Starting phenix.real_space_refine on Fri Dec 27 10:04:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zrr_60403/12_2024/8zrr_60403.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zrr_60403/12_2024/8zrr_60403.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zrr_60403/12_2024/8zrr_60403.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zrr_60403/12_2024/8zrr_60403.map" model { file = "/net/cci-nas-00/data/ceres_data/8zrr_60403/12_2024/8zrr_60403.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zrr_60403/12_2024/8zrr_60403.cif" } resolution = 3.61 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= 0.003 sd= 0.036 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 18 5.16 5 C 2603 2.51 5 N 686 2.21 5 O 758 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 4065 Number of models: 1 Model: "" Number of chains: 4 Chain: "h" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 941 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "l" Number of atoms: 880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 880 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 106} Chain: "A" Number of atoms: 1118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1118 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 11, 'TRANS': 128} Chain: "B" Number of atoms: 1126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1126 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 11, 'TRANS': 129} Time building chain proxies: 3.25, per 1000 atoms: 0.80 Number of scatterers: 4065 At special positions: 0 Unit cell: (99.882, 69.81, 114.918, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 18 16.00 O 758 8.00 N 686 7.00 C 2603 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS h 22 " - pdb=" SG CYS h 96 " distance=2.04 Simple disulfide: pdb=" SG CYS l 23 " - pdb=" SG CYS l 93 " distance=2.04 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: 0.99 Conformation dependent library (CDL) restraints added in 481.1 milliseconds 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 958 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 6 sheets defined 45.5% alpha, 20.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'h' and resid 28 through 32 Processing helix chain 'h' and resid 87 through 91 removed outlier: 3.750A pdb=" N THR h 91 " --> pdb=" O ALA h 88 " (cutoff:3.500A) Processing helix chain 'l' and resid 84 through 88 removed outlier: 4.144A pdb=" N VAL l 88 " --> pdb=" O ALA l 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 6 through 10 Processing helix chain 'A' and resid 12 through 18 removed outlier: 4.223A pdb=" N PHE A 18 " --> pdb=" O GLU A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 43 removed outlier: 3.503A pdb=" N LEU A 30 " --> pdb=" O SER A 26 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N GLU A 40 " --> pdb=" O ALA A 36 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N ALA A 41 " --> pdb=" O LEU A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 75 Processing helix chain 'A' and resid 78 through 92 removed outlier: 3.672A pdb=" N ARG A 82 " --> pdb=" O ASP A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 110 Processing helix chain 'A' and resid 111 through 128 removed outlier: 4.008A pdb=" N GLY A 123 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N VAL A 124 " --> pdb=" O VAL A 120 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N TRP A 125 " --> pdb=" O SER A 121 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE A 126 " --> pdb=" O PHE A 122 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG A 127 " --> pdb=" O GLY A 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 10 removed outlier: 3.819A pdb=" N GLU B 8 " --> pdb=" O PRO B 5 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 18 removed outlier: 3.928A pdb=" N LEU B 16 " --> pdb=" O SER B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 44 removed outlier: 3.524A pdb=" N ARG B 39 " --> pdb=" O SER B 35 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N GLU B 40 " --> pdb=" O ALA B 36 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ALA B 41 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU B 43 " --> pdb=" O ARG B 39 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N SER B 44 " --> pdb=" O GLU B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 75 removed outlier: 3.898A pdb=" N THR B 53 " --> pdb=" O SER B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 91 removed outlier: 4.091A pdb=" N LEU B 84 " --> pdb=" O ALA B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 111 removed outlier: 4.197A pdb=" N ILE B 97 " --> pdb=" O MET B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 128 removed outlier: 3.652A pdb=" N VAL B 115 " --> pdb=" O GLY B 111 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU B 116 " --> pdb=" O ARG B 112 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N GLU B 117 " --> pdb=" O GLU B 