Starting phenix.real_space_refine on Thu Jun 12 07:22:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t5p_25706/06_2025/7t5p_25706.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t5p_25706/06_2025/7t5p_25706.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7t5p_25706/06_2025/7t5p_25706.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t5p_25706/06_2025/7t5p_25706.map" model { file = "/net/cci-nas-00/data/ceres_data/7t5p_25706/06_2025/7t5p_25706.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t5p_25706/06_2025/7t5p_25706.cif" } resolution = 3.4 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= 0.004 sd= 0.048 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: 5 Type Number sf(0) Gaussians S 37 5.16 5 C 4325 2.51 5 N 1157 2.21 5 O 1212 1.98 5 H 6866 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 13597 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 6750 Classifications: {'peptide': 403} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 381} Chain breaks: 2 Chain: "B" Number of atoms: 6847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 6847 Classifications: {'peptide': 419} Link IDs: {'PTRANS': 18, 'TRANS': 400} Chain breaks: 2 Time building chain proxies: 6.82, per 1000 atoms: 0.50 Number of scatterers: 13597 At special positions: 0 Unit cell: (92.988, 74.844, 105.462, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 37 16.00 O 1212 8.00 N 1157 7.00 C 4325 6.00 H 6866 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 3.27 Conformation dependent library (CDL) restraints added in 954.9 milliseconds 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1594 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 0 sheets defined 73.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 430 through 435 removed outlier: 3.542A pdb=" N ARG A 433 " --> pdb=" O CYS A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 450 removed outlier: 3.759A pdb=" N LEU A 450 " --> pdb=" O PHE A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 461 Processing helix chain 'A' and resid 468 through 481 removed outlier: 3.527A pdb=" N GLU A 481 " --> pdb=" O ASN A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 495 Processing helix chain 'A' and resid 502 through 513 Processing helix chain 'A' and resid 520 through 538 removed outlier: 3.684A pdb=" N LEU A 524 " --> pdb=" O THR A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 545 removed outlier: 3.653A pdb=" N VAL A 545 " --> pdb=" O ALA A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 558 Processing helix chain 'A' and resid 565 through 588 Processing helix chain 'A' and resid 595 through 602 removed outlier: 3.836A pdb=" N SER A 602 " --> pdb=" O ASN A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 623 Processing helix chain 'A' and resid 655 through 678 removed outlier: 3.547A pdb=" N THR A 659 " --> pdb=" O LEU A 655 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU A 676 " --> pdb=" O SER A 672 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ASP A 678 " --> pdb=" O ALA A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 698 removed outlier: 3.827A pdb=" N SER A 684 " --> pdb=" O THR A 680 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLY A 694 " --> pdb=" O GLU A 690 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N PHE A 695 " --> pdb=" O MET A 691 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASP A 698 " --> pdb=" O GLY A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 711 removed outlier: 3.851A pdb=" N ARG A 705 " --> pdb=" O GLU A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 729 Processing helix chain 'A' and resid 739 through 750 Processing helix chain 'A' and resid 761 through 787 removed outlier: 4.102A pdb=" N THR A 765 " --> pdb=" O SER A 761 " (cutoff:3.500A) Processing helix chain 'A' and resid 791 through 802 removed outlier: 3.997A pdb=" N ASP A 797 " --> pdb=" O ILE A 793 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 834 Processing helix chain 'A' and resid 838 through 855 removed outlier: 3.501A pdb=" N ALA A 855 " --> pdb=" O LEU A 851 " (cutoff:3.500A) Processing helix chain 'B' and resid 770 through 779 Processing helix chain 'B' and resid 781 through 790 removed outlier: 3.749A pdb=" N ILE B 785 " --> pdb=" O LYS B 781 " (cutoff:3.500A) Processing helix chain 'B' and resid 791 through 797 Processing helix chain 'B' and resid 803 through 817 Processing helix chain 'B' and resid 819 through 841 Processing helix chain 'B' and resid 851 through 863 Processing helix chain 'B' and resid 865 through 870 Processing helix chain 'B' and resid 880 through 892 