Starting phenix.real_space_refine on Tue Feb 11 04:34:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wqz_32716/02_2025/7wqz_32716.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wqz_32716/02_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_32716/02_2025/7wqz_32716.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wqz_32716/02_2025/7wqz_32716.map" model { file = "/net/cci-nas-00/data/ceres_data/7wqz_32716/02_2025/7wqz_32716.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wqz_32716/02_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-5592/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: 3.44, per 1000 atoms: 0.87 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: 0.93 Conformation dependent library (CDL) restraints added in 506.2 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: 0.49 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: 1.02 Time building geometry restraints manager: 1.13 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: 0.010 Normalize map: mean=0, sd=1: 2.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 14.740 Find NCS groups from input model: 0.060 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.370 ------------------------------------------------------------------------------- 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 4070 Z= 0.174 Angle : 0.544 4.798 5541 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 *********************** 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 : 0.397 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: 0.1894 time to fit residues: 25.2374 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 : 0.491 ------------------------------------------------------------------------------- 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: 9.9990 chunk 25 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 38 optimal weight: 5.9990 chunk 14 optimal weight: 8.9990 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 = 43)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.068744 restraints weight = 10390.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.071076 restraints weight = 6298.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.072644 restraints weight = 4719.866| |-----------------------------------------------------------------------------| r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 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 4070 Z= 0.486 Angle : 0.863 10.759 5541 Z= 0.426 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 *********************** 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 : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 723 SER cc_start: 0.9029 (m) cc_final: 0.8824 (p) REVERT: B 785 ILE cc_start: 0.8771 (mp) cc_final: 0.8358 (tt) REVERT: B 873 LYS cc_start: 0.8581 (mmtt) cc_final: 0.8067 (mmmt) outliers start: 13 outliers final: 8 residues processed: 57 average time/residue: 0.2068 time to fit residues: 14.6320 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 : 0.436 ------------------------------------------------------------------------------- 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: 0.9990 chunk 5 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.3923 r_free = 0.3923 target = 0.101027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.070054 restraints weight = 10350.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.072616 restraints weight = 6273.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.074410 restraints weight = 4642.197| |-----------------------------------------------------------------------------| r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.3579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4070 Z= 0.216 Angle : 0.701 10.455 5541 Z= 0.338 Chirality : 0.056 0.737 628 Planarity : 0.003 0.024 720 Dihedral : 7.910 57.985 717 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.20 % Favored : 87.80 % 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: -3.56 (0.36), residues: 492 helix: -1.54 (0.73), residues: 38 sheet: -2.47 (0.48), residues: 106 loop : -2.60 (0.32), residues: 348 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 0.020 0.002 PHE B 991 TYR 0.009 0.001 TYR B 993 ARG 0.004 0.001 ARG A 583 *********************** 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 : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 723 SER cc_start: 0.9064 (m) cc_final: 0.8751 (p) REVERT: B 785 ILE cc_start: 0.8725 (mp) cc_final: 0.8338 (tt) REVERT: B 873 LYS cc_start: 0.8431 (mmtt) cc_final: 0.7938 (mmmt) REVERT: B 891 TYR cc_start: 0.8204 (m-80) cc_final: 0.7961 (m-80) REVERT: B 965 ASP cc_start: 0.7652 (OUTLIER) cc_final: 0.7111 (m-30) outliers start: 16 outliers final: 8 residues processed: 62 average time/residue: 0.1627 time to fit residues: 12.8232 Evaluate side-chains 43 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 34 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 2.9990 chunk 20 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 chunk 41 optimal weight: 0.9990 chunk 26 optimal weight: 6.9990 chunk 45 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 649 GLN ** 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 = 0.3924 r_free = 0.3924 target = 0.101617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.070414 restraints weight = 10458.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.072930 restraints weight = 6386.