113 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N THR B 128 " --> pdb=" O VAL B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 133 removed outlier: 3.506A pdb=" N TYR B 132 " --> pdb=" O PRO B 129 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'h' and resid 3 through 7 removed outlier: 4.121A pdb=" N GLN h 3 " --> pdb=" O SER h 25 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N SER h 25 " --> pdb=" O GLN h 3 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU h 81 " --> pdb=" O LEU h 20 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N CYS h 22 " --> pdb=" O LEU h 79 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'h' and resid 10 through 12 removed outlier: 7.100A pdb=" N MET h 34 " --> pdb=" O TYR h 50 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N TYR h 50 " --> pdb=" O MET h 34 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N TRP h 36 " --> pdb=" O LEU h 48 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N TYR h 50 " --> pdb=" O ASP h 59 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASP h 59 " --> pdb=" O TYR h 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'h' and resid 10 through 12 Processing sheet with id=AA4, first strand: chain 'l' and resid 4 through 7 removed outlier: 3.574A pdb=" N PHE l 76 " --> pdb=" O CYS l 23 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR l 77 " --> pdb=" O SER l 70 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER l 70 " --> pdb=" O THR l 77 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'l' and resid 10 through 12 removed outlier: 3.696A pdb=" N LEU l 11 " --> pdb=" O LYS l 108 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLU l 110 " --> pdb=" O LEU l 11 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N MET l 94 " --> pdb=" O SER l 39 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER l 39 " --> pdb=" O MET l 94 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N PHE l 38 " --> pdb=" O TYR l 54 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N TYR l 54 " --> pdb=" O PHE l 38 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N TRP l 40 " --> pdb=" O LEU l 52 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'l' and resid 10 through 12 removed outlier: 3.696A pdb=" N LEU l 11 " --> pdb=" O LYS l 108 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLU l 110 " --> pdb=" O LEU l 11 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N THR l 102 " --> pdb=" O GLN l 95 " (cutoff:3.500A) 206 hydrogen bonds defined for protein. 540 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.04 Time building geometry restraints manager: 1.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 669 1.30 - 1.43: 1175 1.43 - 1.56: 2305 1.56 - 1.69: 2 1.69 - 1.81: 26 Bond restraints: 4177 Sorted by residual: bond pdb=" C ARG B 98 " pdb=" N GLN B 99 " ideal model delta sigma weight residual 1.335 1.440 -0.106 1.25e-02 6.40e+03 7.18e+01 bond pdb=" C GLY h 26 " pdb=" N PHE h 27 " ideal model delta sigma weight residual 1.330 1.230 0.100 1.26e-02 6.30e+03 6.26e+01 bond pdb=" C LEU A 119 " pdb=" N VAL A 120 " ideal model delta sigma weight residual 1.333 1.237 0.097 1.24e-02 6.50e+03 6.11e+01 bond pdb=" C CYS B 48 " pdb=" N SER B 49 " ideal model delta sigma weight residual 1.331 1.419 -0.087 1.18e-02 7.18e+03 5.49e+01 bond pdb=" C SER A 26 " pdb=" N ILE A 27 " ideal model delta sigma weight residual 1.334 1.421 -0.087 1.22e-02 6.72e+03 5.03e+01 ... (remaining 4172 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 5272 1.69 - 3.37: 312 3.37 - 5.06: 79 5.06 - 6.74: 27 6.74 - 8.43: 4 Bond angle restraints: 5694 Sorted by residual: angle pdb=" CA CYS B 48 " pdb=" C CYS B 48 " pdb=" N SER B 49 " ideal model delta sigma weight residual 119.52 113.93 5.59 7.90e-01 1.60e+00 5.00e+01 angle pdb=" N GLU A 77 " pdb=" CA GLU A 77 " pdb=" C GLU A 77 " ideal model delta sigma weight residual 111.28 117.54 -6.26 1.09e+00 8.42e-01 3.30e+01 angle pdb=" CA ARG B 98 " pdb=" C ARG B 98 " pdb=" N GLN B 99 " ideal model delta sigma weight residual 117.30 110.74 6.56 1.16e+00 7.43e-01 3.20e+01 angle pdb=" C SER B 49 " pdb=" N PRO B 50 " pdb=" CA PRO B 50 " ideal model delta sigma weight residual 119.28 125.45 -6.17 1.10e+00 8.26e-01 3.14e+01 angle pdb=" O ARG B 98 " pdb=" C ARG B 98 " pdb=" N GLN B 99 " ideal model delta sigma weight residual 122.12 127.92 -5.80 1.06e+00 8.90e-01 3.00e+01 ... (remaining 5689 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.32: 2094 16.32 - 32.64: 251 32.64 - 48.97: 83 48.97 - 65.29: 22 65.29 - 81.61: 4 Dihedral angle restraints: 2454 sinusoidal: 962 harmonic: 1492 Sorted by residual: dihedral pdb=" C ASP B 78 " pdb=" N ASP B 78 " pdb=" CA ASP B 78 " pdb=" CB ASP B 78 " ideal model delta harmonic sigma weight residual -122.60 -114.14 -8.46 0 2.50e+00 1.60e-01 1.15e+01 dihedral pdb=" CA GLN h 39 " pdb=" C GLN h 39 " pdb=" N VAL h 40 " pdb=" CA VAL h 40 " ideal