Processing helix chain 'B' and resid 910 through 928 Processing helix chain 'B' and resid 929 through 932 removed outlier: 4.005A pdb=" N TYR B 932 " --> pdb=" O PRO B 929 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 929 through 932' Processing helix chain 'B' and resid 933 through 949 removed outlier: 3.674A pdb=" N LEU B 949 " --> pdb=" O PHE B 945 " (cutoff:3.500A) Processing helix chain 'B' and resid 958 through 972 Processing helix chain 'B' and resid 974 through 989 Proline residue: B 980 - end of helix Processing helix chain 'B' and resid 992 through 1003 removed outlier: 3.534A pdb=" N LEU B 996 " --> pdb=" O HIS B 992 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL B1003 " --> pdb=" O LEU B 999 " (cutoff:3.500A) Processing helix chain 'B' and resid 1007 through 1026 Processing helix chain 'B' and resid 1039 through 1051 Processing helix chain 'B' and resid 1052 through 1068 Processing helix chain 'B' and resid 1074 through 1101 removed outlier: 3.632A pdb=" N CYS B1101 " --> pdb=" O GLY B1097 " (cutoff:3.500A) Processing helix chain 'B' and resid 1108 through 1124 removed outlier: 3.729A pdb=" N HIS B1112 " --> pdb=" O GLY B1108 " (cutoff:3.500A) Processing helix chain 'B' and resid 1134 through 1157 removed outlier: 3.878A pdb=" N THR B1138 " --> pdb=" O LEU B1134 " (cutoff:3.500A) 417 hydrogen bonds defined for protein. 1233 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: 4.30 Time building geometry restraints manager: 4.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 6851 1.03 - 1.23: 18 1.23 - 1.42: 2793 1.42 - 1.61: 4019 1.61 - 1.81: 59 Bond restraints: 13740 Sorted by residual: bond pdb=" CB PRO A 466 " pdb=" CG PRO A 466 " ideal model delta sigma weight residual 1.492 1.561 -0.069 5.00e-02 4.00e+02 1.92e+00 bond pdb=" CB PRO B 871 " pdb=" CG PRO B 871 " ideal model delta sigma weight residual 1.492 1.549 -0.057 5.00e-02 4.00e+02 1.31e+00 bond pdb=" C ILE A 467 " pdb=" N PRO A 468 " ideal model delta sigma weight residual 1.332 1.346 -0.014 1.33e-02 5.65e+03 1.13e+00 bond pdb=" CB PHE A 581 " pdb=" CG PHE A 581 " ideal model delta sigma weight residual 1.502 1.523 -0.021 2.30e-02 1.89e+03 8.57e-01 bond pdb=" CB CYS B 924 " pdb=" SG CYS B 924 " ideal model delta sigma weight residual 1.808 1.778 0.030 3.30e-02 9.18e+02 8.17e-01 ... (remaining 13735 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 24488 1.65 - 3.29: 404 3.29 - 4.94: 38 4.94 - 6.59: 3 6.59 - 8.23: 1 Bond angle restraints: 24934 Sorted by residual: angle pdb=" C GLU A 690 " pdb=" N MET A 691 " pdb=" CA MET A 691 " ideal model delta sigma weight residual 120.31 116.43 3.88 1.52e+00 4.33e-01 6.53e+00 angle pdb=" CA PRO A 466 " pdb=" C PRO A 466 " pdb=" N ILE A 467 " ideal model delta sigma weight residual 114.74 117.23 -2.49 1.03e+00 9.43e-01 5.82e+00 angle pdb=" CA LEU B 949 " pdb=" CB LEU B 949 " pdb=" CG LEU B 949 " ideal model delta sigma weight residual 116.30 124.53 -8.23 3.50e+00 8.16e-02 5.53e+00 angle pdb=" N MET A 691 " pdb=" CA MET A 691 " pdb=" CB MET A 691 " ideal model delta sigma weight residual 110.28 113.71 -3.43 1.55e+00 4.16e-01 4.90e+00 angle pdb=" CA MET A 691 " pdb=" CB MET A 691 " pdb=" CG MET A 691 " ideal model delta sigma weight residual 114.10 118.31 -4.21 2.00e+00 2.50e-01 4.44e+00 ... (remaining 24929 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 5505 17.68 - 35.37: 676 35.37 - 53.05: 176 53.05 - 70.74: 38 70.74 - 88.42: 14 Dihedral angle restraints: 6409 sinusoidal: 3555 harmonic: 2854 Sorted by residual: dihedral pdb=" CA ASP B 763 " pdb=" CB ASP B 763 " pdb=" CG ASP B 763 " pdb=" OD1 ASP B 763 " ideal model delta sinusoidal sigma weight residual -30.00 -88.41 58.41 1 2.00e+01 2.50e-03 1.14e+01 dihedral pdb=" CG ARG A 718 " pdb=" CD ARG A 718 " pdb=" NE ARG A 718 " pdb=" CZ ARG A 718 " ideal model delta sinusoidal sigma weight residual 180.00 136.68 43.32 2 1.50e+01 4.44e-03 1.00e+01 dihedral pdb=" CB GLU B 742 " pdb=" CG GLU B 742 " pdb=" CD GLU B 742 " pdb=" OE1 GLU B 742 " ideal model delta sinusoidal sigma weight residual 0.00 -85.97 85.97 1 3.00e+01 1.11e-03 9.92e+00 ... (remaining 6406 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 795 0.035 - 0.070: 206 0.070 - 0.105: 51 0.105 - 0.140: 18 0.140 - 0.175: 1 Chirality restraints: 1071 Sorted by residual: chirality pdb=" CB THR A 476 " pdb=" CA THR A 476 " pdb=" OG1 THR A 476 " pdb=" CG2 THR A 476 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.18 2.00e-01 2.50e+01 7.69e-01 chirality pdb=" CB VAL A 696 " pdb=" CA VAL A 696 " pdb=" CG1 VAL A 696 " pdb=" CG2 VAL A 696 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.88e-01 