Starting phenix.real_space_refine on Wed Mar 5 23:43:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wqw_32714/03_2025/7wqw_32714.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wqw_32714/03_2025/7wqw_32714.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wqw_32714/03_2025/7wqw_32714.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wqw_32714/03_2025/7wqw_32714.map" model { file = "/net/cci-nas-00/data/ceres_data/7wqw_32714/03_2025/7wqw_32714.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wqw_32714/03_2025/7wqw_32714.cif" } resolution = 3.2 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= -0.001 sd= 0.020 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 2501 2.51 5 N 678 2.21 5 O 775 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-5624/modules/chem_data/mon_lib" Total number of atoms: 3983 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: 1844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1844 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: 3.35, per 1000 atoms: 0.84 Number of scatterers: 3983 At special positions: 0 Unit cell: (64.852, 86.818, 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 775 8.00 N 678 7.00 C 2501 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 725 " " NAG A 802 " - " ASN A 706 " " NAG A 803 " - " ASN A 682 " " NAG A 804 " - " ASN A 630 " " NAG A 805 " - " ASN A 534 " " NAG B1101 " - " ASN B 949 " " NAG B1102 " - " ASN B 909 " " NAG B1103 " - " ASN B 887 " " NAG B1104 " - " ASN B 848 " Time building additional restraints: 0.99 Conformation dependent library (CDL) restraints added in 499.5 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: 5 helices and 7 sheets defined 7.9% alpha, 21.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 671 through 675 removed outlier: 3.550A pdb=" N GLU A 674 " --> pdb=" O GLY A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 719 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 1010 through 1019 removed outlier: 4.079A pdb=" N PHE B1017 " --> pdb=" O TRP B1013 " (cutoff:3.500A) removed outlier: 3.778A 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: 3.565A pdb=" N ALA A 629 " --> pdb=" O PHE A 537 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ASN A 630 " --> pdb=" O PHE A 568 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N PHE A 568 " --> pdb=" O ASN A 630 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 551 through 557 removed outlier: 3.569A pdb=" N CYS A 552 " --> pdb=" O LEU A 616 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU A 616 " --> pdb=" O CYS A 552 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL A 614 " --> pdb=" O TRP A 554 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 688 through 689 Processing sheet with id=AA4, first strand: chain 'A' and resid 693 through 694 Processing sheet with id=AA5, first strand: chain 'A' and resid 702 through 703 removed outlier: 4.693A pdb=" N LEU A 741 " --> pdb=" O CYS A 703 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS A 740 " --> pdb=" O THR A 752 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR A 752 " --> pdb=" O LYS A 740 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE A 750 " --> pdb=" O ASN A 742 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 789 through 790 removed outlier: 3.586A pdb=" N GLN B 929 " --> pdb=" O GLY B 914 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N ASN B 909 " --> pdb=" O GLN B 978 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N GLN B 978 " --> pdb=" O ASN B 909 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ALA B 913 " --> pdb=" O PRO B 974 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLY B 987 " --> pdb=" O LEU B 975 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N CYS B 977 " --> pdb=" O LEU B 985 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N LEU B 985 " --> pdb=" O CYS B 977 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N VAL B1003 " --> pdb=" O SER B 990 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 799 through 804 removed outlier: 3.612A pdb=" N CYS B 810 " --> pdb=" O LEU B 802 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N TYR B 804 " --> pdb=" O LEU B 808 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N LEU B 808 " --> pdb=" O TYR B 804 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLU B 861 " --> pdb=" O HIS B 881 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N TRP B 837 " --> pdb=" O ILE B 859 " (cutoff:3.500A) 82 hydrogen bonds defined for protein. 