 39 optimal weight: 8.9990 chunk 17 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 44 optimal weight: 4.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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** A 768 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.101830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.072091 restraints weight = 11075.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.074594 restraints weight = 6516.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.076149 restraints weight = 4727.983| |-----------------------------------------------------------------------------| r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.4314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4087 Z= 0.197 Angle : 0.744 10.308 5584 Z= 0.353 Chirality : 0.053 0.551 628 Planarity : 0.004 0.027 720 Dihedral : 8.009 57.418 717 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 15.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.04 % Favored : 84.96 % Rotamer: Outliers : 5.21 % Allowed : 15.88 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.33 (0.36), residues: 492 helix: -0.99 (0.84), residues: 36 sheet: -2.02 (0.50), residues: 100 loop : -2.59 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 707 HIS 0.004 0.001 HIS A 665 PHE 0.019 0.002 PHE A 568 TYR 0.008 0.001 TYR B 959 ARG 0.003 0.000 ARG A 583 Details of bonding type rmsd link_NAG-ASN : bond 0.00137 ( 9) link_NAG-ASN : angle 2.74087 ( 27) hydrogen bonds : bond 0.03339 ( 66) hydrogen bonds : angle 6.61671 ( 171) SS BOND : bond 0.00545 ( 8) SS BOND : angle 1.54809 ( 16) covalent geometry : bond 0.00447 ( 4070) covalent geometry : angle 0.71761 ( 5541) *********************** 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 62 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 40 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 564 ILE cc_start: 0.9259 (OUTLIER) cc_final: 0.8989 (mm) REVERT: A 679 ARG cc_start: 0.8730 (ptp-170) cc_final: 0.8529 (mpt-90) REVERT: A 765 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8467 (tt) REVERT: B 785 ILE cc_start: 0.8498 (mp) cc_final: 0.8192 (tt) REVERT: B 858 LEU cc_start: 0.8759 (tt) cc_final: 0.8194 (tt) REVERT: B 860 ASP cc_start: 0.8725 (p0) cc_final: 0.8449 (p0) REVERT: B 873 LYS cc_start: 0.8467 (mmtt) cc_final: 0.7945 (mmmt) REVERT: B 965 ASP cc_start: 0.8074 (OUTLIER) cc_final: 0.7654 (m-30) outliers start: 22 outliers final: 13 residues processed: 58 average time/residue: 0.2229 time to fit residues: 16.1507 Evaluate side-chains 50 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 34 time to evaluate : 0.515 ------------------------------------------------------------------------------- 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 612 MET Chi-restraints excluded: chain A residue 639 ILE 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 809 LEU Chi-restraints excluded: chain B residue 838 THR Chi-restraints excluded: chain B residue 848 ASN Chi-restraints excluded: chain B residue 896 CYS 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 0 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 28 optimal weight: 6.9990 chunk 10 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.4018 r_free = 0.4018 target = 0.101332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.072264 restraints weight = 10280.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.075002 restraints weight = 6216.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.076905 restraints weight = 4534.320| |-----------------------------------------------------------------------------| r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.4468 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= 0.163 Angle : 0.724 10.249 5584 Z= 0.341 Chirality : 0.051 0.478 628 Planarity : 0.003 0.029 720 Dihedral : 7.822 57.592 717 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.04 % Favored : 84.96 % Rotamer: Outliers : 4.74 % Allowed : 17.77 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.29 (0.37), residues: 492 helix: -0.85 (0.87), residues: 36 sheet: -2.28 (0.48), residues: 107 loop : -2.46 (0.33), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 915 HIS 0.003 0.001 HIS A 665 PHE 0.011 0.001 PHE A 568 TYR 0.009 0.001 TYR B 959 ARG 0.002 0.000 ARG A 583 Details of bonding type rmsd link_NAG-ASN : bond 0.00130 ( 9) link_NAG-ASN : angle 2.47839 ( 27) hydrogen bonds : bond 0.03220 ( 66) hydrogen bonds : angle 6.32007 ( 171) SS BOND : bond 0.00439 ( 8) SS BOND : angle 1.80363 ( 16) covalent geometry : bond 0.00371 ( 4070) covalent geometry : angle 0.69944 ( 5541) *********************** 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 59 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 39 time to evaluate : 0.448 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: 