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.074721 restraints weight = 4734.539| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.3877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4070 Z= 0.212 Angle : 0.689 10.459 5541 Z= 0.331 Chirality : 0.053 0.586 628 Planarity : 0.004 0.031 720 Dihedral : 7.787 57.779 717 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.02 % Favored : 85.98 % Rotamer: Outliers : 4.03 % Allowed : 16.82 % 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: -3.30 (0.36), residues: 492 helix: -1.26 (0.80), residues: 36 sheet: -1.87 (0.50), residues: 100 loop : -2.58 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 699 HIS 0.004 0.001 HIS A 700 PHE 0.014 0.002 PHE B 991 TYR 0.013 0.001 TYR B 959 ARG 0.005 0.001 ARG A 679 *********************** 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: 17 poor density : 42 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 604 ASP cc_start: 0.7805 (m-30) cc_final: 0.7568 (m-30) REVERT: B 785 ILE cc_start: 0.8617 (mp) cc_final: 0.8351 (tt) REVERT: B 860 ASP cc_start: 0.8633 (p0) cc_final: 0.8404 (p0) REVERT: B 873 LYS cc_start: 0.8419 (mmtt) cc_final: 0.7916 (mmmt) REVERT: B 965 ASP cc_start: 0.7301 (OUTLIER) cc_final: 0.7005 (m-30) outliers start: 17 outliers final: 10 residues processed: 57 average time/residue: 0.2020 time to fit residues: 14.1226 Evaluate side-chains 44 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 33 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 553 VAL Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 781 ILE Chi-restraints excluded: chain B residue 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: 0.8980 chunk 24 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 39 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 22 optimal weight: 9.9990 chunk 16 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 = 0.3922 r_free = 0.3922 target = 0.102492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.072465 restraints weight = 11044.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.075054 restraints weight = 6455.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.076804 restraints weight = 4667.455| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.4251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4070 Z= 0.258 Angle : 0.699 10.253 5541 Z= 0.336 Chirality : 0.052 0.527 628 Planarity : 0.003 0.026 720 Dihedral : 7.911 57.487 717 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.02 % Favored : 85.98 % 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: -3.27 (0.37), residues: 492 helix: -1.00 (0.84), residues: 36 sheet: -1.90 (0.50), residues: 100 loop : -2.57 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 699 HIS 0.004 0.001 HIS A 665 PHE 0.017 0.002 PHE A 568 TYR 0.007 0.001 TYR B 804 ARG 0.003 0.000 ARG A 583 *********************** 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 66 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 44 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 554 TRP cc_start: 0.8467 (m-90) cc_final: 0.8232 (m-90) REVERT: A 679 ARG cc_start: 0.8747 (ptp-170) cc_final: 0.8509 (mpt-90) REVERT: A 765 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8430 (tt) REVERT: B 785 ILE cc_start: 0.8524 (mp) cc_final: 0.8217 (tt) REVERT: B 858 LEU cc_start: 0.8743 (tt) cc_final: 0.8173 (tt) REVERT: B 860 ASP cc_start: 0.8716 (p0) cc_final: 0.8459 (p0) REVERT: B 873 LYS cc_start: 0.8474 (mmtt) cc_final: 0.7916 (mmmt) REVERT: B 965 ASP cc_start: 0.7938 (OUTLIER) cc_final: 0.7474 (m-30) outliers start: 22 outliers final: 14 residues processed: 63 average time/residue: 0.1835 time to fit residues: 14.2529 Evaluate side-chains 53 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 37 time to evaluate : 0.455 ------------------------------------------------------------------------------- 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 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: 7.9990 chunk 10 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 47 optimal weight: 0.5980 chunk 27 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 = 0.3911 r_free = 0.3911 target = 0.100359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.069176 restraints weight = 10536.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.071658 restraints weight = 6369.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.073416 restraints weight = 4731.554| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.4372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4070 Z= 0.210 Angle : 0.701 10.187 5541 Z= 0.332 Chirality : 0.051 0.448 628 Planarity : 0.003 0.027 720 Dihedral : 7.688 57.880 717 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.62 % Favored : 86.38 % Rotamer: Outliers : 4.50 % Allowed : 17.30 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.20 (0.37), residues: 492 helix: -0.84 (0.87), residues: 36 sheet: -2.09 (0.49), residues: 107 loop : -2.44 (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 680 TYR 0.013 0.001 TYR B 993 ARG 0.002 0.000 ARG A 764 *********************** 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 56 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 37 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 679 ARG cc_start: 0.8776 (ptp-170) cc_final: 0.8502 (mpt-90) REVERT: A 765 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8478 (tt) REVERT: B 785 ILE cc_start: 0.8522 (mp) cc_final: 0.8179 (tt) REVERT: B 860 ASP cc_start: 0.8744 (p0) cc_final: 0.8492 (p0) REVERT: B 873 LYS cc_start: 0.8436 (mmtt) cc_final: 0.7929 (mmmt) REVERT: B 965 ASP cc_start: 0.8176 (OUTLIER) cc_final: 0.7708 (m-30) outliers