210 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: 1.00 Time building geometry restraints manager: 1.20 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: 1312 1.34 - 1.46: 901 1.46 - 1.58: 1831 1.58 - 1.69: 0 1.69 - 1.81: 36 Bond restraints: 4080 Sorted by residual: bond pdb=" C1 NAG A 804 " pdb=" O5 NAG A 804 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.48e+00 bond pdb=" C1 NAG A 802 " pdb=" O5 NAG A 802 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.30e+00 bond pdb=" C1 NAG A 805 " pdb=" O5 NAG A 805 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.16e+00 bond pdb=" C1 NAG A 801 " pdb=" O5 NAG A 801 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.08e+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 2.03e+00 ... (remaining 4075 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.91: 5220 0.91 - 1.82: 248 1.82 - 2.74: 72 2.74 - 3.65: 11 3.65 - 4.56: 3 Bond angle restraints: 5554 Sorted by residual: angle pdb=" N GLY A 585 " pdb=" CA GLY A 585 " pdb=" C GLY A 585 " ideal model delta sigma weight residual 113.18 117.25 -4.07 2.37e+00 1.78e-01 2.96e+00 angle pdb=" C ASN A 575 " pdb=" N ILE A 576 " pdb=" CA ILE A 576 " ideal model delta sigma weight residual 120.62 123.15 -2.53 1.64e+00 3.72e-01 2.38e+00 angle pdb=" C ASN A 682 " pdb=" N GLY A 683 " pdb=" CA GLY A 683 " ideal model delta sigma weight residual 122.80 121.37 1.43 9.70e-01 1.06e+00 2.19e+00 angle pdb=" CA GLN A 759 " pdb=" CB GLN A 759 " pdb=" CG GLN A 759 " ideal model delta sigma weight residual 114.10 117.04 -2.94 2.00e+00 2.50e-01 2.16e+00 angle pdb=" NE ARG B 830 " pdb=" CZ ARG B 830 " pdb=" NH1 ARG B 830 " ideal model delta sigma weight residual 121.50 120.05 1.45 1.00e+00 1.00e+00 2.11e+00 ... (remaining 5549 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.35: 2391 16.35 - 32.69: 113 32.69 - 49.04: 28 49.04 - 65.38: 10 65.38 - 81.73: 2 Dihedral angle restraints: 2544 sinusoidal: 1132 harmonic: 1412 Sorted by residual: dihedral pdb=" CA SER A 539 " pdb=" C SER A 539 " pdb=" N THR A 540 " pdb=" CA THR A 540 " ideal model delta harmonic sigma weight residual 180.00 162.41 17.59 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" N ASN B 848 " pdb=" CA ASN B 848 " pdb=" CB ASN B 848 " pdb=" CG ASN B 848 " ideal model delta sinusoidal sigma weight residual -180.00 -121.53 -58.47 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" N CYS A 662 " pdb=" CA CYS A 662 " pdb=" CB CYS A 662 " pdb=" SG CYS A 662 " ideal model delta sinusoidal sigma weight residual -60.00 -117.30 57.30 3 1.50e+01 4.44e-03 9.43e+00 ... (remaining 2541 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 416 0.035 - 0.069: 132 0.069 - 0.104: 55 0.104 - 0.138: 24 0.138 - 0.173: 1 Chirality restraints: 628 Sorted by residual: chirality pdb=" C1 NAG A 804 " pdb=" ND2 ASN A 630 " pdb=" C2 NAG A 804 " pdb=" O5 NAG A 804 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-01 2.50e+01 7.48e-01 chirality pdb=" CA VAL B 919 " pdb=" N VAL B 919 " pdb=" C VAL B 919 " pdb=" CB VAL B 919 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.95e-01 chirality pdb=" CA ILE B 862 " pdb=" N ILE B 862 " pdb=" C ILE B 862 " pdb=" CB ILE B 862 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.58e-01 ... (remaining 625 not shown) Planarity restraints: 731 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 542 " -0.020 5.00e-02 4.00e+02 2.93e-02 1.38e+00 pdb=" N PRO A 543 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO A 543 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 543 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 526 " 0.017 5.00e-02 4.00e+02 2.51e-02 1.01e+00 pdb=" N PRO A 527 " -0.043 5.00e-02 4.00e+02 pdb=" CA PRO A 527 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 527 " 0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 532 " -0.016 5.00e-02 4.00e+02 2.44e-02 9.54e-01 pdb=" N PRO A 533 " 0.042 5.00e-02 4.00e+02 pdb=" CA PRO A 533 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 533 " -0.014 5.00e-02 4.00e+02 ... (remaining 728 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 1028 2.80 - 3.32: 3674 3.32 - 3.85: 6640 3.85 - 4.37: 7574 4.37 - 4.90: 12826 Nonbonded interactions: 31742 Sorted by model distance: nonbonded pdb=" OD1 ASP A 584 " pdb=" OG1 THR A 609 " model vdw 2.272 3.040 nonbonded pdb=" OD1 ASP B 874 " pdb=" OG1 THR B 951 " model vdw 2.306 3.040 nonbonded pdb=" OD2 ASP A 584 " pdb=" OG1 THR A 608 " model vdw 2.309 3.040 nonbonded pdb=" OD2 ASP B 874 " pdb=" ND2 ASN B 875 " model vdw 2.319 3.120 nonbonded pdb=" NZ LYS A 740 " pdb=" O SER A 754 " model vdw 2.359 3.120 ... (remaining 31737 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 individual isotropic 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: 