0.8909 (OUTLIER) cc_final: 0.8371 (tt) REVERT: B 785 ILE cc_start: 0.8531 (mp) cc_final: 0.8216 (tt) REVERT: B 860 ASP cc_start: 0.8572 (p0) cc_final: 0.8256 (p0) REVERT: B 873 LYS cc_start: 0.8487 (mmtt) cc_final: 0.8036 (mmmt) REVERT: B 965 ASP cc_start: 0.8186 (OUTLIER) cc_final: 0.7755 (m-30) outliers start: 20 outliers final: 13 residues processed: 56 average time/residue: 0.1848 time to fit residues: 13.0378 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 : 0.454 ------------------------------------------------------------------------------- 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 748 HIS 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 809 LEU Chi-restraints excluded: chain B residue 838 THR Chi-restraints excluded: chain B residue 848 ASN Chi-restraints excluded: chain B residue 896 CYS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 20 optimal weight: 2.9990 chunk 28 optimal weight: 6.9990 chunk 14 optimal weight: 0.7980 chunk 43 optimal weight: 0.0770 chunk 31 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 38 optimal weight: 7.9990 chunk 45 optimal weight: 0.8980 chunk 17 optimal weight: 0.3980 chunk 21 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4055 r_free = 0.4055 target = 0.103702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.075208 restraints weight = 10190.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.078142 restraints weight = 5982.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.080220 restraints weight = 4282.261| |-----------------------------------------------------------------------------| r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.4448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4087 Z= 0.124 Angle : 0.713 11.224 5584 Z= 0.331 Chirality : 0.050 0.421 628 Planarity : 0.003 0.028 720 Dihedral : 7.467 58.004 717 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.60 % Favored : 87.40 % Rotamer: Outliers : 4.50 % Allowed : 17.54 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.12 (0.37), residues: 492 helix: -0.91 (0.85), residues: 38 sheet: -2.02 (0.49), residues: 107 loop : -2.38 (0.33), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 915 HIS 0.002 0.001 HIS A 700 PHE 0.010 0.001 PHE A 680 TYR 0.007 0.001 TYR B 959 ARG 0.002 0.000 ARG A 624 Details of bonding type rmsd link_NAG-ASN : bond 0.00191 ( 9) link_NAG-ASN : angle 2.30543 ( 27) hydrogen bonds : bond 0.02945 ( 66) hydrogen bonds : angle 5.97936 ( 171) SS BOND : bond 0.00339 ( 8) SS BOND : angle 1.51989 ( 16) covalent geometry : bond 0.00277 ( 4070) covalent geometry : angle 0.69255 ( 5541) *********************** 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 59 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 40 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 765 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8346 (tt) REVERT: B 785 ILE cc_start: 0.8489 (mp) cc_final: 0.8257 (tt) REVERT: B 860 ASP cc_start: 0.8518 (p0) cc_final: 0.8241 (p0) REVERT: B 873 LYS cc_start: 0.8427 (mmtt) cc_final: 0.7924 (mmmt) REVERT: B 965 ASP cc_start: 0.8237 (OUTLIER) cc_final: 0.7549 (m-30) outliers start: 19 outliers final: 14 residues processed: 56 average time/residue: 0.1825 time to fit residues: 12.6436 Evaluate side-chains 50 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 34 time to evaluate : 0.413 ------------------------------------------------------------------------------- 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 765 LEU Chi-restraints excluded: chain A residue 781 ILE Chi-restraints excluded: chain B residue 809 LEU Chi-restraints excluded: chain B residue 838 THR Chi-restraints excluded: chain B residue 848 ASN Chi-restraints excluded: chain B residue 896 CYS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 13 optimal weight: 7.9990 chunk 16 optimal weight: 10.0000 chunk 45 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 26 optimal weight: 10.0000 chunk 39 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 chunk 46 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.4043 r_free = 0.4043 target = 0.102540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.073482 restraints weight = 10030.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.076355 restraints weight = 5993.