model delta harmonic sigma weight residual 180.00 163.71 16.29 0 5.00e+00 4.00e-02 1.06e+01 dihedral pdb=" CA LEU A 37 " pdb=" C LEU A 37 " pdb=" N TYR A 38 " pdb=" CA TYR A 38 " ideal model delta harmonic sigma weight residual -180.00 -164.36 -15.64 0 5.00e+00 4.00e-02 9.79e+00 ... (remaining 2451 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 445 0.045 - 0.090: 106 0.090 - 0.134: 59 0.134 - 0.179: 6 0.179 - 0.224: 8 Chirality restraints: 624 Sorted by residual: chirality pdb=" CA LEU A 31 " pdb=" N LEU A 31 " pdb=" C LEU A 31 " pdb=" CB LEU A 31 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CA ILE A 97 " pdb=" N ILE A 97 " pdb=" C ILE A 97 " pdb=" CB ILE A 97 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CA GLN l 95 " pdb=" N GLN l 95 " pdb=" C GLN l 95 " pdb=" CB GLN l 95 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 621 not shown) Planarity restraints: 731 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR l 14 " -0.074 5.00e-02 4.00e+02 1.08e-01 1.85e+01 pdb=" N PRO l 15 " 0.186 5.00e-02 4.00e+02 pdb=" CA PRO l 15 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO l 15 " -0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER B 74 " -0.019 2.00e-02 2.50e+03 3.82e-02 1.46e+01 pdb=" C SER B 74 " 0.066 2.00e-02 2.50e+03 pdb=" O SER B 74 " -0.025 2.00e-02 2.50e+03 pdb=" N ASN B 75 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY h 99 " -0.013 2.00e-02 2.50e+03 2.72e-02 7.39e+00 pdb=" C GLY h 99 " 0.047 2.00e-02 2.50e+03 pdb=" O GLY h 99 " -0.018 2.00e-02 2.50e+03 pdb=" N PHE h 100 " -0.016 2.00e-02 2.50e+03 ... (remaining 728 not shown) Histogram of nonbonded interaction distances: 1.34 - 2.06: 3 2.06 - 2.77: 750 2.77 - 3.48: 5707 3.48 - 4.19: 8607 4.19 - 4.90: 14908 Nonbonded interactions: 29975 Sorted by model distance: nonbonded pdb=" OH TYR h 53 " pdb=" OE1 GLU B 83 " model vdw 1.345 3.040 nonbonded pdb=" OD1 ASN l 33 " pdb=" CD1 LEU A 84 " model vdw 1.710 3.460 nonbonded pdb=" OH TYR h 53 " pdb=" CD GLU B 83 " model vdw 2.039 3.270 nonbonded pdb=" O ALA A 80 " pdb=" N GLU A 83 " model vdw 2.282 3.120 nonbonded pdb=" OD2 ASP A 78 " pdb=" N SER A 81 " model vdw 2.284 3.120 ... (remaining 29970 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 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 3 through 142) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.410 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: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 14.260 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6990 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 : 0.008 0.106 4177 Z= 0.543 Angle : 0.991 8.431 5694 Z= 0.694 Chirality : 0.053 0.224 624 Planarity : 0.007 0.108 731 Dihedral : 16.463 81.610 1490 Min Nonbonded Distance : 1.345 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.79 % Allowed : 3.54 % Favored : 95.67 % Rotamer: Outliers : 3.81 % Allowed : 27.13 % Favored : 69.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 0.51 (0.38), residues: 508 helix: 1.03 (0.38), residues: 173 sheet: 1.02 (0.59), residues: 81 loop : -0.31 (0.41), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 71 HIS 0.004 0.001 HIS h 35 PHE 0.029 0.002 PHE l 38 TYR 0.015 0.002 TYR A 6 ARG 0.006 0.001 ARG A 56 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 173 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: h 36 TRP cc_start: 0.7281 (m100) cc_final: 0.7057 (m100) REVERT: h 38 ARG cc_start: 0.6982 (tmm-80) cc_final: 0.6739 (ttp-170) REVERT: h 39 GLN cc_start: 0.7120 (tt0) cc_final: 0.6877 (tm-30) REVERT: h 47 TRP cc_start: 0.8430 (t60) cc_final: 0.7896 (t60) REVERT: h 69 THR cc_start: 0.7607 (t) cc_final: 0.7304 (p) REVERT: h 83 MET cc_start: 0.7099 (mtm) cc_final: 0.6618 (mtm) REVERT: l 68 SER cc_start: 0.8016 (t) cc_final: 0.7594 (p) REVERT: l 78 LEU cc_start: 0.8672 (tp) cc_final: 0.8373 (tp) REVERT: A 31 LEU cc_start: 0.8283 (mm) cc_final: 0.7922 (mm) REVERT: A 124 VAL cc_start: 0.8249 (t) cc_final: 0.8036 (p) REVERT: B 19 LEU cc_start: 0.8123 (tp) cc_final: 0.7777 (tp) REVERT: B 38 TYR cc_start: 0.7284 (m-80) cc_final: 0.6902 (m-10) REVERT: B 42 LEU cc_start: 0.8095 (tt) cc_final: 0.7882 (tp) REVERT: B 66 MET cc_start: 0.7491 (OUTLIER) cc_final: 0.7233 (mmt) REVERT: B 103 PHE cc_start: 0.8418 (t80) cc_final: 0.8064 (t80) outliers start: 17 outliers final: 7 residues processed: 178 average time/residue: 0.1278 time to fit residues: 29.1656 Evaluate side-chains 162 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 154 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain h residue 106 LEU Chi-restraints excluded: chain A residue 75 ASN Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain B residue 66 MET Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 108 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 43 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 24 optimal weight: 0.0470 chunk 29 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 overall best weight: 0.7280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** l 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 GLN ** B 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7071 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4177 Z= 0.198 Angle : 0.653 7.022 5694 Z= 0.339 Chirality : 0.044 0.137 624 Planarity : 0.005 0.057 731 Dihedral : 6.810 58.731 581 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 5.83 % Allowed : 23.77 % Favored : 70.