start: 19 outliers final: 11 residues processed: 53 average time/residue: 0.1875 time to fit residues: 12.5037 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 : 0.427 ------------------------------------------------------------------------------- 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 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: 3.9990 chunk 28 optimal weight: 8.9990 chunk 14 optimal weight: 6.9990 chunk 43 optimal weight: 0.0870 chunk 31 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 38 optimal weight: 9.9990 chunk 45 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 21 optimal weight: 6.9990 chunk 25 optimal weight: 3.9990 overall best weight: 1.2560 ------------------------------------------------------------------------------- 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 = 0.4019 r_free = 0.4019 target = 0.101264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.072769 restraints weight = 10341.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.075598 restraints weight = 6092.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.077550 restraints weight = 4388.204| |-----------------------------------------------------------------------------| r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.4568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4070 Z= 0.258 Angle : 0.738 11.144 5541 Z= 0.348 Chirality : 0.051 0.426 628 Planarity : 0.003 0.025 720 Dihedral : 7.638 57.595 717 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 15.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.23 % Favored : 85.77 % Rotamer: Outliers : 4.50 % Allowed : 18.48 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.16 (0.37), residues: 492 helix: -0.79 (0.88), residues: 36 sheet: -2.06 (0.50), residues: 107 loop : -2.42 (0.33), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 915 HIS 0.003 0.001 HIS A 665 PHE 0.012 0.001 PHE A 568 TYR 0.009 0.001 TYR B 959 ARG 0.002 0.000 ARG A 583 *********************** 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 56 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 37 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 765 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8427 (tt) REVERT: B 785 ILE cc_start: 0.8567 (mp) cc_final: 0.8244 (tt) REVERT: B 860 ASP cc_start: 0.8578 (p0) cc_final: 0.8276 (p0) REVERT: B 873 LYS cc_start: 0.8482 (mmtt) cc_final: 0.7975 (mmmt) REVERT: B 965 ASP cc_start: 0.8275 (OUTLIER) cc_final: 0.7575 (m-30) outliers start: 19 outliers final: 13 residues processed: 53 average time/residue: 0.1893 time to fit residues: 12.5468 Evaluate side-chains 47 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 32 time to evaluate : 0.455 ------------------------------------------------------------------------------- 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 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: 8.9990 chunk 16 optimal weight: 4.9990 chunk 45 optimal weight: 0.3980 chunk 1 optimal weight: 1.9990 chunk 26 optimal weight: 9.9990 chunk 39 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 40 optimal weight: 6.9990 chunk 46 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 = 0.101082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.072714 restraints weight = 10115.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.075443 restraints weight = 5975.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.077398 restraints weight = 4329.098| |-----------------------------------------------------------------------------| r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.4735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4070 Z= 0.250 Angle : 0.732 10.592 5541 Z= 0.345 Chirality : 0.050 0.418 628 Planarity : 0.004 0.035 720 Dihedral : 7.575 57.588 717 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 16.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.63 % Favored : 85.37 % 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 : 0.00 % 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: -3.10 (0.37), residues: 492 helix: -0.87 (0.85), residues: 38 sheet: -1.66 (0.51), residues: 100 loop : -2.50 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 699 HIS 0.003 0.001 HIS A 665 PHE 0.010 0.001 PHE A 568 TYR 0.009 0.001 TYR B 959 ARG 0.003 0.001 ARG A 679 *********************** 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 55 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 34 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 765 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8442 (tt) REVERT: B 785 ILE cc_start: 0.8518 (mp) cc_final: 0.8238 (tt) REVERT: B 845 MET cc_start: 0.6562 (tpp) cc_final: 0.5892 (tpp) REVERT: B 860 ASP cc_start: 0.8560 (p0) cc_final: 0.8266 (p0) REVERT: B 873 LYS cc_start: 0.8469 (mmtt) cc_final: 0.8022 (mmmt) REVERT: B 965 ASP cc_start: 0.8236 (OUTLIER) cc_final: 0.7582 (m-30) outliers start: 21 outliers final: 16 residues processed: 50 average time/residue: 0.1628 time to fit residues: 10.6716 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 : 0.640 ------------------------------------------------------------------------------- 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 695 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 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: 1.9990 chunk 24 optimal weight: 2.9990 chunk 40 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 = 0.3978 r_free = 0.3978 target = 0.098572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.070232 restraints weight = 10452.