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.078363 restraints weight = 4334.995| |-----------------------------------------------------------------------------| r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.4600 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= 0.138 Angle : 0.735 10.132 5584 Z= 0.344 Chirality : 0.050 0.394 628 Planarity : 0.003 0.026 720 Dihedral : 7.332 57.828 717 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.01 % Favored : 86.99 % Rotamer: Outliers : 5.21 % Allowed : 17.54 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.07 (0.36), residues: 492 helix: -0.90 (0.85), residues: 38 sheet: -1.93 (0.50), residues: 107 loop : -2.36 (0.32), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 983 HIS 0.002 0.001 HIS A 665 PHE 0.009 0.001 PHE A 680 TYR 0.013 0.001 TYR B 993 ARG 0.002 0.000 ARG B 982 Details of bonding type rmsd link_NAG-ASN : bond 0.00157 ( 9) link_NAG-ASN : angle 2.18568 ( 27) hydrogen bonds : bond 0.02910 ( 66) hydrogen bonds : angle 5.81200 ( 171) SS BOND : bond 0.00375 ( 8) SS BOND : angle 1.39592 ( 16) covalent geometry : bond 0.00320 ( 4070) covalent geometry : angle 0.71801 ( 5541) *********************** 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 56 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 34 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 765 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8366 (tt) REVERT: B 785 ILE cc_start: 0.8513 (mp) cc_final: 0.8238 (tt) REVERT: B 845 MET cc_start: 0.8180 (OUTLIER) cc_final: 0.7951 (tpt) REVERT: B 860 ASP cc_start: 0.8566 (p0) cc_final: 0.8304 (p0) REVERT: B 873 LYS cc_start: 0.8412 (mmtt) cc_final: 0.7916 (mmmt) REVERT: B 965 ASP cc_start: 0.8230 (OUTLIER) cc_final: 0.7541 (m-30) outliers start: 22 outliers final: 15 residues processed: 51 average time/residue: 0.1760 time to fit residues: 11.5028 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 : 0.526 ------------------------------------------------------------------------------- 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 738 PHE 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 809 LEU Chi-restraints excluded: chain B residue 838 THR Chi-restraints excluded: chain B residue 845 MET Chi-restraints excluded: chain B residue 848 ASN Chi-restraints excluded: chain B residue 896 CYS 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 14 optimal weight: 10.0000 chunk 24 optimal weight: 0.5980 chunk 40 optimal weight: 5.9990 chunk 32 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 46 optimal weight: 0.6980 overall best weight: 1.3984 ------------------------------------------------------------------------------- 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 = 0.4006 r_free = 0.4006 target = 0.100186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.071771 restraints weight = 10390.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.074430 restraints weight = 6227.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.076335 restraints weight = 4516.173| |-----------------------------------------------------------------------------| r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.4810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4087 Z= 0.189 Angle : 0.760 9.871 5584 Z= 0.360 Chirality : 0.050 0.386 628 Planarity : 0.003 0.028 720 Dihedral : 7.537 57.538 717 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 16.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.46 % Favored : 83.54 % Rotamer: Outliers : 4.74 % Allowed : 18.01 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.07 (0.36), residues: 492 helix: -0.81 (0.85), residues: 38 sheet: -1.82 (0.53), residues: 90 loop : -2.42 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 983 HIS 0.003 0.001 HIS A 665 PHE 0.010 0.001 PHE A 606 TYR 0.009 0.001 TYR B 993 ARG 0.002 0.000 ARG B 908 Details of bonding type rmsd link_NAG-ASN : bond 0.00102 ( 9) link_NAG-ASN : angle 2.15693 ( 27) hydrogen bonds : bond 0.03095 ( 66) hydrogen bonds : angle 6.24789 ( 171) SS BOND : bond 0.00527 ( 8) SS BOND : angle 1.82841 ( 16) covalent geometry : bond 0.00436 ( 4070) covalent geometry : angle 0.74133 ( 5541) *********************** 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 55 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 35 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 785 ILE cc_start: 0.8495 (mp) cc_final: 0.8169 (tt) REVERT: B 845 MET cc_start: 0.8163 (OUTLIER) cc_final: 0.7935 (tpt) REVERT: B 860 ASP cc_start: 0.8545 (p0) cc_final: 0.8250 (p0) REVERT: B 873 LYS cc_start: 0.8436 (mmtt) cc_final: 0.7938 (mmmt) REVERT: B 965 ASP cc_start: 0.8284 (OUTLIER) cc_final: 0.7673 (m-30) outliers start: 20 outliers final: 16 residues processed: 50 average time/residue: 0.1818 time to fit residues: 11.9582 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 : 0.440 ------------------------------------------------------------------------------- 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 738 PHE 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 809 LEU Chi-restraints excluded: chain B residue 838 THR Chi-restraints excluded: chain B residue 845 MET Chi-restraints excluded: chain B residue 848 ASN Chi-restraints excluded: chain B residue 896 CYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 3 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 11 optimal weight: 0.4980 chunk 30 optimal weight: 0.6980 chunk 37 optimal weight: 0.0980 chunk 31 optimal weight: 0.9990 chunk 44 optimal weight: 6.9990 chunk 46 optimal weight: 0.7980 chunk 15 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.4047 r_free = 0.4047 target = 0.102944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.074497 restraints weight = 10223.