1.830 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 15.020 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 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 4080 Z= 0.165 Angle : 0.488 4.561 5554 Z= 0.249 Chirality : 0.043 0.173 628 Planarity : 0.003 0.029 722 Dihedral : 10.247 81.731 1616 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 4.47 % Allowed : 6.59 % Favored : 88.94 % 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: -4.30 (0.31), residues: 492 helix: -2.87 (0.53), residues: 36 sheet: -2.55 (0.41), residues: 127 loop : -3.18 (0.29), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP B 796 HIS 0.001 0.000 HIS A 665 PHE 0.004 0.001 PHE A 537 TYR 0.003 0.000 TYR B 828 ARG 0.002 0.000 ARG A 624 *********************** 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 137 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 118 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 535 THR cc_start: 0.6611 (p) cc_final: 0.6247 (p) REVERT: A 648 PHE cc_start: 0.8536 (t80) cc_final: 0.8301 (t80) REVERT: A 700 HIS cc_start: 0.5600 (OUTLIER) cc_final: 0.4602 (p90) REVERT: B 848 ASN cc_start: 0.7394 (OUTLIER) cc_final: 0.6981 (m-40) REVERT: B 968 GLN cc_start: 0.7087 (pm20) cc_final: 0.6774 (pt0) outliers start: 19 outliers final: 5 residues processed: 133 average time/residue: 0.2086 time to fit residues: 32.6521 Evaluate side-chains 71 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 64 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 630 ASN Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 700 HIS Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 772 CYS Chi-restraints excluded: chain B residue 848 ASN Chi-restraints excluded: chain B residue 977 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 41 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 20 optimal weight: 5.9990 chunk 12 optimal weight: 0.0980 chunk 25 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 23 optimal weight: 8.9990 chunk 28 optimal weight: 0.6980 chunk 44 optimal weight: 0.3980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 636 HIS ** A 717 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 769 HIS B 875 ASN B 881 HIS B 921 GLN B 944 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.139299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.102971 restraints weight = 6357.314| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 3.16 r_work: 0.3379 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.2972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4080 Z= 0.213 Angle : 0.590 5.118 5554 Z= 0.306 Chirality : 0.046 0.180 628 Planarity : 0.004 0.031 722 Dihedral : 7.372 58.181 728 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 4.24 % Allowed : 14.59 % Favored : 81.18 % 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: -3.72 (0.34), residues: 492 helix: -2.03 (0.67), residues: 38 sheet: -2.33 (0.39), residues: 140 loop : -2.72 (0.32), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 983 HIS 0.019 0.002 HIS A 636 PHE 0.011 0.001 PHE B1017 TYR 0.011 0.001 TYR B 993 ARG 0.010 0.001 ARG A 764 *********************** 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 82 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 64 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 535 THR cc_start: 0.7441 (p) cc_final: 0.7023 (p) REVERT: A 647 HIS cc_start: 0.6388 (m170) cc_final: 0.6091 (m170) REVERT: A 648 PHE cc_start: 0.8657 (t80) cc_final: 0.8270 (t80) REVERT: A 693 PHE cc_start: 0.8731 (m-80) cc_final: 0.8213 (m-80) REVERT: A 700 HIS cc_start: 0.6022 (OUTLIER) cc_final: 0.4207 (p90) REVERT: A 750 ILE cc_start: 0.8459 (mp) cc_final: 0.8147 (tt) REVERT: A 772 CYS cc_start: 0.6990 (OUTLIER) cc_final: 0.6731 (t) REVERT: B 793 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7773 (pt0) REVERT: B 848 ASN cc_start: 0.7743 (OUTLIER) cc_final: 0.7157 (m-40) outliers start: 18 outliers final: 8 residues processed: 77 average time/residue: 0.1842 time to fit residues: 17.2470 Evaluate side-chains 66 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 54 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 630 ASN Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 700 HIS Chi-restraints excluded: chain A residue 738 PHE Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 772 CYS Chi-restraints excluded: chain B residue 793 GLU Chi-restraints excluded: chain B residue 848 ASN Chi-restraints excluded: chain B residue 896 CYS Chi-restraints excluded: chain B residue 952 GLU Chi-restraints excluded: chain B residue 977 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 