chirality pdb=" CA ILE A 699 " pdb=" N ILE A 699 " pdb=" C ILE A 699 " pdb=" CB ILE A 699 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.65e-01 ... (remaining 1068 not shown) Planarity restraints: 1952 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 467 " -0.037 5.00e-02 4.00e+02 5.68e-02 5.16e+00 pdb=" N PRO A 468 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO A 468 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 468 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 501 " -0.030 5.00e-02 4.00e+02 4.51e-02 3.26e+00 pdb=" N PRO A 502 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 502 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 502 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS B 992 " 0.028 5.00e-02 4.00e+02 4.30e-02 2.96e+00 pdb=" N PRO B 993 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO B 993 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 993 " 0.024 5.00e-02 4.00e+02 ... (remaining 1949 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 1246 2.20 - 2.80: 28766 2.80 - 3.40: 39043 3.40 - 4.00: 46977 4.00 - 4.60: 73505 Nonbonded interactions: 189537 Sorted by model distance: nonbonded pdb=" O LEU A 736 " pdb="HE21 GLN A 742 " model vdw 1.602 2.450 nonbonded pdb=" O ILE A 725 " pdb=" HG SER A 729 " model vdw 1.612 2.450 nonbonded pdb=" O GLN B 876 " pdb="HH22 ARG B 935 " model vdw 1.621 2.450 nonbonded pdb=" OE1 GLU B 873 " pdb=" H GLU B 873 " model vdw 1.624 2.450 nonbonded pdb=" O LYS B 970 " pdb=" HZ2 LYS B 970 " model vdw 1.666 2.450 ... (remaining 189532 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: 0.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.240 Extract box with map and model: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 29.610 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 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: 0.010 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 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 0.069 6874 Z= 0.129 Angle : 0.590 8.231 9307 Z= 0.311 Chirality : 0.036 0.175 1071 Planarity : 0.004 0.057 1175 Dihedral : 17.853 88.424 2606 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 0.39 % Allowed : 32.69 % Favored : 66.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 1.09 (0.29), residues: 810 helix: 1.54 (0.21), residues: 551 sheet: None (None), residues: 0 loop : -1.05 (0.39), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B1006 HIS 0.004 0.001 HIS A 782 PHE 0.026 0.001 PHE A 825 TYR 0.010 0.001 TYR A 554 ARG 0.008 0.000 ARG B1011 Details of bonding type rmsd hydrogen bonds : bond 0.13448 ( 417) hydrogen bonds : angle 6.17496 ( 1233) covalent geometry : bond 0.00303 ( 6874) covalent geometry : angle 0.59038 ( 9307) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 245 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 771 GLU cc_start: 0.7107 (mm-30) cc_final: 0.6788 (mm-30) outliers start: 3 outliers final: 3 residues processed: 246 average time/residue: 0.4332 time to fit residues: 139.3667 Evaluate side-chains 241 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 238 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 576 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 68 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 781 GLN B 790 GLN B 817 HIS B 952 GLN B1005 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.097613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.080359 restraints weight = 51086.243| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 4.67 r_work: 0.3360 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.0826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6874 Z= 0.174 Angle : 0.587 5.899 9307 Z= 0.318 Chirality : 0.036 0.155 1071 Planarity : 0.005 0.059 1175 Dihedral : 4.625 44.265 885 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 2.71 % Allowed : 30.49 % Favored : 66.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 1.15 (0.29), residues: 810 helix: 1.55 (0.21), residues: 564 sheet: None (None), residues: 0 loop : -1.08 (0.40), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 549 HIS 0.004 0.001 HIS B 739 PHE 0.015 0.001 PHE B 840 TYR 0.006 0.001 TYR B1047 ARG 0.005 0.001 ARG A 433 Details of bonding type rmsd hydrogen bonds : bond 0.04732 ( 417) hydrogen bonds : angle 5.18468 ( 1233) covalent geometry : bond 0.00364 ( 6874) covalent geometry : angle 0.58693 ( 9307) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 250 time to evaluate : 1.