Starting phenix.real_space_refine on Wed Mar 4 12:37:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t5p_25706/03_2026/7t5p_25706.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t5p_25706/03_2026/7t5p_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 { model { file = "/net/cci-nas-00/data/ceres_data/7t5p_25706/03_2026/7t5p_25706.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t5p_25706/03_2026/7t5p_25706.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7t5p_25706/03_2026/7t5p_25706.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t5p_25706/03_2026/7t5p_25706.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 2.89, per 1000 atoms: 0.21 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: 1.33 Conformation dependent library (CDL) restraints added in 460.2 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: 0.30 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: 2.99 Time building geometry restraints manager: 1.83 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: 0.510 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: 0.070 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.040 Find NCS groups from input model: 0.050 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:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.460 ------------------------------------------------------------------------------- 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 : 15.16 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.008 0.000 ARG B1011 TYR 0.010 0.001 TYR A 554 PHE 0.026 0.001 PHE A 825 TRP 0.008 0.001 TRP B1006 HIS 0.004 0.001 HIS A 782 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 6874) covalent geometry : angle 0.59038 ( 9307) hydrogen bonds : bond 0.13448 ( 417) hydrogen bonds : angle 6.17496 ( 1233) *********************** 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 : 0.333 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: 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: 0.2058 time to fit residues: 66.2729 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 : 0.374 ------------------------------------------------------------------------------- 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 49 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 6.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 952 GLN B1005 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.097201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.079924 restraints weight = 51476.902| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 4.64 r_work: 0.3353 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.0855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 6874 Z= 0.190 Angle : 0.594 5.916 9307 Z= 0.324 Chirality : 0.037 0.157 1071 Planarity : 0.005 0.060 1175 Dihedral : 4.683 44.340 885 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.71 % Allowed : 30.23 % Favored : 67.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.29), residues: 810 helix: 1.35 (0.21), residues: 573 sheet: None (None), residues: 0 loop : -1.03 (0.41), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 433 TYR 0.007 0.001 TYR A 554 PHE 0.016 0.001 PHE B 840 TRP 0.009 0.001 TRP A 549 HIS 0.005 0.001 HIS B 739 Details of bonding type rmsd covalent geometry : bond 0.00394 ( 6874) covalent geometry : angle 0.59389 ( 9307) hydrogen bonds : bond 0.04766 ( 417) hydrogen bonds : angle 5.23807 ( 1233) *********************** 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 272 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 251 time to evaluate : 0.372 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: symmetry clash outliers start: 21 outliers final: 17 residues processed: 255 average time/residue: 0.2150 time to fit residues: 70.8577 Evaluate side-chains 258 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 241 time to evaluate : 0.369 ------------------------------------------------------------------------------- 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 1057 LEU 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 9 optimal weight: 3.9990 chunk 18 optimal weight: 0.5980 chunk 24 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 62 optimal weight: 0.4980 chunk 15 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- 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 = 0.3796 r_free = 0.3796 target = 0.097631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.080572 restraints weight = 51377.786| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 4.63 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: 0.7727 moved from start: 0.1099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6874 Z= 0.151 Angle : 0.573 6.311 9307 Z= 0.307 Chirality : 0.036 0.157 1071 Planarity : 0.005 0.064 1175 Dihedral : 4.350 24.292 883 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 2.58 % Allowed : 31.27 % Favored : 66.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.29), residues: 810 helix: 1.52 (0.21), residues: 573 sheet: None (None), residues: 0 loop : -0.92 (0.41), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1011 TYR 0.006 0.001 TYR A 554 PHE 0.011 0.001 PHE B 840 TRP 0.008 0.001 TRP A 763 HIS 0.004 0.001 HIS A 508 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 6874) covalent geometry : angle 0.57289 ( 9307) hydrogen bonds : bond 0.04398 ( 417) hydrogen bonds : angle 5.01272 ( 1233) *********************** 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 266 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 246 time to evaluate : 0.516 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: A 771 GLU cc_start: 0.7925 (mm-30) cc_final: 0.7413 (mm-30) REVERT: B 902 TYR cc_start: 0.7014 (m-80) cc_final: 0.6720 (m-80) outliers start: 20 outliers final: 15 residues processed: 254 average time/residue: 0.2160 time to fit residues: 70.6921 Evaluate side-chains 251 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 236 time to evaluate : 0.346 ------------------------------------------------------------------------------- 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 697 LEU Chi-restraints excluded: chain A residue 719 CYS Chi-restraints excluded: chain A residue 765 THR 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 