Starting phenix.real_space_refine on Tue Feb 11 04:30:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wqw_32714/02_2025/7wqw_32714.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wqw_32714/02_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_32714/02_2025/7wqw_32714.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wqw_32714/02_2025/7wqw_32714.map" model { file = "/net/cci-nas-00/data/ceres_data/7wqw_32714/02_2025/7wqw_32714.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wqw_32714/02_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-5592/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: 2.88, per 1000 atoms: 0.72 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: 0.72 Conformation dependent library (CDL) restraints added in 485.4 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: 0.46 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: 0.99 Time building geometry restraints manager: 0.89 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: 0.000 Normalize map: mean=0, sd=1: 0.840 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: 0.160 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.390 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.300 ------------------------------------------------------------------------------- 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 : 0.424 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: 0.2027 time to fit residues: 32.0705 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 : 0.445 ------------------------------------------------------------------------------- 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: 0.2980 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 636 HIS A 713 ASN A 769 HIS B 875 ASN B 881 HIS B 921 GLN B 944 GLN B 968 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.139123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.102824 restraints weight = 6359.043| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 3.16 r_work: 0.3377 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.3036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4080 Z= 0.208 Angle : 0.590 5.183 5554 Z= 0.306 Chirality : 0.046 0.182 628 Planarity : 0.004 0.031 722 Dihedral : 7.362 58.186 728 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 4.94 % Allowed : 14.35 % Favored : 80.71 % 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: -3.69 (0.34), residues: 492 helix: -2.03 (0.67), residues: 38 sheet: -2.38 (0.38), residues: 148 loop : -2.64 (0.33), residues: 306 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 0.010 0.001 PHE B1017 TYR 0.011 0.001 TYR B 993 ARG 0.007 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 85 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 64 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 535 THR cc_start: 0.7447 (p) cc_final: 0.7028 (p) REVERT: A 573 LEU cc_start: 0.7976 (OUTLIER) cc_final: 0.7644 (mt) REVERT: A 647 HIS cc_start: 0.6423 (m170) cc_final: 0.6137 (m170) REVERT: A 648 PHE cc_start: 0.8656 (t80) cc_final: 0.8275 (t80) REVERT: A 693 PHE cc_start: 0.8737 (m-80) cc_final: 0.8208 (m-80) REVERT: A 700 HIS cc_start: 0.5989 (OUTLIER) cc_final: 0.4172 (p90) REVERT: A 750 ILE cc_start: 0.8450 (mp) cc_final: 0.8130 (tt) REVERT: A 772 CYS cc_start: 0.7029 (OUTLIER) cc_final: 0.6757 (t) REVERT: B 793 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7771 (pt0) REVERT: B 848 ASN cc_start: 0.7737 (OUTLIER) cc_final: 0.7145 (m-40) outliers start: 21 outliers final: 10 residues processed: 79 average time/residue: 0.1799 time to fit residues: 17.3664 Evaluate side-chains 70 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 55 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 540 THR Chi-restraints excluded: chain A residue 573 LEU 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 884 PHE 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: 0.0470 chunk 6 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 24 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 chunk 27 optimal weight: 0.3980 chunk 1 optimal weight: 1.9990 overall best weight: 0.6280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 978 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.136286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.099963 restraints weight = 6278.984| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 3.10 r_work: 0.3328 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.3643 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= 0.201 Angle : 0.556 6.276 5554 Z= 0.286 Chirality : 0.046 0.189 628 Planarity : 0.004 0.035 722 Dihedral : 7.013 58.730 726 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.54 % Favored : 91.46 % Rotamer: Outliers : 4.71 % Allowed : 15.76 % 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: -3.27 (0.35), residues: 492 helix: -1.41 (0.75), residues: 38 sheet: -2.15 (0.37), residues: 159 loop : -2.34 (0.34), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 983 HIS 0.004 0.001 HIS A 636 PHE 0.014 0.001 PHE A 681 TYR 0.011 0.001 TYR B 993 ARG 0.003 0.001 ARG A 764 *********************** 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 80 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 60 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 535 THR cc_start: 0.7610 (p) cc_final: 0.7161 (p) REVERT: A 573 LEU cc_start: 0.8077 (OUTLIER) cc_final: 0.7635 (mt) REVERT: A 624 ARG cc_start: 0.7422 (mmm-85) cc_final: 0.7111 (mtp180) REVERT: A 647 HIS cc_start: 0.6540 (m170) cc_final: 0.6261 (m170) REVERT: A 679 ARG cc_start: 0.7675 (ptt90) cc_final: 0.7321 (ptt90) REVERT: A 693 PHE cc_start: 0.8770 (m-80) cc_final: 0.8390 (m-80) REVERT: A 700 HIS cc_start: 0.5760 (OUTLIER) cc_final: 0.4975 (p90) REVERT: A 750 ILE cc_start: 0.8485 (mp) cc_final: 0.8146 (tt) REVERT: A 772 CYS cc_start: 0.7000 (OUTLIER) cc_final: 0.6646 (t) REVERT: B 848 ASN cc_start: 0.7702 (OUTLIER) cc_final: 0.7237 (m-40) outliers start: 20 outliers final: 11 residues processed: 76 average time/residue: 0.1805 time to fit residues: 16.9679 Evaluate side-chains 68 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 53 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 541 ASN Chi-restraints excluded: chain A residue 573 LEU 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 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 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: 1.9990 chunk 42 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 16 optimal weight: 6.9990 chunk 20 optimal weight: 6.9990 chunk 13 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 2 optimal weight: 5.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 687 ASN B 844 HIS B 875 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.130187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.093785 restraints weight = 6406.711| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 3.15 r_work: 0.3231 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.4376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 4080 Z= 0.315 Angle : 0.594 5.529 5554 Z= 0.308 Chirality : 0.047 0.189 628 Planarity : 0.005 0.072 722 Dihedral : 7.246 59.795 726 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.35 % Favored : 90.65 % Rotamer: Outliers : 4.71 % Allowed : 14.82 % Favored : 80.47 % 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: -3.06 (0.36), residues: 492 helix: -1.27 (0.76), residues: 38 sheet: -2.40 (0.39), residues: 143 loop : -2.00 (0.35), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 983 HIS 0.004 0.001 HIS A 665 PHE 0.011 0.001 PHE A 537 TYR 0.010 0.001 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 74 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 54 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 639 ILE cc_start: 0.8725 (OUTLIER) cc_final: 0.8461 (pt) REVERT: A 647 HIS cc_start: 0.6648 (m90) cc_final: 0.6401 (m170) REVERT: A 693 PHE cc_start: 0.8806 (m-80) cc_final: 0.8500 (m-80) REVERT: A 750 ILE cc_start: 0.8540 (mp) cc_final: 0.8197 (tt) REVERT: A 772 CYS cc_start: 0.7168 (OUTLIER) cc_final: 0.6833 (t) REVERT: B 803 TYR cc_start: 0.8359 (m-80) cc_final: 0.8154 (m-80) REVERT: B 848 ASN cc_start: 0.7705 (OUTLIER) cc_final: 0.7277 (m-40) REVERT: B 954 MET cc_start: 0.8203 (mtm) cc_final: 0.7996 (mtt) outliers start: 20 outliers final: 10 residues processed: 70 average time/residue: 0.1630 time to fit residues: 14.6455 Evaluate side-chains 57 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 44 time to evaluate : 0.441 ------------------------------------------------------------------------------- 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 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 743 THR 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: 0.9980 chunk 0 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 25 optimal weight: 0.0670 chunk 14 optimal weight: 4.9990 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 548 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.131248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.094978 restraints weight = 6553.923| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 3.20 r_work: 0.3252 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.4579 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= 0.210 Angle : 0.556 6.106 5554 Z= 0.290 Chirality : 0.046 0.230 628 Planarity : 0.004 0.061 722 Dihedral : 6.784 59.189 722 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer: Outliers : 4.47 % Allowed : 16.24 % Favored : 79.29 % 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: -2.84 (0.36), residues: 492 helix: -1.02 (0.81), residues: 38 sheet: -1.87 (0.39), residues: 139 loop : -2.08 (0.34), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 983 HIS 0.004 0.001 HIS A 636 PHE 0.021 0.001 PHE A 681 TYR 0.006 0.001 TYR B 920 ARG 0.003 0.000 ARG A 679 *********************** 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: 19 poor density : 52 time to evaluate : 0.379 Fit side-chains revert: symmetry clash REVERT: A 647 HIS cc_start: 0.6655 (m90) cc_final: 0.6084 (m170) REVERT: A 681 PHE cc_start: 0.7540 (t80) cc_final: 0.7079 (t80) REVERT: A 692 ARG cc_start: 0.7741 (tpp80) cc_final: 0.7348 (tpt-90) REVERT: A 700 HIS cc_start: 0.6080 (OUTLIER) cc_final: 0.4276 (p90) REVERT: A 750 ILE cc_start: 0.8465 (mp) cc_final: 0.8146 (tt) REVERT: A 772 CYS cc_start: 0.7124 (OUTLIER) cc_final: 0.6853 (t) REVERT: B 845 MET cc_start: 0.8530 (mtm) cc_final: 0.8205 (mtp) REVERT: B 848 ASN cc_start: 0.7676 (OUTLIER) cc_final: 0.7346 (m-40) outliers start: 19 outliers final: 9 residues processed: 69 average time/residue: 0.1576 time to fit residues: 13.7609 Evaluate side-chains 62 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 50 time to evaluate : 0.501 ------------------------------------------------------------------------------- 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 656 VAL 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 22 optimal weight: 6.9990 chunk 26 optimal weight: 0.0470 chunk 0 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 29 optimal weight: 0.0980 chunk 30 optimal weight: 0.6980 chunk 33 optimal weight: 0.5980 chunk 39 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 48 optimal weight: 0.7980 chunk 32 optimal weight: 0.3980 overall best weight: 0.3678 ------------------------------------------------------------------------------- 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 = 0.3945 r_free = 0.3945 target = 0.133329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.097034 restraints weight = 6356.210| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 3.15 r_work: 0.3286 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.4626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 4080 Z= 0.163 Angle : 0.542 5.726 5554 Z= 0.282 Chirality : 0.046 0.238 628 Planarity : 0.004 0.056 722 Dihedral : 6.704 58.926 722 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 4.00 % Allowed : 17.18 % 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: -2.70 (0.36), residues: 492 helix: -0.98 (0.81), residues: 38 sheet: -1.83 (0.40), residues: 137 loop : -1.95 (0.35), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 796 HIS 0.010 0.001 HIS A 636 PHE 0.017 0.001 PHE A 681 TYR 0.012 0.001 TYR A 546 ARG 0.003 0.000 ARG A 624 *********************** 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 70 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 53 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 570 GLU cc_start: 0.7174 (tp30) cc_final: 0.6923 (tp30) REVERT: A 647 HIS cc_start: 0.6709 (m90) cc_final: 0.6455 (m170) REVERT: A 681 PHE cc_start: 0.7495 (t80) cc_final: 0.7293 (t80) REVERT: A 693 PHE cc_start: 0.8762 (OUTLIER) cc_final: 0.8500 (m-10) REVERT: A 700 HIS cc_start: 0.6102 (OUTLIER) cc_final: 0.5240 (p90) REVERT: A 750 ILE cc_start: 0.8510 (mp) cc_final: 0.8205 (tt) REVERT: A 772 CYS cc_start: 0.7096 (OUTLIER) cc_final: 0.6845 (t) REVERT: B 845 MET cc_start: 0.8511 (mtm) cc_final: 0.8217 (mtp) REVERT: B 848 ASN cc_start: 0.7675 (OUTLIER) cc_final: 0.7316 (m-40) outliers start: 17 outliers final: 11 residues processed: 68 average time/residue: 0.1555 time to fit residues: 13.5824 Evaluate side-chains 64 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 49 time to evaluate : 0.417 ------------------------------------------------------------------------------- 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 656 VAL Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 693 PHE 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 5 optimal weight: 0.4980 chunk 17 optimal weight: 3.9990 chunk 11 optimal weight: 0.2980 chunk 40 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3929 r_free = 0.3929 target = 0.132107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.096024 restraints weight = 6416.579| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 3.12 r_work: 0.3268 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.4800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4080 Z= 0.202 Angle : 0.554 5.783 5554 Z= 0.288 Chirality : 0.046 0.232 628 Planarity : 0.004 0.056 722 Dihedral : 6.764 58.764 722 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 4.00 % Allowed : 17.65 % Favored : 78.35 % 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 (0.36), residues: 492 helix: -0.94 (0.82), residues: 