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1125 LYS cc_start: 0.7590 (tmmt) cc_final: 0.7324 (tmmt) outliers start: 21 outliers final: 16 residues processed: 256 average time/residue: 0.4420 time to fit residues: 148.0191 Evaluate side-chains 257 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 241 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 719 CYS Chi-restraints excluded: chain A residue 765 THR Chi-restraints excluded: chain A residue 786 GLU Chi-restraints excluded: chain B residue 767 ILE Chi-restraints excluded: chain B residue 794 THR Chi-restraints excluded: chain B residue 810 LEU Chi-restraints excluded: chain B residue 829 THR Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 1005 ASN Chi-restraints excluded: chain B residue 1008 SER Chi-restraints excluded: chain B residue 1078 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 70 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 16 optimal weight: 0.1980 chunk 23 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 74 optimal weight: 6.9990 chunk 19 optimal weight: 0.8980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 781 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.098145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.081048 restraints weight = 51221.847| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 4.65 r_work: 0.3375 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.1096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6874 Z= 0.140 Angle : 0.569 6.293 9307 Z= 0.303 Chirality : 0.036 0.157 1071 Planarity : 0.005 0.063 1175 Dihedral : 4.301 24.097 883 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 2.71 % Allowed : 30.75 % Favored : 66.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 1.35 (0.30), residues: 810 helix: 1.62 (0.21), residues: 573 sheet: None (None), residues: 0 loop : -0.87 (0.41), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 763 HIS 0.004 0.001 HIS B 817 PHE 0.012 0.001 PHE B 840 TYR 0.005 0.001 TYR B1047 ARG 0.005 0.000 ARG B1011 Details of bonding type rmsd hydrogen bonds : bond 0.04308 ( 417) hydrogen bonds : angle 4.93930 ( 1233) covalent geometry : bond 0.00306 ( 6874) covalent geometry : angle 0.56938 ( 9307) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 246 time to evaluate : 1.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 676 GLU cc_start: 0.7949 (mm-30) cc_final: 0.7679 (mm-30) REVERT: A 734 THR cc_start: 0.9092 (OUTLIER) cc_final: 0.8877 (m) REVERT: A 771 GLU cc_start: 0.7926 (mm-30) cc_final: 0.7507 (mm-30) REVERT: B 902 TYR cc_start: 0.7002 (m-80) cc_final: 0.6718 (m-80) REVERT: B 1125 LYS cc_start: 0.7535 (tmmt) cc_final: 0.7271 (tmmt) outliers start: 21 outliers final: 15 residues processed: 255 average time/residue: 0.4441 time to fit residues: 147.6899 Evaluate side-chains 256 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 240 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 719 CYS Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 765 THR Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain B residue 794 THR Chi-restraints excluded: chain B residue 810 LEU Chi-restraints excluded: chain B residue 829 THR Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 1008 SER Chi-restraints excluded: chain B residue 1078 HIS Chi-restraints excluded: chain B residue 1095 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 0.3980 chunk 29 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 7 optimal weight: 0.0000 chunk 75 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 781 GLN B1068 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.097843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.080578 restraints weight = 51208.024| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 4.65 r_work: 0.3366 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 6874 Z= 0.151 Angle : 0.560 5.916 9307 Z= 0.299 Chirality : 0.036 0.156 1071 Planarity : 0.005 0.063 1175 Dihedral : 4.218 23.915 882 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 3.36 % Allowed : 29.84 % Favored : 66.