976 ASN 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 9 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 12 optimal weight: 0.4980 chunk 61 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 561 GLN A 781 GLN B1005 ASN B1068 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.098354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.081010 restraints weight = 51192.122| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 4.65 r_work: 0.3376 rms_B_bonded: 4.91 restraints_weight: 0.5000 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.1316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6874 Z= 0.136 Angle : 0.559 5.897 9307 Z= 0.296 Chirality : 0.036 0.156 1071 Planarity : 0.004 0.062 1175 Dihedral : 4.193 24.106 882 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 3.23 % Allowed : 30.23 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.30), residues: 810 helix: 1.70 (0.21), residues: 573 sheet: None (None), residues: 0 loop : -0.86 (0.41), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1011 TYR 0.007 0.001 TYR A 554 PHE 0.009 0.001 PHE A 825 TRP 0.009 0.001 TRP B1006 HIS 0.003 0.001 HIS A 508 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 6874) covalent geometry : angle 0.55936 ( 9307) hydrogen bonds : bond 0.04052 ( 417) hydrogen bonds : angle 4.81739 ( 1233) *********************** 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 271 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 246 time to evaluate : 0.325 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 771 GLU cc_start: 0.8031 (mm-30) cc_final: 0.7521 (mm-30) REVERT: B 902 TYR cc_start: 0.7028 (m-80) cc_final: 0.6669 (m-80) REVERT: B 998 TRP cc_start: 0.8763 (t-100) cc_final: 0.8358 (t-100) outliers start: 25 outliers final: 21 residues processed: 255 average time/residue: 0.2132 time to fit residues: 70.0831 Evaluate side-chains 263 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 242 time to evaluate : 0.259 ------------------------------------------------------------------------------- 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 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 A residue 804 LYS 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 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 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 60 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 17 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 overall best weight: 1.6784 ------------------------------------------------------------------------------- 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 ** B 817 HIS ** 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 = 0.3786 r_free = 0.3786 target = 0.097057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.079867 restraints weight = 51990.906| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 4.65 r_work: 0.3348 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 6874 Z= 0.192 Angle : 0.581 5.891 9307 Z= 0.318 Chirality : 0.037 0.155 1071 Planarity : 0.005 0.065 1175 Dihedral : 4.289 23.661 882 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 3.75 % Allowed : 30.23 % Favored : 66.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.29), residues: 810 helix: 1.48 (0.21), residues: 573 sheet: None (None), residues: 0 loop : -1.01 (0.40), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1011 TYR 0.009 0.001 TYR A 780 PHE 0.009 0.001 PHE B 840 TRP 0.009 0.001 TRP A 549 HIS 0.004 0.001 HIS A 782 Details of bonding type rmsd covalent geometry : bond 0.00404 ( 6874) covalent geometry : angle 0.58116 ( 9307) hydrogen bonds : bond 0.04204 ( 417) hydrogen bonds : angle 4.99537 ( 1233) *********************** 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 273 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 244 time to evaluate : 0.337 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: A 697 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8384 (mt) REVERT: A 771 GLU cc_start: 0.8091 (mm-30) cc_final: 0.7549 (mm-30) REVERT: B 998 TRP cc_start: 0.8816 (t-100) cc_final: 0.8412 (t-100) outliers start: 29 outliers final: 25 residues processed: 254 average time/residue: 0.2010 time to fit residues: 66.4948 Evaluate side-chains 266 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 240 time to evaluate : 0.377 ------------------------------------------------------------------------------- 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 530 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 697 LEU Chi-restraints excluded: chain A residue 719 CYS 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 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 976 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 1095 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 19 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 47 optimal weight: 0.3980 chunk 65 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 73 optimal weight: 0.1980 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 561 GLN A 781 GLN ** B 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.097858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.080329 restraints weight = 51402.284| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 4.72 r_work: 0.3358 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.1578 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= 0.142 Angle : 0.569 6.022 9307 Z= 0.302 Chirality : 0.036 0.156 1071 Planarity : 0.005 0.065 1175 Dihedral : 4.222 24.269 882 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 3.75 % Allowed : 30.88 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.30), residues: 810 helix: 1.63 (0.21), residues: 574 sheet: None (None), residues: 0 loop : -0.93 (0.41), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1011 TYR 0.007 0.001 TYR A 780 PHE 0.011 0.001 PHE A 825 TRP 0.010 0.001 TRP B1006 HIS 0.004 0.001 HIS A 782 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 6874) covalent geometry : angle 0.56878 ( 9307) hydrogen bonds : bond 0.03967 ( 417) hydrogen bonds : angle 4.80424 ( 1233) *********************** 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 273 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 244 time to