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.077530 restraints weight = 6019.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.079615 restraints weight = 4304.715| |-----------------------------------------------------------------------------| r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.4776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4087 Z= 0.126 Angle : 0.728 10.018 5584 Z= 0.342 Chirality : 0.050 0.384 628 Planarity : 0.003 0.027 720 Dihedral : 7.320 57.825 717 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.40 % Favored : 87.60 % Rotamer: Outliers : 4.27 % Allowed : 18.25 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.03 (0.36), residues: 492 helix: -0.83 (0.84), residues: 38 sheet: -2.12 (0.52), residues: 97 loop : -2.27 (0.32), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 983 HIS 0.002 0.001 HIS A 647 PHE 0.008 0.001 PHE A 680 TYR 0.011 0.001 TYR B 993 ARG 0.002 0.000 ARG A 624 Details of bonding type rmsd link_NAG-ASN : bond 0.00228 ( 9) link_NAG-ASN : angle 2.16464 ( 27) hydrogen bonds : bond 0.02782 ( 66) hydrogen bonds : angle 5.65974 ( 171) SS BOND : bond 0.00293 ( 8) SS BOND : angle 1.81564 ( 16) covalent geometry : bond 0.00288 ( 4070) covalent geometry : angle 0.70847 ( 5541) ********************** 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 55 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 37 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 575 ASN cc_start: 0.7932 (m-40) cc_final: 0.7683 (p0) REVERT: B 785 ILE cc_start: 0.8422 (mp) cc_final: 0.8218 (tt) REVERT: B 845 MET cc_start: 0.8156 (OUTLIER) cc_final: 0.7907 (tpt) REVERT: B 860 ASP cc_start: 0.8555 (p0) cc_final: 0.8298 (p0) REVERT: B 873 LYS cc_start: 0.8392 (mmtt) cc_final: 0.7870 (mmmt) REVERT: B 965 ASP cc_start: 0.8218 (OUTLIER) cc_final: 0.7581 (m-30) outliers start: 18 outliers final: 16 residues processed: 50 average time/residue: 0.1811 time to fit residues: 12.1199 Evaluate side-chains 52 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 34 time to evaluate : 0.457 ------------------------------------------------------------------------------- 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 738 PHE 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 809 LEU Chi-restraints excluded: chain B residue 838 THR Chi-restraints excluded: chain B residue 845 MET Chi-restraints excluded: chain B residue 848 ASN Chi-restraints excluded: chain B residue 896 CYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 18 optimal weight: 0.9980 chunk 21 optimal weight: 10.0000 chunk 42 optimal weight: 0.0670 chunk 46 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 16 optimal weight: 9.9990 chunk 41 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 overall best weight: 0.7522 ------------------------------------------------------------------------------- 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 = 0.4045 r_free = 0.4045 target = 0.102639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.073997 restraints weight = 10121.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.076901 restraints weight = 5960.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.078950 restraints weight = 4286.784| |-----------------------------------------------------------------------------| r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.4822 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= 0.139 Angle : 0.769 10.894 5584 Z= 0.364 Chirality : 0.051 0.364 628 Planarity : 0.003 0.026 720 Dihedral : 7.332 57.809 717 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.62 % Favored : 86.38 % Rotamer: Outliers : 4.98 % Allowed : 17.54 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.93 (0.36), residues: 492 helix: -0.82 (0.84), residues: 38 sheet: -1.71 (0.53), residues: 92 loop : -2.31 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 915 HIS 0.002 0.001 HIS A 665 PHE 0.008 0.001 PHE A 680 TYR 0.010 0.001 TYR B 993 ARG 0.002 0.000 ARG A 624 Details of bonding type rmsd link_NAG-ASN : bond 0.00194 ( 9) link_NAG-ASN : angle 2.11267 ( 27) hydrogen bonds : bond 0.02738 ( 66) hydrogen bonds : angle 5.78771 ( 171) SS BOND : bond 0.00292 ( 8) SS BOND : angle 3.00186 ( 16) covalent geometry : bond 0.00319 ( 4070) covalent geometry : angle 0.74022 ( 5541) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2821.14 seconds wall clock time: 51 minutes 26.34 seconds (3086.34 seconds total)