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 1.36 (0.30), residues: 810 helix: 1.63 (0.21), residues: 573 sheet: None (None), residues: 0 loop : -0.89 (0.41), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B1006 HIS 0.004 0.001 HIS B 817 PHE 0.009 0.001 PHE B 840 TYR 0.008 0.001 TYR A 554 ARG 0.006 0.000 ARG B1011 Details of bonding type rmsd hydrogen bonds : bond 0.04111 ( 417) hydrogen bonds : angle 4.85871 ( 1233) covalent geometry : bond 0.00326 ( 6874) covalent geometry : angle 0.56018 ( 9307) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 247 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 676 GLU cc_start: 0.7971 (mm-30) cc_final: 0.7612 (mm-30) REVERT: A 771 GLU cc_start: 0.8021 (mm-30) cc_final: 0.7509 (mm-30) REVERT: B 902 TYR cc_start: 0.7046 (m-80) cc_final: 0.6693 (m-80) REVERT: B 998 TRP cc_start: 0.8785 (t-100) cc_final: 0.8311 (t-100) REVERT: B 1125 LYS cc_start: 0.7580 (tmmt) cc_final: 0.7327 (tmmt) outliers start: 26 outliers final: 21 residues processed: 257 average time/residue: 0.4427 time to fit residues: 147.8155 Evaluate side-chains 264 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 243 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 719 CYS Chi-restraints excluded: chain A residue 765 THR Chi-restraints excluded: chain A residue 767 ASP Chi-restraints excluded: chain A residue 786 GLU Chi-restraints excluded: chain B residue 767 ILE Chi-restraints excluded: chain B residue 794 THR Chi-restraints excluded: chain B residue 810 LEU Chi-restraints excluded: chain B residue 829 THR Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 915 LEU Chi-restraints excluded: chain B residue 960 ASP Chi-restraints excluded: chain B residue 1008 SER Chi-restraints excluded: chain B residue 1057 LEU Chi-restraints excluded: chain B residue 1078 HIS Chi-restraints excluded: chain B residue 1095 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 15 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 75 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 781 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.094775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.077791 restraints weight = 51999.902| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 4.56 r_work: 0.3304 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 6874 Z= 0.279 Angle : 0.630 5.892 9307 Z= 0.357 Chirality : 0.038 0.157 1071 Planarity : 0.005 0.072 1175 Dihedral : 4.609 22.757 882 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 4.26 % Allowed : 30.62 % Favored : 65.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.50 (0.28), residues: 810 helix: 1.00 (0.21), residues: 572 sheet: None (None), residues: 0 loop : -1.21 (0.40), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 549 HIS 0.006 0.001 HIS B 739 PHE 0.013 0.002 PHE B 840 TYR 0.010 0.001 TYR A 554 ARG 0.006 0.001 ARG B1011 Details of bonding type rmsd hydrogen bonds : bond 0.04694 ( 417) hydrogen bonds : angle 5.34233 ( 1233) covalent geometry : bond 0.00565 ( 6874) covalent geometry : angle 0.63024 ( 9307) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 246 time to evaluate : 1.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 676 GLU cc_start: 0.8079 (mm-30) cc_final: 0.7701 (mm-30) REVERT: A 771 GLU cc_start: 0.8081 (mm-30) cc_final: 0.7485 (mm-30) REVERT: B 1125 LYS cc_start: 0.7780 (tmmt) cc_final: 0.7491 (tmmt) outliers start: 33 outliers final: 30 residues processed: 260 average time/residue: 0.4660 time to fit residues: 160.9163 Evaluate side-chains 276 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 246 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 CYS Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 579 ASP Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 765 THR Chi-restraints excluded: chain A residue 767 ASP Chi-restraints excluded: chain A residue 786 GLU Chi-restraints excluded: chain B residue 767 ILE Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain B residue 794 THR Chi-restraints excluded: chain B residue 810 LEU Chi-restraints excluded: chain B residue 814 MET Chi-restraints excluded: chain B residue 817 HIS Chi-restraints excluded: chain B residue 829 THR Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 960 ASP Chi-restraints excluded: chain B residue 976 ASN Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1005 ASN Chi-restraints excluded: chain B residue 1008 SER Chi-restraints excluded: chain B residue 1057 LEU Chi-restraints excluded: chain B residue 1078 HIS Chi-restraints excluded: chain B residue 1080 GLU Chi-restraints excluded: chain B residue 1095 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 30 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 7 optimal weight: 0.0020 chunk 34 optimal weight: 0.1980 chunk 8 optimal weight: 0.4980 chunk 14 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 overall best weight: 0.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 561 GLN A 781 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.098972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.081605 restraints weight = 51260.728| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 4.67 r_work: 0.3379 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6874 Z= 0.117 Angle : 0.568 5.963 9307 Z= 0.299 Chirality : 0.036 0.157 1071 Planarity : 0.005 0.064 1175 Dihedral : 4.258 25.201 882 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.23 % Allowed : 30.88 % Favored : 65.