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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 (0.38), residues: 508 helix: 1.87 (0.39), residues: 176 sheet: 0.54 (0.57), residues: 92 loop : 0.01 (0.42), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP l 101 HIS 0.006 0.001 HIS B 104 PHE 0.012 0.002 PHE l 67 TYR 0.020 0.002 TYR h 101 ARG 0.003 0.000 ARG h 38 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 151 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: h 43 LYS cc_start: 0.8639 (mmtt) cc_final: 0.8371 (mmtt) REVERT: h 47 TRP cc_start: 0.8234 (t60) cc_final: 0.7879 (t60) REVERT: h 70 ILE cc_start: 0.8513 (tt) cc_final: 0.8261 (tt) REVERT: h 83 MET cc_start: 0.7088 (mtm) cc_final: 0.6546 (ttm) REVERT: h 111 GLN cc_start: 0.8132 (mm-40) cc_final: 0.7511 (tm-30) REVERT: l 33 ASN cc_start: 0.7313 (t0) cc_final: 0.7075 (t0) REVERT: l 50 GLN cc_start: 0.7220 (OUTLIER) cc_final: 0.6947 (mp10) REVERT: l 68 SER cc_start: 0.8050 (t) cc_final: 0.7641 (p) REVERT: l 78 LEU cc_start: 0.8707 (tp) cc_final: 0.8458 (tp) REVERT: l 94 MET cc_start: 0.7082 (tmt) cc_final: 0.6811 (tmt) REVERT: l 95 GLN cc_start: 0.7895 (tm-30) cc_final: 0.7090 (tm-30) REVERT: A 37 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7931 (tp) REVERT: A 61 CYS cc_start: 0.8668 (m) cc_final: 0.7879 (m) REVERT: A 66 MET cc_start: 0.7430 (tpp) cc_final: 0.7171 (mpp) REVERT: A 108 LEU cc_start: 0.8558 (tp) cc_final: 0.8111 (tp) REVERT: B 19 LEU cc_start: 0.8131 (OUTLIER) cc_final: 0.7810 (tp) REVERT: B 38 TYR cc_start: 0.7498 (m-80) cc_final: 0.7292 (m-10) REVERT: B 83 GLU cc_start: 0.6554 (OUTLIER) cc_final: 0.5926 (mt-10) outliers start: 26 outliers final: 12 residues processed: 160 average time/residue: 0.1324 time to fit residues: 26.8161 Evaluate side-chains 164 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 148 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain h residue 30 ASN Chi-restraints excluded: chain h residue 101 TYR Chi-restraints excluded: chain h residue 115 VAL Chi-restraints excluded: chain h residue 116 ILE Chi-restraints excluded: chain l residue 50 GLN Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 96 LYS Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 139 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 25 optimal weight: 0.0570 chunk 14 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 12 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 41 optimal weight: 0.0010 chunk 15 optimal weight: 3.9990 chunk 37 optimal weight: 0.2980 chunk 45 optimal weight: 4.9990 overall best weight: 0.6706 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** l 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7104 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4177 Z= 0.177 Angle : 0.603 8.329 5694 Z= 0.304 Chirality : 0.043 0.265 624 Planarity : 0.005 0.042 731 Dihedral : 5.783 58.664 571 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 5.83 % Allowed : 23.77 % Favored : 70.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 1.40 (0.38), residues: 508 helix: 2.33 (0.38), residues: 176 sheet: 0.52 (0.56), residues: 92 loop : 0.10 (0.41), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP h 36 HIS 0.004 0.001 HIS A 104 PHE 0.020 0.002 PHE B 103 TYR 0.020 0.002 TYR h 101 ARG 0.005 0.000 ARG B 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 147 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: h 38 ARG cc_start: 0.7349 (ttp-170) cc_final: 0.7085 (ttp-170) REVERT: h 43 LYS cc_start: 0.8656 (mmtt) cc_final: 0.8360 (mmtt) REVERT: h 47 TRP cc_start: 0.8248 (t60) cc_final: 0.7884 (t60) REVERT: h 70 ILE cc_start: 0.8500 (tt) cc_final: 0.8225 (tt) REVERT: h 83 MET cc_start: 0.7318 (mtm) cc_final: 0.6972 (mtm) REVERT: h 111 GLN cc_start: 0.8147 (mm-40) cc_final: 0.7517 (tm-30) REVERT: l 33 ASN cc_start: 0.7446 (t0) cc_final: 0.7136 (t0) REVERT: l 50 GLN cc_start: 0.7257 (OUTLIER) cc_final: 0.6937 (mp10) REVERT: l 68 SER cc_start: 0.8040 (t) cc_final: 0.7596 (p) REVERT: l 78 LEU cc_start: 0.8692 (tp) cc_final: 0.8467 (tp) REVERT: l 94 MET cc_start: 0.7058 (tmt) cc_final: 0.6778 (tmt) REVERT: l 95 GLN cc_start: 0.8015 (tm-30) cc_final: 0.7286 (tm-30) REVERT: A 37 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7932 (tp) REVERT: A 66 MET cc_start: 0.7451 (tpp) cc_final: 0.7247 (tpp) REVERT: A 108 LEU cc_start: 0.8536 (tp) cc_final: 