evaluate : 0.362 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: A 771 GLU cc_start: 0.8175 (mm-30) cc_final: 0.7617 (mm-30) REVERT: B 981 GLU cc_start: 0.8864 (mp0) cc_final: 0.8209 (mp0) REVERT: B 998 TRP cc_start: 0.8778 (t-100) cc_final: 0.8426 (t-100) outliers start: 29 outliers final: 27 residues processed: 253 average time/residue: 0.2064 time to fit residues: 67.6032 Evaluate side-chains 268 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 241 time to evaluate : 0.470 ------------------------------------------------------------------------------- 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 576 THR Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 719 CYS 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 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 44 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 73 optimal weight: 0.0050 chunk 72 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 overall best weight: 1.3598 ------------------------------------------------------------------------------- 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 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 561 GLN A 781 GLN ** B 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.097434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.080228 restraints weight = 51155.979| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 4.63 r_work: 0.3353 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 6874 Z= 0.165 Angle : 0.575 6.044 9307 Z= 0.311 Chirality : 0.036 0.157 1071 Planarity : 0.005 0.067 1175 Dihedral : 4.273 23.887 882 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 3.36 % Allowed : 31.14 % Favored : 65.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.29), residues: 810 helix: 1.53 (0.21), residues: 574 sheet: None (None), residues: 0 loop : -0.97 (0.41), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B1011 TYR 0.014 0.001 TYR A 780 PHE 0.011 0.001 PHE A 825 TRP 0.009 0.001 TRP A 549 HIS 0.004 0.001 HIS A 782 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 6874) covalent geometry : angle 0.57545 ( 9307) hydrogen bonds : bond 0.04023 ( 417) hydrogen bonds : angle 4.88069 ( 1233) *********************** 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 271 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 245 time to evaluate : 0.354 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: A 697 LEU cc_start: 0.8581 (mt) cc_final: 0.8362 (mt) REVERT: A 771 GLU cc_start: 0.8169 (mm-30) cc_final: 0.7617 (mm-30) REVERT: B 971 ASN cc_start: 0.8064 (m110) cc_final: 0.7790 (m110) REVERT: B 981 GLU cc_start: 0.8849 (mp0) cc_final: 0.8338 (mp0) REVERT: B 998 TRP cc_start: 0.8813 (t-100) cc_final: 0.8467 (t-100) outliers start: 26 outliers final: 25 residues processed: 252 average time/residue: 0.1941 time to fit residues: 63.1956 Evaluate side-chains 265 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 240 time to evaluate : 0.345 ------------------------------------------------------------------------------- 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 576 THR Chi-restraints excluded: chain A residue 719 CYS Chi-restraints excluded: chain A residue 761 SER 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 19 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 chunk 74 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 68 optimal weight: 3.9990 chunk 57 optimal weight: 0.0020 chunk 9 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 overall best weight: 2.1594 ------------------------------------------------------------------------------- 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 ** B 817 HIS ** 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 = 0.3755 r_free = 0.3755 target = 0.095534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.078612 restraints weight = 51727.942| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 4.59 r_work: 0.3317 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 6874 Z= 0.241 Angle : 0.618 6.264 9307 Z= 0.346 Chirality : 0.038 0.162 1071 Planarity : 0.005 0.072 1175 Dihedral : 4.513 22.916 882 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 4.13 % Allowed : 31.91 % Favored : 63.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.29), residues: 810 helix: 1.10 (0.21), residues: 575 sheet: None (None), residues: 0 loop : -1.19 (0.41), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B1011 TYR 0.016 0.001 TYR A 780 PHE 0.021 0.002 PHE B 754 TRP 0.011 0.002 TRP A 549 HIS 0.005 0.001 HIS A 782 Details of bonding type rmsd covalent geometry : bond 0.00493 ( 6874) covalent geometry : angle 0.61841 ( 9307) hydrogen bonds : bond 0.04451 ( 417) hydrogen bonds : angle 5.17824 ( 1233) *********************** 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 272 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 240 time to evaluate : 0.402 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: A 771 GLU cc_start: 0.8126 (mm-30) cc_final: 0.7578 (mm-30) REVERT: B 971 ASN cc_start: 0.8168 (m110) cc_final: 0.7863 (m110) REVERT: B 981 GLU cc_start: 0.8944 (mp0) cc_final: 0.8400 (mp0) REVERT: B 1125 LYS cc_start: 0.7848 (tmmt) cc_final: 0.7610 (tmmt) outliers start: 32 outliers final: 29 residues processed: 252 average time/residue: 0.1976 time to fit residues: 64.8253 Evaluate side-chains 264 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 235 time to evaluate : 0.442 ------------------------------------------------------------------------------- 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 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 576 THR 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 21 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 51 optimal weight: 0.0870 chunk 27 optimal weight: 0.7980 chunk 55 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 overall best weight: 0.9762 ------------------------------------------------------------------------------- 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 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 561 GLN A 781 GLN ** B 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.097745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.080441 restraints weight = 51019.077| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 4.71 r_work: 0.3358 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.1872 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= 0.143 Angle : 0.596 6.664 9307 Z= 0.319 Chirality : 0.037 0.171 1071 Planarity : 0.005 0.069 1175 Dihedral : 4.375 24.232 882 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 2.97 % Allowed : 33.07 % Favored : 63.