11 optimal weight: 2.9990 chunk 6 optimal weight: 0.0070 chunk 0 optimal weight: 2.9990 chunk 44 optimal weight: 0.4980 chunk 38 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 24 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 968 GLN B 978 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.137000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.100703 restraints weight = 6287.859| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 3.12 r_work: 0.3346 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.3505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 4080 Z= 0.190 Angle : 0.555 6.851 5554 Z= 0.285 Chirality : 0.045 0.188 628 Planarity : 0.004 0.035 722 Dihedral : 7.001 58.882 726 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.54 % Favored : 91.46 % Rotamer: Outliers : 5.18 % Allowed : 14.82 % Favored : 80.00 % 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 (0.35), residues: 492 helix: -1.47 (0.74), residues: 38 sheet: -2.17 (0.37), residues: 159 loop : -2.35 (0.34), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 983 HIS 0.005 0.001 HIS A 636 PHE 0.014 0.001 PHE A 681 TYR 0.010 0.001 TYR B 993 ARG 0.003 0.001 ARG A 692 *********************** 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 84 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 62 time to evaluate : 0.466 Fit side-chains revert: symmetry clash REVERT: A 535 THR cc_start: 0.7547 (p) cc_final: 0.7108 (p) REVERT: A 636 HIS cc_start: 0.6328 (p90) cc_final: 0.6098 (p-80) REVERT: A 647 HIS cc_start: 0.6533 (m170) cc_final: 0.6257 (m170) REVERT: A 693 PHE cc_start: 0.8760 (m-80) cc_final: 0.8366 (m-80) REVERT: A 700 HIS cc_start: 0.5653 (OUTLIER) cc_final: 0.4696 (p90) REVERT: A 750 ILE cc_start: 0.8473 (mp) cc_final: 0.8153 (tt) REVERT: A 772 CYS cc_start: 0.7031 (OUTLIER) cc_final: 0.6712 (t) REVERT: B 848 ASN cc_start: 0.7701 (OUTLIER) cc_final: 0.7174 (m-40) REVERT: B 970 ASP cc_start: 0.7575 (t0) cc_final: 0.7361 (t0) outliers start: 22 outliers final: 13 residues processed: 78 average time/residue: 0.2054 time to fit residues: 19.7619 Evaluate side-chains 73 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 57 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 541 ASN Chi-restraints excluded: chain A residue 630 ASN Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 700 HIS Chi-restraints excluded: chain A residue 738 PHE Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 772 CYS Chi-restraints excluded: chain B residue 848 ASN Chi-restraints excluded: chain B residue 884 PHE Chi-restraints excluded: chain B residue 896 CYS Chi-restraints excluded: chain B residue 951 THR Chi-restraints excluded: chain B residue 977 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 28 optimal weight: 3.9990 chunk 4 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 16 optimal weight: 6.9990 chunk 20 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 2 optimal weight: 5.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 548 ASN A 687 ASN B 844 HIS B 875 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.128000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.091524 restraints weight = 6501.127| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 3.15 r_work: 0.3194 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.4594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 4080 Z= 0.424 Angle : 0.671 5.879 5554 Z= 0.347 Chirality : 0.049 0.190 628 Planarity : 0.005 0.071 722 Dihedral : 7.696 59.685 726 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.77 % Favored : 89.23 % Rotamer: Outliers : 4.94 % Allowed : 15.06 % Favored : 80.00 % 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: -3.15 (0.36), residues: 492 helix: -1.40 (0.72), residues: 38 sheet: -2.49 (0.39), residues: 143 loop : -2.03 (0.35), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 983 HIS 0.006 0.001 HIS A 636 PHE 0.019 0.002 PHE A 681 TYR 0.013 0.002 TYR B 868 ARG 0.003 0.001 ARG A 764 *********************** 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 76 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 55 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 639 ILE cc_start: 0.8829 (OUTLIER) cc_final: 0.8619 (pt) REVERT: A 647 HIS cc_start: 0.6611 (m90) cc_final: 0.6372 (m170) REVERT: A 693 PHE cc_start: 0.8778 (m-80) cc_final: 0.8442 (m-80) REVERT: A 705 GLU cc_start: 0.7784 (mm-30) cc_final: 0.7404 (mm-30) REVERT: A 750 ILE cc_start: 0.8558 (mp) cc_final: 0.8239 (tt) REVERT: A 772 CYS cc_start: 0.7197 (OUTLIER) cc_final: 0.6844 (t) REVERT: B 803 TYR cc_start: 0.8361 (m-80) cc_final: 0.8142 (m-80) REVERT: B 848 ASN cc_start: 0.7672 (OUTLIER) cc_final: 0.7276 (m-40) outliers start: 21 outliers final: 10 residues processed: 72 average time/residue: 0.1738 time to fit residues: 15.6559 Evaluate side-chains 60 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 47 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 541 ASN Chi-restraints excluded: chain A residue 630 ASN Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 772 CYS Chi-restraints excluded: chain B residue 800 VAL Chi-restraints excluded: chain B residue 848 ASN Chi-restraints excluded: chain B residue 884 PHE Chi-restraints excluded: chain B residue 896 CYS Chi-restraints excluded: chain B residue 977 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 1 optimal weight: 0.3980 chunk 0 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 chunk 37 optimal weight: 0.0980 chunk 11 optimal weight: 0.0970 chunk 41 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 14 optimal weight: 6.9990 overall best weight: 0.3578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 779 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 = 0.3932 r_free = 0.3932 target = 0.132294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.096279 restraints weight = 6524.707| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 3.13 r_work: 0.3282 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.4591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4080 Z= 0.160 Angle : 0.548 6.384 5554 Z= 0.284 Chirality : 0.046 0.191 628 Planarity : 0.004 0.060 722 Dihedral : 6.758 59.021 724 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 4.00 % Allowed : 15.76 % Favored : 80.24 % 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: -2.86 (0.35), residues: 492 helix: -1.09 (0.79), residues: 38 sheet: -1.74 (0.42), residues: 120 loop : -2.18 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 796 HIS 0.004 0.001 HIS A 636 PHE 0.009 0.001 PHE A 537 TYR 0.005 0.001 TYR B 803 ARG 0.002 0.000 ARG A 692 *********************** 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 71 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 54 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 570 GLU cc_start: 0.7139 (tp30) cc_final: 0.6839 (tp30) REVERT: A 636 HIS cc_start: 0.6564 (p90) cc_final: 0.6326 (p-80) REVERT: A 639 ILE cc_start: 0.8760 (OUTLIER) cc_final: 0.8558 (pt) REVERT: A 647 HIS cc_start: 0.6612 (m90) cc_final: 0.6056 (m170) REVERT: A 693 PHE cc_start: 0.8834 (m-80) cc_final: 0.8580 (m-80) REVERT: A 700 HIS cc_start: 0.6088 (OUTLIER) cc_final: 0.5028 (p90) REVERT: A 705 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7534 (mm-30) REVERT: A 750 ILE cc_start: 0.8444 (mp) cc_final: 0.8128 (tt) REVERT: A 772 CYS cc_start: 0.7141 (OUTLIER) cc_final: 0.6853 (t) REVERT: B 848 ASN cc_start: 0.7660 (OUTLIER) cc_final: 0.7233 (m-40) REVERT: B 954 MET cc_start: 0.8170 (mtt) cc_final: 0.7786 (mtt) outliers start: 17 outliers final: 10 residues processed: 68 average time/residue: 0.1689 time to fit residues: 14.4964 Evaluate side-chains 63 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 49 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 541 ASN Chi-restraints excluded: chain A residue 630 ASN Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 700 HIS Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 772 CYS Chi-restraints excluded: chain B residue 848 ASN Chi-restraints excluded: chain B residue 884 PHE Chi-restraints excluded: chain B residue 896 CYS Chi-restraints excluded: chain B residue 971 SER Chi-restraints excluded: chain B residue 977 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 22 optimal weight: 7.9990 chunk 26 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 768 ASN ** A 779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.127313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.091530 restraints weight = 6484.522| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 3.08 r_work: 0.3201 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.5110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 4080 Z= 0.368 Angle : 0.634 6.171 5554 Z= 0.327 Chirality : 0.048 0.193 628 Planarity : 0.005 0.059 722 Dihedral : 7.439 59.525 724 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.37 % Favored : 89.63 % Rotamer: Outliers : 5.18 % Allowed : 15.29 % Favored : 79.53 % 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: -2.80 (0.36), residues: 492 helix: -1.27 (0.76), residues: 38 sheet: -2.01 (0.43), residues: 120 loop : -1.97 (0.34), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 796 HIS 0.004 0.001 HIS A 636 PHE 0.015 