0.8149 (tp) REVERT: B 19 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7809 (tp) REVERT: B 83 GLU cc_start: 0.6531 (OUTLIER) cc_final: 0.5932 (mt-10) outliers start: 26 outliers final: 18 residues processed: 154 average time/residue: 0.1402 time to fit residues: 27.5015 Evaluate side-chains 168 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 146 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain h residue 11 VAL Chi-restraints excluded: chain h residue 30 ASN Chi-restraints excluded: chain h residue 71 SER Chi-restraints excluded: chain h residue 116 ILE Chi-restraints excluded: chain l residue 4 MET Chi-restraints excluded: chain l residue 5 THR Chi-restraints excluded: chain l residue 20 SER Chi-restraints excluded: chain l residue 50 GLN Chi-restraints excluded: chain l residue 75 SER Chi-restraints excluded: chain A residue 28 ARG Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 139 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 34 optimal weight: 4.9990 chunk 24 optimal weight: 0.0970 chunk 5 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 46 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 chunk 44 optimal weight: 0.0980 chunk 13 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 51 HIS B 104 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.3688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4177 Z= 0.215 Angle : 0.641 8.490 5694 Z= 0.327 Chirality : 0.044 0.152 624 Planarity : 0.005 0.041 731 Dihedral : 5.770 57.529 571 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 6.50 % Allowed : 25.78 % Favored : 67.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 1.24 (0.38), residues: 508 helix: 2.14 (0.37), residues: 176 sheet: 0.18 (0.54), residues: 97 loop : 0.19 (0.42), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 125 HIS 0.004 0.001 HIS B 51 PHE 0.012 0.002 PHE l 67 TYR 0.018 0.002 TYR l 54 ARG 0.006 0.000 ARG B 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 157 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: h 43 LYS cc_start: 0.8615 (mmtt) cc_final: 0.8322 (mmtt) REVERT: h 47 TRP cc_start: 0.8308 (t60) cc_final: 0.7988 (t60) REVERT: h 70 ILE cc_start: 0.8553 (tt) cc_final: 0.8202 (tt) REVERT: h 81 LEU cc_start: 0.7679 (tp) cc_final: 0.7287 (tp) REVERT: h 83 MET cc_start: 0.7656 (mtm) cc_final: 0.6802 (mtm) REVERT: h 111 GLN cc_start: 0.8122 (mm-40) cc_final: 0.7521 (tm-30) REVERT: l 33 ASN cc_start: 0.7571 (t0) cc_final: 0.7230 (t0) REVERT: l 50 GLN cc_start: 0.7235 (OUTLIER) cc_final: 0.6875 (mp10) REVERT: l 78 LEU cc_start: 0.8660 (tp) cc_final: 0.8440 (tp) REVERT: l 94 MET cc_start: 0.7236 (tmt) cc_final: 0.7034 (tmt) REVERT: l 95 GLN cc_start: 0.8108 (tm-30) cc_final: 0.7280 (tm-30) REVERT: A 6 TYR cc_start: 0.8165 (m-80) cc_final: 0.7868 (m-80) REVERT: A 66 MET cc_start: 0.7533 (tpp) cc_final: 0.7323 (tpp) REVERT: B 19 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7846 (tp) REVERT: B 24 PHE cc_start: 0.9029 (m-10) cc_final: 0.8765 (m-10) REVERT: B 71 TRP cc_start: 0.8251 (t60) cc_final: 0.7799 (t-100) REVERT: B 83 GLU cc_start: 0.6655 (OUTLIER) cc_final: 0.6042 (mt-10) outliers start: 29 outliers final: 18 residues processed: 165 average time/residue: 0.1288 time to fit residues: 27.5193 Evaluate side-chains 176 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 155 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain h residue 11 VAL Chi-restraints excluded: chain h residue 30 ASN Chi-restraints excluded: chain h residue 71 SER Chi-restraints excluded: chain h residue 116 ILE Chi-restraints excluded: chain l residue 20 SER Chi-restraints excluded: chain l residue 21 ILE Chi-restraints excluded: chain l residue 50 GLN Chi-restraints excluded: chain l residue 57 SER Chi-restraints excluded: chain l residue 75 SER Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 96 LYS Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 142 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 0 optimal weight: 7.9990 chunk 36 optimal weight: 0.0030 chunk 20 optimal weight: 10.0000 chunk 42 optimal weight: 1.9990 chunk 34 optimal weight: 0.3980 chunk 25 optimal weight: 2.9990 chunk 44 optimal weight: 0.4980 chunk 12 optimal weight: 2.9990 chunk 16 optimal weight: 0.2980 chunk 9 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 overall best weight: 0.4392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: l 32 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 moved from start: 0.3891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4177 Z= 0.152 Angle : 0.638 8.853 5694 Z= 0.307 Chirality : 0.042 0.176 624 Planarity : 0.004 0.037 731 Dihedral : 5.498 59.203 569 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 4.93 % Allowed : 27.35 % Favored : 67.