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 1.49 (0.30), residues: 810 helix: 1.74 (0.21), residues: 573 sheet: None (None), residues: 0 loop : -0.86 (0.41), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 763 HIS 0.004 0.001 HIS B 817 PHE 0.021 0.001 PHE B 754 TYR 0.008 0.001 TYR A 554 ARG 0.004 0.000 ARG B1011 Details of bonding type rmsd hydrogen bonds : bond 0.03901 ( 417) hydrogen bonds : angle 4.65253 ( 1233) covalent geometry : bond 0.00264 ( 6874) covalent geometry : angle 0.56833 ( 9307) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 253 time to evaluate : 1.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 676 GLU cc_start: 0.7994 (mm-30) cc_final: 0.7654 (mm-30) REVERT: A 771 GLU cc_start: 0.8109 (mm-30) cc_final: 0.7589 (mm-30) REVERT: B 971 ASN cc_start: 0.8008 (m110) cc_final: 0.7730 (m110) REVERT: B 998 TRP cc_start: 0.8767 (t-100) cc_final: 0.8378 (t-100) REVERT: B 1125 LYS cc_start: 0.7578 (tmmt) cc_final: 0.7288 (tmmt) outliers start: 25 outliers final: 21 residues processed: 263 average time/residue: 0.4439 time to fit residues: 151.6457 Evaluate side-chains 267 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 246 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 CYS Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 719 CYS Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 767 ASP Chi-restraints excluded: chain A residue 786 GLU Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain B residue 810 LEU Chi-restraints excluded: chain B residue 829 THR Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 915 LEU Chi-restraints excluded: chain B residue 938 MET Chi-restraints excluded: chain B residue 1078 HIS Chi-restraints excluded: chain B residue 1095 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 78 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 76 optimal weight: 0.0670 chunk 43 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 overall best weight: 1.1722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 781 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.097835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.080410 restraints weight = 51143.281| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 4.73 r_work: 0.3358 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6874 Z= 0.154 Angle : 0.584 8.255 9307 Z= 0.311 Chirality : 0.036 0.155 1071 Planarity : 0.004 0.064 1175 Dihedral : 4.259 24.250 882 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 3.36 % Allowed : 31.27 % Favored : 65.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 1.44 (0.30), residues: 810 helix: 1.79 (0.21), residues: 564 sheet: None (None), residues: 0 loop : -1.02 (0.40), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 549 HIS 0.004 0.001 HIS A 782 PHE 0.016 0.001 PHE A 825 TYR 0.012 0.001 TYR B 799 ARG 0.004 0.000 ARG B1011 Details of bonding type rmsd hydrogen bonds : bond 0.04031 ( 417) hydrogen bonds : angle 4.77055 ( 1233) covalent geometry : bond 0.00333 ( 6874) covalent geometry : angle 0.58386 ( 9307) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 251 time to evaluate : 1.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 561 GLN cc_start: 0.3073 (OUTLIER) cc_final: 0.2851 (pt0) REVERT: A 676 GLU cc_start: 0.8107 (mm-30) cc_final: 0.7763 (mm-30) REVERT: A 771 GLU cc_start: 0.8170 (mm-30) cc_final: 0.7621 (mm-30) REVERT: B 971 ASN cc_start: 0.8064 (m110) cc_final: 0.7778 (m110) REVERT: B 998 TRP cc_start: 0.8823 (t-100) cc_final: 0.8401 (t-100) REVERT: B 1125 LYS cc_start: 0.7726 (tmmt) cc_final: 0.7473 (tmmt) outliers start: 26 outliers final: 24 residues processed: 260 average time/residue: 0.4375 time to fit residues: 147.9438 Evaluate side-chains 270 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 245 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 CYS Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 561 GLN Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 719 CYS Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 767 ASP Chi-restraints excluded: chain A residue 786 GLU Chi-restraints excluded: chain B residue 767 ILE Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain B residue 794 THR Chi-restraints excluded: chain B residue 810 LEU Chi-restraints excluded: chain B residue 829 THR Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 915 LEU Chi-restraints excluded: chain B residue 938 MET Chi-restraints excluded: chain B residue 1005 ASN Chi-restraints excluded: chain B residue 1078 HIS Chi-restraints excluded: chain B residue 1095 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 6 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 29 optimal weight: 0.7980 chunk 60 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 21 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 781 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.095322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.078284 restraints weight = 52025.056| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 4.62 r_work: 0.3312 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 6874 Z= 0.257 Angle : 0.636 6.213 9307 Z= 0.356 Chirality : 0.038 0.157 1071 Planarity : 0.005 0.073 1175 Dihedral : 4.608 23.052 882 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 3.75 % Allowed : 31.91 % Favored : 64.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.57 (0.29), residues: 810 helix: 1.07 (0.21), residues: 570 sheet: None (None), residues: 0 loop : -1.24 (0.40), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 549 HIS 0.006 0.001 HIS A 782 PHE 0.015 0.002 PHE A 825 TYR 0.013 0.002 TYR A 554 ARG 0.005 0.001 ARG A 679 Details of bonding type rmsd hydrogen bonds : bond 0.04643 ( 417) hydrogen bonds : angle 5.18807 ( 1233) covalent geometry : bond 0.00528 ( 6874) covalent geometry : angle 0.63574 ( 9307) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 249 time to evaluate : 1.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 676 GLU cc_start: 0.8176 (mm-30) cc_final: 0.7843 (mm-30) REVERT: A 771 GLU cc_start: 0.8118 (mm-30) cc_final: 0.7540 (mm-30) REVERT: B 1125 LYS cc_start: 0.7867 (tmmt) cc_final: 0.7632 (tmmt) outliers start: 29 outliers final: 27 residues processed: 259 average time/residue: 0.4420 time to fit residues: 150.0182 Evaluate side-chains 269 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 242 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 CYS Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 561 GLN Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 767 ASP Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain A residue 786 GLU Chi-restraints excluded: chain B residue 767 ILE Chi-restraints excluded: chain B residue 794 THR Chi-restraints excluded: chain B residue 810 LEU Chi-restraints excluded: chain B residue 814 MET Chi-restraints excluded: chain B residue 817 HIS Chi-restraints excluded: chain B residue 829 THR Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 915 LEU Chi-restraints excluded: chain B residue 960 ASP Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1005 ASN Chi-restraints excluded: chain B residue 1078 HIS Chi-restraints excluded: chain B residue 1095 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 55 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 34 optimal weight: 0.2980 chunk 36 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 35 optimal weight: 0.1980 chunk 3 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 781 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.097836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.080468 restraints weight = 50614.879| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 4.71 r_work: 0.3356 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6874 Z= 0.137 Angle : 0.602 6.688 9307 Z= 0.318 Chirality : 0.037 0.156 1071 Planarity : 0.005 0.069 1175 Dihedral : 4.360 24.907 882 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 3.23 % Allowed : 32.56 % Favored : 64.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 1.26 (0.29), residues: 810 helix: 1.69 (0.21), residues: 558 sheet: None (None), residues: 0 loop : -1.14 (0.39), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 763 HIS 0.004 0.001 HIS A 782 PHE 0.013 0.001 PHE A 825 TYR 0.011 0.001 TYR B 797 ARG 0.003 0.000 ARG B1011 Details of bonding type rmsd hydrogen bonds : bond 0.04060 ( 417) hydrogen bonds : angle 4.75541 ( 1233) covalent geometry : bond 0.00307 ( 6874) covalent geometry : angle 0.60234 ( 9307) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 242 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 676 GLU cc_start: 0.8124 (mm-30) cc_final: 0.7781 (mm-30) REVERT: A 771 GLU cc_start: 0.8174 (mm-30) cc_final: 0.7613 (mm-30) REVERT: B 938 MET cc_start: 0.7905 (OUTLIER) cc_final: 0.7473 (tpp) REVERT: B 971 ASN cc_start: 0.8098 (m110) cc_final: 0.7801 (m110) REVERT: B 998 TRP cc_start: 0.8841 (t-100) cc_final: 0.8458 (t-100) REVERT: B 1125 LYS cc_start: 0.7792 (tmmt) cc_final: 0.7568 (tmmt) outliers start: 25 outliers final: 20 residues processed: 250 average time/residue: 0.4458 time to fit