0.002 PHE A 681 TYR 0.009 0.002 TYR B 868 ARG 0.003 0.000 ARG B 908 *********************** 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 71 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 49 time to evaluate : 0.430 Fit side-chains revert: symmetry clash REVERT: A 647 HIS cc_start: 0.6616 (m90) cc_final: 0.6389 (m170) REVERT: A 648 PHE cc_start: 0.8527 (t80) cc_final: 0.8226 (t80) REVERT: A 679 ARG cc_start: 0.8045 (ptt90) cc_final: 0.7594 (ptt90) REVERT: A 693 PHE cc_start: 0.8840 (m-80) cc_final: 0.8601 (m-80) REVERT: A 700 HIS cc_start: 0.6428 (OUTLIER) cc_final: 0.5265 (p90) REVERT: A 705 GLU cc_start: 0.7954 (mm-30) cc_final: 0.7642 (mm-30) REVERT: A 750 ILE cc_start: 0.8508 (mp) cc_final: 0.8178 (tt) REVERT: A 772 CYS cc_start: 0.7226 (OUTLIER) cc_final: 0.6893 (t) REVERT: B 845 MET cc_start: 0.8583 (mtm) cc_final: 0.8283 (mtp) REVERT: B 848 ASN cc_start: 0.7656 (OUTLIER) cc_final: 0.7339 (m-40) REVERT: B 880 MET cc_start: 0.8887 (mtt) cc_final: 0.8600 (mtt) outliers start: 22 outliers final: 13 residues processed: 67 average time/residue: 0.1973 time to fit residues: 16.6053 Evaluate side-chains 61 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 45 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 541 ASN Chi-restraints excluded: chain A residue 630 ASN Chi-restraints excluded: chain A residue 651 LYS Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 700 HIS Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 772 CYS Chi-restraints excluded: chain B residue 800 VAL Chi-restraints excluded: chain B residue 848 ASN Chi-restraints excluded: chain B residue 896 CYS Chi-restraints excluded: chain B residue 971 SER Chi-restraints excluded: chain B residue 977 CYS Chi-restraints excluded: chain B residue 995 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 5 optimal weight: 0.6980 chunk 17 optimal weight: 0.0270 chunk 11 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 32 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 2 optimal weight: 7.9990 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 779 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.129938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.094059 restraints weight = 6471.955| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 3.14 r_work: 0.3241 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.5077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4080 Z= 0.203 Angle : 0.577 6.040 5554 Z= 0.301 Chirality : 0.046 0.189 628 Planarity : 0.004 0.056 722 Dihedral : 6.959 59.274 724 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.35 % Favored : 90.65 % Rotamer: Outliers : 4.47 % Allowed : 16.71 % Favored : 78.82 % 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: -2.71 (0.36), residues: 492 helix: -1.03 (0.80), residues: 38 sheet: -1.93 (0.44), residues: 113 loop : -1.95 (0.34), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 915 HIS 0.004 0.001 HIS A 636 PHE 0.013 0.001 PHE A 681 TYR 0.010 0.001 TYR B 993 ARG 0.003 0.000 ARG A 692 *********************** 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 69 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 50 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 636 HIS cc_start: 0.6692 (p90) cc_final: 0.6456 (p-80) REVERT: A 647 HIS cc_start: 0.6705 (m90) cc_final: 0.6467 (m170) REVERT: A 648 PHE cc_start: 0.8537 (t80) cc_final: 0.8201 (t80) REVERT: A 679 ARG cc_start: 0.8067 (ptt90) cc_final: 0.7601 (ptt90) REVERT: A 693 PHE cc_start: 0.8862 (m-80) cc_final: 0.8601 (m-80) REVERT: A 700 HIS cc_start: 0.6200 (OUTLIER) cc_final: 0.5332 (p90) REVERT: A 705 GLU cc_start: 0.7999 (mm-30) cc_final: 0.7631 (mm-30) REVERT: A 750 ILE cc_start: 0.8548 (mp) cc_final: 0.8152 (tt) REVERT: A 772 CYS cc_start: 0.7199 (OUTLIER) cc_final: 0.6935 (t) REVERT: B 845 MET cc_start: 0.8375 (OUTLIER) cc_final: 0.8084 (mtp) outliers start: 19 outliers final: 12 residues processed: 66 average time/residue: 0.1611 time to fit residues: 13.6771 Evaluate side-chains 63 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 48 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 541 ASN Chi-restraints excluded: chain A residue 630 ASN Chi-restraints excluded: chain A residue 651 LYS Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 700 HIS Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 772 CYS Chi-restraints excluded: chain B residue 800 VAL Chi-restraints excluded: chain B residue 845 MET Chi-restraints excluded: chain B residue 848 ASN Chi-restraints excluded: chain B residue 884 PHE Chi-restraints excluded: chain B residue 896 CYS Chi-restraints excluded: chain