38 sheet: -1.81 (0.40), residues: 137 loop : -1.89 (0.35), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 796 HIS 0.004 0.001 HIS A 636 PHE 0.015 0.001 PHE A 681 TYR 0.013 0.002 TYR B 803 ARG 0.002 0.000 ARG A 679 *********************** 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 66 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 49 time to evaluate : 0.503 Fit side-chains revert: symmetry clash REVERT: A 647 HIS cc_start: 0.6700 (m90) cc_final: 0.6443 (m170) REVERT: A 692 ARG cc_start: 0.7681 (tpp80) cc_final: 0.7470 (tpp80) REVERT: A 693 PHE cc_start: 0.8759 (m-10) cc_final: 0.8467 (m-10) REVERT: A 695 ILE cc_start: 0.7998 (OUTLIER) cc_final: 0.7790 (mm) REVERT: A 700 HIS cc_start: 0.6166 (OUTLIER) cc_final: 0.4514 (p90) REVERT: A 750 ILE cc_start: 0.8518 (mp) cc_final: 0.8211 (tt) REVERT: A 772 CYS cc_start: 0.7248 (OUTLIER) cc_final: 0.6964 (t) REVERT: B 803 TYR cc_start: 0.8364 (m-80) cc_final: 0.8162 (m-80) REVERT: B 845 MET cc_start: 0.8478 (mtm) cc_final: 0.8074 (mtp) REVERT: B 848 ASN cc_start: 0.7683 (OUTLIER) cc_final: 0.7327 (m-40) outliers start: 17 outliers final: 9 residues processed: 64 average time/residue: 0.1686 time to fit residues: 13.7896 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 : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 541 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 37 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 26 optimal weight: 0.3980 chunk 11 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 14 optimal weight: 9.9990 chunk 12 optimal weight: 7.9990 chunk 17 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.3914 r_free = 0.3914 target = 0.131008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.095195 restraints weight = 6317.749| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 3.06 r_work: 0.3253 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.4958 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= 0.226 Angle : 0.573 5.487 5554 Z= 0.300 Chirality : 0.046 0.225 628 Planarity : 0.004 0.054 722 Dihedral : 6.838 58.739 722 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.94 % Favored : 91.06 % Rotamer: Outliers : 3.29 % Allowed : 18.35 % Favored : 78.35 % 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: -2.60 (0.37), residues: 492 helix: -0.95 (0.81), residues: 38 sheet: -1.94 (0.42), residues: 125 loop : -1.81 (0.34), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 796 HIS 0.004 0.001 HIS A 636 PHE 0.012 0.001 PHE B1017 TYR 0.014 0.002 TYR B 803 ARG 0.003 0.000 ARG A 624 *********************** 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 62 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 48 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 647 HIS cc_start: 0.6665 (m90) cc_final: 0.6418 (m170) REVERT: A 692 ARG cc_start: 0.7717 (tpp80) cc_final: 0.7493 (tpp80) REVERT: A 693 PHE cc_start: 0.8754 (m-10) cc_final: 0.8411 (m-10) REVERT: A 695 ILE cc_start: 0.7986 (OUTLIER) cc_final: 0.7780 (mm) REVERT: A 700 HIS cc_start: 0.6274 (OUTLIER) cc_final: 0.4613 (p90) REVERT: A 750 ILE cc_start: 0.8472 (mp) cc_final: 0.8146 (tt) REVERT: B 803 TYR cc_start: 0.8403 (m-80) cc_final: 0.8144 (m-80) REVERT: B 845 MET cc_start: 0.8320 (mtm) cc_final: 0.8077 (mtp) outliers start: 14 outliers final: 10 residues processed: 60 average time/residue: 0.1661 time to fit residues: 12.7588 Evaluate side-chains 58 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 46 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 541 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 739 VAL Chi-restraints excluded: chain A residue 743 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 46 optimal weight: 0.6980 chunk 22 optimal weight: 3.9990 chunk 13 optimal weight: 9.9990 chunk 15 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 47 optimal weight: 0.4980 chunk 5 optimal weight: 0.0060 chunk 9 optimal weight: 0.5980 overall best weight: 0.5196 ------------------------------------------------------------------------------- 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 = 0.3927 r_free = 0.3927 target = 0.131840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.095910 restraints weight = 6362.196| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 3.14 r_work: 0.3272 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.4998 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= 0.187 Angle : 0.563 5.805 5554 Z= 0.296 Chirality : 0.046 0.236 628 Planarity : 0.004 0.053 722 Dihedral : 6.495 58.694 721 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 2.82 % Allowed : 18.59 % 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: -2.53 (0.37), residues: 492 helix: -0.90 (0.81), residues: 38 sheet: -1.74 (0.42), residues: 137 loop : -1.80 (0.35), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 915 HIS 0.004 0.001 HIS A 636 PHE 0.012 0.001 PHE B1017 TYR 0.013 0.001 TYR A 546 ARG 0.002 0.000 ARG A 679 *********************** 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 61 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 49 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 647 HIS cc_start: 0.6640 (m90) cc_final: 0.6392 (m170) REVERT: A 693 PHE cc_start: 0.8744 (m-10) cc_final: 0.8438 (m-10) REVERT: A 695 ILE cc_start: 0.7972 (OUTLIER) cc_final: 0.7760 (mm) REVERT: A 700 HIS cc_start: 0.6223 (OUTLIER) cc_final: 0.4508 (p90) REVERT: A 750 ILE cc_start: 0.8508 (mp) cc_final: 0.8139 (tt) REVERT: B 803 TYR cc_start: 0.8425 (m-80) cc_final: 0.8192 (m-80) REVERT: B 845 MET cc_start: 0.8343 (mtm) cc_final: 0.8081 (mtp) outliers start: 12 outliers final: 10 residues processed: 59 average time/residue: 0.1900 time to fit residues: 14.3051 Evaluate side-chains 59 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 47 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 541 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 739 VAL Chi-restraints excluded: chain A residue 743 THR 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 0 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 11 optimal weight: 0.0270 chunk 35 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 37 optimal weight: 0.4980 chunk 2 optimal weight: 0.0170 chunk 8 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 overall best weight: 0.4076 ------------------------------------------------------------------------------- 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 = 0.3936 r_free = 0.3936 target = 0.132559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.096797 restraints weight = 6334.886| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 3.12 r_work: 0.3284 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.5012 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= 0.172 Angle : 0.569 5.464 5554 Z= 0.299 Chirality : 0.046 0.238 628 Planarity : 0.004 0.053 722 Dihedral : 6.453 58.983 721 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.94 % Favored : 91.06 % Rotamer: Outliers : 2.35 % Allowed : 19.76 % 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: -2.47 (0.37), residues: 492 helix: -0.92 (0.81), residues: 38 sheet: -1.71 (0.42), residues: 137 loop : -1.75 (0.35), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 915 HIS 0.005 0.001 HIS A 769 PHE 0.014 0.001 PHE B1017 TYR 0.012 0.001 TYR B 803 ARG 0.005 0.000 ARG A 679 ********************** 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 58 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 48 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 647 HIS cc_start: 0.6671 (m90) cc_final: 0.6422 (m170) REVERT: A 693 PHE cc_start: 0.8725 (m-10) cc_final: 0.8400 (m-10) REVERT: A 700 HIS cc_start: 0.6028 (OUTLIER) cc_final: 0.5269 (p90) REVERT: A 750 ILE cc_start: 0.8521 (mp) cc_final: 0.8146 (tt) REVERT: B 803 TYR cc_start: 0.8466 (m-80) cc_final: 0.8220 (m-80) REVERT: B 845 MET cc_start: 0.8357 (mtm) cc_final: 0.8104 (mtp) outliers start: 10 outliers final: 9 residues processed: 57 average time/residue: 0.1693 time to fit residues: 12.3221 Evaluate side-chains 57 residues out of total 425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 541 ASN 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 743 THR 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: 0.0010 chunk 9 optimal weight: 0.8980 chunk 18 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 chunk 15 optimal weight: 7.9990 chunk 23 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 overall best weight: 0.6986 ------------------------------------------------------------------------------- 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 = 0.3915 r_free = 0.3915 target = 0.130882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.094849 restraints weight = 6340.833| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 3.17 r_work: 0.3255 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.5118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4080 Z= 0.220 Angle : 0.586 5.868 5554 Z= 0.308 Chirality : 0.046 0.226 628 Planarity : 0.005 0.053 722 Dihedral : 6.608 59.176 721 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % 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: -2.46 (0.37), residues: 492 helix: -0.91 (0.82), residues: 38 sheet: -1.66 (0.46), residues: 113 loop : -1.80 (0.34), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 699 HIS 0.006 0.001 HIS A 769 PHE 0.014 0.001 PHE B1017 TYR 0.013 0.002 TYR B 803 ARG 0.005 0.001 ARG A 679 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2341.39 seconds wall clock time: 42 minutes 20.82 seconds (2540.82 seconds total)