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.072946 restraints weight = 6208.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.074784 restraints weight = 4487.679| |-----------------------------------------------------------------------------| r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.4982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 4070 Z= 0.325 Angle : 0.767 10.415 5541 Z= 0.369 Chirality : 0.051 0.421 628 Planarity : 0.004 0.042 720 Dihedral : 7.776 57.225 717 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 18.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.67 % Favored : 83.33 % 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: -3.09 (0.37), residues: 492 helix: -0.83 (0.84), residues: 38 sheet: -1.82 (0.55), residues: 86 loop : -2.44 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 915 HIS 0.003 0.001 HIS A 647 PHE 0.012 0.002 PHE A 568 TYR 0.011 0.002 TYR B 959 ARG 0.004 0.001 ARG A 583 *********************** 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 54 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 34 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 845 MET cc_start: 0.6626 (tpp) cc_final: 0.5971 (tpp) REVERT: B 860 ASP cc_start: 0.8558 (p0) cc_final: 0.8297 (p0) REVERT: B 873 LYS cc_start: 0.8456 (mmtt) cc_final: 0.7958 (mmmt) REVERT: B 965 ASP cc_start: 0.8347 (OUTLIER) cc_final: 0.7758 (m-30) outliers start: 20 outliers final: 16 residues processed: 50 average time/residue: 0.1612 time to fit residues: 10.4471 Evaluate side-chains 51 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 34 time to evaluate : 0.449 ------------------------------------------------------------------------------- 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 748 HIS 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 3 optimal weight: 1.9990 chunk 20 optimal weight: 0.0370 chunk 11 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 overall best weight: 1.4064 ------------------------------------------------------------------------------- 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 = 0.3986 r_free = 0.3986 target = 0.098995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.070751 restraints weight = 10345.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.073457 restraints weight = 6134.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.075359 restraints weight = 4431.813| |-----------------------------------------------------------------------------| r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.5076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 4070 Z= 0.272 Angle : 0.748 10.347 5541 Z= 0.359 Chirality : 0.051 0.425 628 Planarity : 0.004 0.047 720 Dihedral : 7.676 57.555 717 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 16.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.63 % Favored : 85.37 % Rotamer: Outliers : 3.79 % Allowed : 19.19 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.09 (0.37), residues: 492 helix: -0.90 (0.82), residues: 38 sheet: -2.20 (0.53), residues: 93 loop : -2.30 (0.33), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 915 HIS 0.003 0.001 HIS A 647 PHE 0.010 0.001 PHE A 568 TYR 0.011 0.001 TYR B 959 ARG 0.002 0.000 ARG A 583 ********************** 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 48 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 32 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 845 MET cc_start: 0.6677 (tpp) cc_final: 0.6023 (tpp) REVERT: B 860 ASP cc_start: 0.8620 (p0) cc_final: 0.8388 (p0) REVERT: B 873 LYS cc_start: 0.8427 (mmtt) cc_final: 0.7910 (mmmt) REVERT: B 965 ASP cc_start: 0.8235 (OUTLIER) cc_final: 0.7680 (m-30) outliers start: 16 outliers final: 15 residues processed: 45 average time/residue: 0.1612 time to fit residues: 9.3918 Evaluate side-chains 47 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 31 time to evaluate : 0.465 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 18 optimal weight: 0.6980 chunk 21 optimal weight: 0.0970 chunk 42 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 16 optimal weight: 10.0000 chunk 41 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 20 optimal weight: 7.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- 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 = 0.4021 r_free = 0.4021 target = 0.101095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.072890 restraints weight = 10172.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.075627 restraints weight = 6067.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.077415 restraints weight = 4387.893| |-----------------------------------------------------------------------------| r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.5010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 4070 Z= 0.186 Angle : 0.744 10.467 5541 Z= 0.355 Chirality : 0.050 0.400 628 Planarity : 0.004 0.043 720 Dihedral : 7.509 58.136 717 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.02 % Favored : 85.98 % Rotamer: Outliers : 4.50 % Allowed : 18.48 % Favored : 77.01 % 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: -3.02 (0.37), residues: 492 helix: -0.90 (0.82), residues: 38 sheet: -2.12 (0.52), residues: 97 loop : -2.25 (0.32), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 915 HIS 0.003 0.001 HIS A 647 PHE 0.007 0.001 PHE B 991 TYR 0.008 0.001 TYR B 959 ARG 0.002 0.000 ARG A 764 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1836.19 seconds wall clock time: 33 minutes 41.09 seconds (2021.09 seconds total)