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.29), residues: 810 helix: 1.55 (0.21), residues: 565 sheet: None (None), residues: 0 loop : -1.15 (0.40), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 812 TYR 0.014 0.001 TYR A 780 PHE 0.011 0.001 PHE A 825 TRP 0.010 0.001 TRP B1006 HIS 0.004 0.001 HIS A 782 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 6874) covalent geometry : angle 0.59621 ( 9307) hydrogen bonds : bond 0.04115 ( 417) hydrogen bonds : angle 4.81681 ( 1233) *********************** 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 261 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 238 time to evaluate : 0.263 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: A 771 GLU cc_start: 0.8166 (mm-30) cc_final: 0.7608 (mm-30) REVERT: B 971 ASN cc_start: 0.8118 (m110) cc_final: 0.7832 (m110) REVERT: B 981 GLU cc_start: 0.8815 (mp0) cc_final: 0.8162 (mp0) REVERT: B 998 TRP cc_start: 0.8813 (t-100) cc_final: 0.8398 (t-100) REVERT: B 1125 LYS cc_start: 0.7796 (tmmt) cc_final: 0.7500 (tmmt) outliers start: 23 outliers final: 22 residues processed: 246 average time/residue: 0.2091 time to fit residues: 66.7807 Evaluate side-chains 258 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 236 time to evaluate : 0.355 ------------------------------------------------------------------------------- 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 530 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 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 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 1078 HIS Chi-restraints excluded: chain B residue 1095 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 6 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 38 optimal weight: 0.0970 chunk 46 optimal weight: 2.9990 chunk 77 optimal weight: 7.9990 chunk 55 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 overall best weight: 0.9780 ------------------------------------------------------------------------------- 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 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 561 GLN A 781 GLN ** B 817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.097843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.080707 restraints weight = 50563.037| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 4.69 r_work: 0.3363 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.1961 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= 0.144 Angle : 0.603 9.767 9307 Z= 0.318 Chirality : 0.037 0.175 1071 Planarity : 0.005 0.066 1175 Dihedral : 4.294 24.170 882 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 2.84 % Allowed : 33.33 % Favored : 63.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.29), residues: 810 helix: 1.66 (0.21), residues: 564 sheet: None (None), residues: 0 loop : -1.15 (0.40), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1011 TYR 0.013 0.001 TYR A 780 PHE 0.020 0.001 PHE A 825 TRP 0.010 0.001 TRP B1006 HIS 0.005 0.001 HIS A 782 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 6874) covalent geometry : angle 0.60286 ( 9307) hydrogen bonds : bond 0.04026 ( 417) hydrogen bonds : angle 4.79202 ( 1233) ********************** 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 261 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 239 time to evaluate : 0.484 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: A 771 GLU cc_start: 0.8188 (mm-30) cc_final: 0.7622 (mm-30) REVERT: B 971 ASN cc_start: 0.8142 (m110) cc_final: 0.7853 (m110) REVERT: B 981 GLU cc_start: 0.8825 (mp0) cc_final: 0.8167 (mp0) REVERT: B 998 TRP cc_start: 0.8815 (t-100) cc_final: 0.8405 (t-100) REVERT: B 1125 LYS cc_start: 0.7792 (tmmt) cc_final: 0.7505 (tmmt) outliers start: 22 outliers final: 21 residues processed: 247 average time/residue: 0.1921 time to fit residues: 61.2079 Evaluate side-chains 256 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 235 time to evaluate : 0.357 ------------------------------------------------------------------------------- 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 530 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 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 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 1078 HIS Chi-restraints excluded: chain B residue 1095 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 16 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 55 optimal weight: 0.6980 chunk 41 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 76 optimal weight: 0.4980 chunk 47 optimal weight: 0.5980 chunk 69 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 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 = 0.3812 r_free = 0.3812 target = 0.098612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.081486 restraints weight = 50374.099| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 4.70 r_work: 0.3380 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.2046 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= 0.129 Angle : 0.602 7.508 9307 Z= 0.316 Chirality : 0.037 0.180 1071 Planarity : 0.005 0.063 1175 Dihedral : 4.210 24.597 882 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.71 % Allowed : 33.46 % Favored : 63.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.30), residues: 810 helix: 1.81 (0.22), residues: 564 sheet: None (None), residues: 0 loop : -1.08 (0.40), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1011 TYR 0.013 0.001 TYR A 780 PHE 0.016 0.001 PHE A 825 TRP 0.010 0.001 TRP B1006 HIS 0.004 0.001 HIS A 782 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 6874) covalent geometry : angle 0.60198 ( 9307) hydrogen bonds : bond 0.03865 ( 417) hydrogen bonds : angle 4.67931 ( 1233) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3468.80 seconds wall clock time: 59 minutes 36.18 seconds (3576.18 seconds total)