B residue 977 CYS Chi-restraints excluded: chain B residue 995 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 37 optimal weight: 0.5980 chunk 4 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 11 optimal weight: 0.2980 chunk 30 optimal weight: 0.7980 chunk 46 optimal weight: 0.7980 chunk 14 optimal weight: 9.9990 chunk 12 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 48 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.129799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.094305 restraints weight = 6339.076| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 3.09 r_work: 0.3241 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.5134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4080 Z= 0.201 Angle : 0.561 5.755 5554 Z= 0.292 Chirality : 0.046 0.189 628 Planarity : 0.004 0.056 722 Dihedral : 6.917 59.325 724 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.55 % Favored : 90.45 % Rotamer: Outliers : 4.47 % Allowed : 16.94 % Favored : 78.59 % 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: -2.66 (0.37), residues: 492 helix: -0.98 (0.79), residues: 38 sheet: -1.91 (0.40), residues: 140 loop : -1.84 (0.36), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 915 HIS 0.003 0.001 HIS A 636 PHE 0.016 0.001 PHE A 681 TYR 0.011 0.001 TYR A 546 ARG 0.002 0.000 ARG A 692 *********************** 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 68 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 49 time to evaluate : 1.033 Fit side-chains revert: symmetry clash REVERT: A 570 GLU cc_start: 0.7204 (tp30) cc_final: 0.6943 (tp30) REVERT: A 647 HIS cc_start: 0.6720 (m90) cc_final: 0.6491 (m170) REVERT: A 648 PHE cc_start: 0.8537 (t80) cc_final: 0.8207 (t80) REVERT: A 679 ARG cc_start: 0.8056 (ptt90) cc_final: 0.7594 (ptt90) REVERT: A 693 PHE cc_start: 0.8851 (m-80) cc_final: 0.8563 (m-80) REVERT: A 700 HIS cc_start: 0.6126 (OUTLIER) cc_final: 0.5333 (p90) REVERT: A 705 GLU cc_start: 0.7989 (mm-30) cc_final: 0.7665 (mm-30) REVERT: A 750 ILE cc_start: 0.8576 (mp) cc_final: 0.8190 (tt) REVERT: A 772 CYS cc_start: 0.7167 (OUTLIER) cc_final: 0.6916 (t) REVERT: B 845 MET cc_start: 0.8335 (OUTLIER) cc_final: 0.8121 (mtp) REVERT: B 884 PHE cc_start: 0.7976 (OUTLIER) cc_final: 0.7733 (m-80) outliers start: 19 outliers final: 12 residues processed: 65 average time/residue: 0.2416 time to fit residues: 20.2022 Evaluate side-chains 65 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 49 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 541 ASN Chi-restraints excluded: chain A residue 651 LYS Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 700 HIS Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 772 CYS Chi-restraints excluded: chain B residue 800 VAL Chi-restraints excluded: chain B residue 809 LEU Chi-restraints excluded: chain B residue 845 MET Chi-restraints excluded: chain B residue 848 ASN Chi-restraints excluded: chain B residue 884 PHE Chi-restraints excluded: chain B residue 896 CYS Chi-restraints excluded: chain B residue 977 CYS Chi-restraints excluded: chain B residue 995 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 46 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 13 optimal weight: 7.9990 chunk 15 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.127160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.091948 restraints weight = 6487.433| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 3.00 r_work: 0.3204 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.5394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 4080 Z= 0.350 Angle : 0.636 6.411 5554 Z= 0.332 Chirality : 0.048 0.212 628 Planarity : 0.005 0.057 722 Dihedral : 7.386 59.626 722 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.76 % Favored : 90.24 % Rotamer: Outliers : 4.00 % Allowed : 18.12 % Favored : 77.88 % 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: -2.64 (0.37), residues: 492 helix: -1.14 (0.78), residues: 38 sheet: -1.57 (0.43), residues: 124 loop : -2.00 (0.35), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 796 HIS 0.004 0.001 HIS A 636 PHE 0.014 0.002 PHE A 606 TYR 0.018 0.002 TYR B 959 ARG 0.003 0.000 ARG A 692 *********************** 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 66 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 49 time to evaluate : 0.519 Fit side-chains revert: symmetry clash REVERT: A 570 GLU cc_start: 0.7424 (tp30) cc_final: 0.7113 (tp30) REVERT: A 647 HIS cc_start: 0.6749 (m90) cc_final: 0.6525 (m170) REVERT: A 648 PHE cc_start: 0.8488 (t80) cc_final: 0.8178 (t80) REVERT: A 693 PHE cc_start: 0.8795 (m-80) cc_final: 