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 1.43 (0.38), residues: 508 helix: 2.35 (0.38), residues: 176 sheet: 0.12 (0.53), residues: 102 loop : 0.33 (0.43), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 125 HIS 0.004 0.001 HIS A 104 PHE 0.019 0.001 PHE B 103 TYR 0.021 0.002 TYR B 118 ARG 0.003 0.000 ARG B 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 161 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: h 43 LYS cc_start: 0.8602 (mmtt) cc_final: 0.8188 (mmtt) REVERT: h 47 TRP cc_start: 0.8257 (t60) cc_final: 0.7864 (t60) REVERT: h 70 ILE cc_start: 0.8512 (tt) cc_final: 0.8154 (tt) REVERT: h 81 LEU cc_start: 0.7563 (tp) cc_final: 0.7286 (tp) REVERT: h 83 MET cc_start: 0.7541 (mtm) cc_final: 0.6773 (mtm) REVERT: h 111 GLN cc_start: 0.8093 (mm-40) cc_final: 0.7508 (tm-30) REVERT: l 50 GLN cc_start: 0.7287 (OUTLIER) cc_final: 0.6899 (mp10) REVERT: l 95 GLN cc_start: 0.8057 (tm-30) cc_final: 0.7317 (tm-30) REVERT: A 4 ASP cc_start: 0.7499 (m-30) cc_final: 0.7188 (m-30) REVERT: A 6 TYR cc_start: 0.8088 (m-80) cc_final: 0.7824 (m-80) REVERT: A 37 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7866 (tp) REVERT: B 19 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7641 (tt) REVERT: B 24 PHE cc_start: 0.9018 (m-10) cc_final: 0.8668 (m-10) REVERT: B 71 TRP cc_start: 0.8267 (t60) cc_final: 0.7850 (t-100) outliers start: 22 outliers final: 17 residues processed: 167 average time/residue: 0.1219 time to fit residues: 26.3236 Evaluate side-chains 179 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 159 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain h residue 11 VAL Chi-restraints excluded: chain h residue 30 ASN Chi-restraints excluded: chain h residue 48 LEU Chi-restraints excluded: chain h residue 69 THR Chi-restraints excluded: chain h residue 116 ILE Chi-restraints excluded: chain l residue 50 GLN Chi-restraints excluded: chain l residue 75 SER Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 66 MET Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 142 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 12 optimal weight: 3.9990 chunk 49 optimal weight: 0.0170 chunk 40 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 25 optimal weight: 4.9990 chunk 47 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 36 optimal weight: 0.0050 overall best weight: 0.5836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: l 33 ASN ** B 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 moved from start: 0.4148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4177 Z= 0.154 Angle : 0.670 11.275 5694 Z= 0.314 Chirality : 0.044 0.319 624 Planarity : 0.004 0.036 731 Dihedral : 5.500 58.878 569 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 4.93 % Allowed : 27.58 % Favored : 67.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 1.51 (0.38), residues: 508 helix: 2.34 (0.38), residues: 177 sheet: 0.36 (0.54), residues: 98 loop : 0.34 (0.42), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 102 HIS 0.005 0.001 HIS B 104 PHE 0.010 0.001 PHE l 67 TYR 0.031 0.001 TYR B 118 ARG 0.003 0.000 ARG B 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 149 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: h 34 MET cc_start: 0.7015 (mmm) cc_final: 0.6804 (mmm) REVERT: h 43 LYS cc_start: 0.8563 (mmtt) cc_final: 0.8186 (mmtt) REVERT: h 47 TRP cc_start: 0.8242 (t60) cc_final: 0.7877 (t60) REVERT: h 70 ILE cc_start: 0.8523 (tt) cc_final: 0.8165 (tt) REVERT: h 81 LEU cc_start: 0.7455 (tp) cc_final: 0.7191 (tp) REVERT: h 83 MET cc_start: 0.7556 (mtm) cc_final: 0.6850 (mtm) REVERT: l 95 GLN cc_start: 0.8053 (tm-30) cc_final: 0.7531 (tm-30) REVERT: A 37 LEU cc_start: 0.8138 (OUTLIER) cc_final: 0.7890 (tp) REVERT: A 38 TYR cc_start: 0.6741 (m-80) cc_final: 0.6499 (m-80) REVERT: A 66 MET cc_start: 0.7603 (tpp) cc_final: 0.7314 (mpp) REVERT: B 19 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7611 (tt) REVERT: B 24 PHE cc_start: 0.9014 (m-10) cc_final: 0.8680 (m-10) REVERT: B 27 ILE cc_start: 0.7280 (OUTLIER) cc_final: 0.6983 (mm) REVERT: B 71 TRP cc_start: 0.8254 (t60) cc_final: 0.7844 (t-100) outliers start: 22 outliers final: 17 residues processed: 155 average time/residue: 0.1290 time to fit residues: 25.4304 Evaluate side-chains 168 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 148 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain h residue 30 ASN Chi-restraints excluded: chain h residue 48 LEU Chi-restraints excluded: chain h residue 69 THR Chi-restraints excluded: chain l residue 33 ASN Chi-restraints excluded: chain l residue 75 SER Chi-restraints excluded: chain A residue 28 ARG Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 66 MET Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 142 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 27 optimal weight: 0.5980 chunk 41 optimal weight: 0.0980 chunk 49 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 chunk 22 optimal weight: 4.9990 chunk 19 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7159 moved from start: 0.4282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 4177 Z= 0.155 Angle : 0.674 14.587 5694 Z= 0.313 Chirality : 0.045 0.384 624 Planarity : 0.004 0.035 731 Dihedral : 5.442 58.548 569 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 5.61 % Allowed : 27.13 % Favored : 67.