residues: 144.8051 Evaluate side-chains 257 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 236 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 CYS Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 719 CYS Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 767 ASP Chi-restraints excluded: chain A residue 786 GLU Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain B residue 767 ILE Chi-restraints excluded: chain B residue 810 LEU Chi-restraints excluded: chain B residue 829 THR Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 915 LEU Chi-restraints excluded: chain B residue 938 MET Chi-restraints excluded: chain B residue 960 ASP Chi-restraints excluded: chain B residue 1057 LEU Chi-restraints excluded: chain B residue 1078 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 43 optimal weight: 0.0870 chunk 21 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 49 optimal weight: 0.0980 chunk 2 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 561 GLN A 781 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.099007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.081527 restraints weight = 51009.031| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 4.77 r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6874 Z= 0.122 Angle : 0.599 7.017 9307 Z= 0.313 Chirality : 0.036 0.154 1071 Planarity : 0.004 0.064 1175 Dihedral : 4.192 24.940 882 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.97 % Allowed : 32.95 % Favored : 64.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 1.56 (0.30), residues: 810 helix: 1.93 (0.21), residues: 558 sheet: None (None), residues: 0 loop : -1.06 (0.39), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B1006 HIS 0.005 0.001 HIS B 817 PHE 0.013 0.001 PHE A 825 TYR 0.010 0.001 TYR B1047 ARG 0.003 0.000 ARG B1011 Details of bonding type rmsd hydrogen bonds : bond 0.03783 ( 417) hydrogen bonds : angle 4.60637 ( 1233) covalent geometry : bond 0.00282 ( 6874) covalent geometry : angle 0.59911 ( 9307) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 246 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 676 GLU cc_start: 0.7886 (mm-30) cc_final: 0.7524 (mm-30) REVERT: A 771 GLU cc_start: 0.7726 (mm-30) cc_final: 0.7135 (mm-30) REVERT: B 971 ASN cc_start: 0.7784 (m110) cc_final: 0.7506 (m110) REVERT: B 998 TRP cc_start: 0.8760 (t-100) cc_final: 0.8373 (t-100) REVERT: B 1125 LYS cc_start: 0.7712 (tmmt) cc_final: 0.7496 (tmmt) outliers start: 23 outliers final: 20 residues processed: 253 average time/residue: 0.4483 time to fit residues: 147.7569 Evaluate side-chains 260 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 240 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 CYS Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 509 ILE Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 719 CYS Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 767 ASP Chi-restraints excluded: chain A residue 786 GLU Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain B residue 767 ILE Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain B residue 794 THR Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 915 LEU Chi-restraints excluded: chain B residue 960 ASP Chi-restraints excluded: chain B residue 1057 LEU Chi-restraints excluded: chain B residue 1078 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 35 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 6 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 781 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.097267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.080347 restraints weight = 51274.089| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 4.55 r_work: 0.3357 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 6874 Z= 0.185 Angle : 0.619 6.987 9307 Z= 0.333 Chirality : 0.037 0.154 1071 Planarity : 0.005 0.067 1175 Dihedral : 4.306 24.078 882 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 2.20 % Allowed : 33.59 % Favored : 64.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 1.18 (0.29), residues: 810 helix: 1.64 (0.21), residues: 564 sheet: None (None), residues: 0 loop : -1.27 (0.40), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 549 HIS 0.008 0.001 HIS B 817 PHE 0.011 0.001 PHE A 825 TYR 0.014 0.001 TYR A 780 ARG 0.003 0.000 ARG A 679 Details of bonding type rmsd hydrogen bonds : bond 0.04057 ( 417) hydrogen bonds : angle 4.84791 ( 1233) covalent geometry : bond 0.00393 ( 6874) covalent geometry : angle 0.61872 ( 9307) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7174.18 seconds wall clock time: 122 minutes 27.60 seconds (7347.60 seconds total)