0.8515 (m-80) REVERT: A 700 HIS cc_start: 0.6257 (OUTLIER) cc_final: 0.5135 (p90) REVERT: A 705 GLU cc_start: 0.8020 (mm-30) cc_final: 0.7764 (mm-30) REVERT: A 750 ILE cc_start: 0.8574 (mp) cc_final: 0.8215 (tt) REVERT: A 772 CYS cc_start: 0.7548 (OUTLIER) cc_final: 0.7339 (t) outliers start: 17 outliers final: 11 residues processed: 63 average time/residue: 0.2329 time to fit residues: 19.5884 Evaluate side-chains 61 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 48 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 541 ASN Chi-restraints excluded: chain A residue 651 LYS Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 700 HIS Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 772 CYS Chi-restraints excluded: chain B residue 800 VAL Chi-restraints excluded: chain B residue 848 ASN Chi-restraints excluded: chain B residue 850 THR Chi-restraints excluded: chain B residue 896 CYS Chi-restraints excluded: chain B residue 977 CYS Chi-restraints excluded: chain B residue 995 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 0 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.127906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.092574 restraints weight = 6470.135| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 2.99 r_work: 0.3221 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.5514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4080 Z= 0.286 Angle : 0.625 6.058 5554 Z= 0.328 Chirality : 0.047 0.197 628 Planarity : 0.005 0.057 722 Dihedral : 7.337 59.861 722 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.37 % Favored : 89.63 % Rotamer: Outliers : 3.29 % Allowed : 19.06 % Favored : 77.65 % 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: -2.72 (0.37), residues: 492 helix: -1.08 (0.77), residues: 38 sheet: -1.74 (0.42), residues: 122 loop : -2.01 (0.35), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 796 HIS 0.004 0.001 HIS A 567 PHE 0.012 0.001 PHE A 681 TYR 0.011 0.002 TYR B 993 ARG 0.002 0.000 ARG A 692 ********************** 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 60 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 46 time to evaluate : 0.496 Fit side-chains revert: symmetry clash REVERT: A 647 HIS cc_start: 0.6746 (m90) cc_final: 0.6533 (m170) REVERT: A 648 PHE cc_start: 0.8541 (t80) cc_final: 0.8234 (t80) REVERT: A 693 PHE cc_start: 0.8763 (m-80) cc_final: 0.8469 (m-80) REVERT: A 700 HIS cc_start: 0.6327 (OUTLIER) cc_final: 0.5397 (p90) REVERT: A 705 GLU cc_start: 0.7998 (mm-30) cc_final: 0.7708 (mm-30) REVERT: A 750 ILE cc_start: 0.8641 (mp) cc_final: 0.8182 (tt) outliers start: 14 outliers final: 11 residues processed: 59 average time/residue: 0.1828 time to fit residues: 13.9098 Evaluate side-chains 57 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 45 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 541 ASN Chi-restraints excluded: chain A residue 651 LYS Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 700 HIS Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain B residue 800 VAL Chi-restraints excluded: chain B residue 848 ASN Chi-restraints excluded: chain B residue 896 CYS Chi-restraints excluded: chain B residue 977 CYS Chi-restraints excluded: chain B residue 995 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 3 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 15 optimal weight: 6.9990 chunk 23 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 chunk 11 optimal weight: 0.5980 chunk 1 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 5 optimal weight: 0.4980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.129287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.093910 restraints weight = 6431.822| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 3.07 r_work: 0.3240 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.5504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4080 Z= 0.219 Angle : 0.608 6.096 5554 Z= 0.321 Chirality : 0.047 0.215 628 Planarity : 0.005 0.055 722 Dihedral : 6.902 59.969 721 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.76 % Favored : 90.24 % Rotamer: Outliers : 2.59 % Allowed : 19.29 % Favored : 78.12 % 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: -2.65 (0.37), residues: 492 helix: -1.00 (0.79), residues: 38 sheet: -1.87 (0.42), residues: 133 loop : -1.86 (0.35), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 915 HIS 0.004 0.001 HIS A 769 PHE 0.013 0.001 PHE A 681 TYR 0.012 0.001 TYR B 993 ARG 0.002 0.000 ARG A 679 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2699.30 seconds wall clock time: 49 minutes 19.58 seconds (2959.58 seconds total)