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 1.54 (0.38), residues: 508 helix: 2.37 (0.38), residues: 177 sheet: 0.41 (0.54), residues: 98 loop : 0.35 (0.42), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 102 HIS 0.007 0.001 HIS l 31 PHE 0.020 0.001 PHE B 103 TYR 0.020 0.001 TYR B 118 ARG 0.002 0.000 ARG B 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 150 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: h 43 LYS cc_start: 0.8538 (mmtt) cc_final: 0.8188 (mmtt) REVERT: h 47 TRP cc_start: 0.8250 (t60) cc_final: 0.7898 (t60) REVERT: h 70 ILE cc_start: 0.8530 (tt) cc_final: 0.8169 (tt) REVERT: h 81 LEU cc_start: 0.7424 (tp) cc_final: 0.7171 (tp) REVERT: h 83 MET cc_start: 0.7537 (mtm) cc_final: 0.6821 (mtm) REVERT: l 95 GLN cc_start: 0.8041 (tm-30) cc_final: 0.7477 (tm-30) REVERT: l 114 THR cc_start: 0.7823 (p) cc_final: 0.7519 (t) REVERT: A 66 MET cc_start: 0.7580 (tpp) cc_final: 0.7290 (mpp) REVERT: A 93 MET cc_start: 0.8098 (tpt) cc_final: 0.7870 (tpp) REVERT: B 19 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7603 (tt) REVERT: B 24 PHE cc_start: 0.9018 (m-10) cc_final: 0.8672 (m-10) REVERT: B 27 ILE cc_start: 0.7410 (OUTLIER) cc_final: 0.7097 (mm) REVERT: B 71 TRP cc_start: 0.8274 (t60) cc_final: 0.7865 (t-100) REVERT: B 83 GLU cc_start: 0.6606 (OUTLIER) cc_final: 0.6002 (mt-10) outliers start: 25 outliers final: 21 residues processed: 158 average time/residue: 0.1438 time to fit residues: 29.3511 Evaluate side-chains 174 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 150 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain h residue 30 ASN Chi-restraints excluded: chain h residue 48 LEU Chi-restraints excluded: chain h residue 69 THR Chi-restraints excluded: chain l residue 10 SER Chi-restraints excluded: chain l residue 33 ASN Chi-restraints excluded: chain l residue 57 SER Chi-restraints excluded: chain l residue 75 SER Chi-restraints excluded: chain l residue 94 MET Chi-restraints excluded: chain A residue 28 ARG Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 96 LYS Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 66 MET Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 142 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 24 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 38 optimal weight: 0.0970 chunk 44 optimal weight: 0.7980 chunk 47 optimal weight: 0.4980 chunk 42 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 chunk 27 optimal weight: 0.1980 chunk 19 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 14 optimal weight: 0.5980 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 moved from start: 0.4434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 4177 Z= 0.150 Angle : 0.682 13.613 5694 Z= 0.311 Chirality : 0.044 0.376 624 Planarity : 0.004 0.037 731 Dihedral : 5.403 56.471 569 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 4.71 % Allowed : 27.80 % Favored : 67.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 1.59 (0.38), residues: 508 helix: 2.36 (0.39), residues: 177 sheet: 0.27 (0.53), residues: 103 loop : 0.51 (0.43), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 102 HIS 0.005 0.001 HIS B 104 PHE 0.012 0.001 PHE l 67 TYR 0.020 0.001 TYR B 118 ARG 0.002 0.000 ARG B 127 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 148 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: h 43 LYS cc_start: 0.8591 (mmtt) cc_final: 0.8304 (mmtt) REVERT: h 46 GLU cc_start: 0.6906 (tt0) cc_final: 0.6657 (tt0) REVERT: h 47 TRP cc_start: 0.8210 (t60) cc_final: 0.7856 (t60) REVERT: h 70 ILE cc_start: 0.8526 (tt) cc_final: 0.8163 (tt) REVERT: h 83 MET cc_start: 0.7513 (mtm) cc_final: 0.6776 (mtm) REVERT: l 95 GLN cc_start: 0.8026 (tm-30) cc_final: 0.7733 (tm-30) REVERT: l 114 THR cc_start: 0.7774 (p) cc_final: 0.7463 (t) REVERT: A 38 TYR cc_start: 0.6635 (m-80) cc_final: 0.6407 (m-80) REVERT: A 66 MET cc_start: 0.7666 (tpp) cc_final: 0.7399 (mpp) REVERT: A 93 MET cc_start: 0.8036 (tpt) cc_final: 0.7830 (tpp) REVERT: B 19 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.7696 (tt) REVERT: B 24 PHE cc_start: 0.9009 (m-10) cc_final: 0.8676 (m-10) REVERT: B 27 ILE cc_start: 0.7415 (OUTLIER) cc_final: 0.7089 (mm) REVERT: B 71 TRP cc_start: 0.8297 (t60) cc_final: 0.7909 (t-100) REVERT: B 83 GLU cc_start: 0.6589 (OUTLIER) cc_final: 0.5986 (mt-10) outliers start: 21 outliers final: 14 residues processed: 154 average time/residue: 0.1358 time to fit residues: 26.6841 Evaluate side-chains 163 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 146 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain h residue 30 ASN Chi-restraints excluded: chain h residue 48 LEU Chi-restraints excluded: chain h residue 69 THR Chi-restraints excluded: chain l residue 33 ASN Chi-restraints excluded: chain l residue 75 SER Chi-restraints excluded: chain l residue 94 MET Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 66 MET Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 108 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 41 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 48 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 50 optimal weight: 0.0770 chunk 46 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 overall best weight: 0.9342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 0.4630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4177 Z= 0.190 Angle : 0.696 13.152 5694 Z= 0.327 Chirality : 0.046 0.393 624 Planarity : 0.004 0.038 731 Dihedral : 5.544 59.050 569 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 4.48 % Allowed : 28.03 % Favored : 67.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 1.64 (0.38), residues: 508 helix: 2.38 (0.38), residues: 177 sheet: 0.29 (0.53), residues: 103 loop : 0.57 (0.43), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 102 HIS 0.004 0.001 HIS B 104 PHE 0.024 0.002 PHE B 103 TYR 0.008 0.001 TYR l 54 ARG 0.002 0.000 ARG B 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 155 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: h 38 ARG cc_start: 0.7365 (ttp-170) cc_final: 0.6391 (mtp-110) REVERT: h 46 GLU cc_start: 0.6907 (tt0) cc_final: 0.6566 (tt0) REVERT: h 47 TRP cc_start: 0.8269 (t60) cc_final: 0.7907 (t60) REVERT: h 70 ILE cc_start: 0.8520 (tt) cc_final: 0.8171 (tt) REVERT: h 83 MET cc_start: 0.7480 (mtm) cc_final: 0.6567 (mtm) REVERT: h 94 TYR cc_start: 0.7833 (m-10) cc_final: 0.7511 (m-10) REVERT: l 95 GLN cc_start: 0.7920 (tm-30) cc_final: 0.7644 (tm-30) REVERT: l 114 THR cc_start: 0.7829 (p) cc_final: 0.7536 (t) REVERT: A 66 MET cc_start: 0.7700 (tpp) cc_final: 0.7441 (mpp) REVERT: B 19 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.7741 (tt) REVERT: B 24 PHE cc_start: 0.8992 (m-10) cc_final: 0.8630 (m-10) REVERT: B 27 ILE cc_start: 0.7584 (OUTLIER) cc_final: 0.7224 (mm) REVERT: B 71 TRP cc_start: 0.8380 (t60) cc_final: 0.7962 (t-100) REVERT: B 83 GLU cc_start: 0.6607 (OUTLIER) cc_final: 0.5999 (mt-10) REVERT: B 103 PHE cc_start: 0.8774 (t80) cc_final: 0.8415 (t80) outliers start: 20 outliers final: 17 residues processed: 163 average time/residue: 0.1402 time to fit residues: 28.8214 Evaluate side-chains 175 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 155 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain h residue 11 VAL Chi-restraints excluded: chain h residue 30 ASN Chi-restraints excluded: chain h residue 69 THR Chi-restraints excluded: chain h residue 96 CYS Chi-restraints excluded: chain l residue 21 ILE Chi-restraints excluded: chain l residue 33 ASN Chi-restraints excluded: chain l residue 75 SER Chi-restraints excluded: chain l residue 94 MET Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 96 LYS Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 66 MET Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 114 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 4 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 24 optimal weight: 0.3980 chunk 32 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 12 optimal weight: 0.0570 chunk 37 optimal weight: 1.9990 chunk 5 optimal weight: 0.3980 chunk 11 optimal weight: 6.9990 chunk 40 optimal weight: 0.5980 chunk 16 optimal weight: 0.3980 overall best weight: 0.3698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7152 moved from start: 0.4791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 4177 Z= 0.151 Angle : 0.721 14.409 5694 Z= 0.325 Chirality : 0.046 0.418 624 Planarity : 0.004 0.038 731 Dihedral : 5.423 55.712 569 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.36 % Allowed : 29.37 % Favored : 67.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 1.84 (0.39), residues: 508 helix: 2.45 (0.39), residues: 177 sheet: 0.70 (0.55), residues: 97 loop : 0.60 (0.43), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP h 36 HIS 0.004 0.001 HIS B 104 PHE 0.022 0.001 PHE B 103 TYR 0.009 0.001 TYR A 38 ARG 0.004 0.000 ARG h 87 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1016 Ramachandran restraints generated. 508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 152 time to evaluate : 0.444 Fit side-chains revert: symmetry clash REVERT: h 46 GLU cc_start: 0.6895 (tt0) cc_final: 0.6643 (tt0) REVERT: h 47 TRP cc_start: 0.8225 (t60) cc_final: 0.7816 (t60) REVERT: h 70 ILE cc_start: 0.8496 (tt) cc_final: 0.8158 (tt) REVERT: h 83 MET cc_start: 0.7319 (mtm) cc_final: 0.6584 (mtm) REVERT: l 95 GLN cc_start: 0.8055 (tm-30) cc_final: 0.7757 (tm-30) REVERT: l 103 PHE cc_start: 0.8793 (m-80) cc_final: 0.8368 (m-80) REVERT: l 114 THR cc_start: 0.7893 (p) cc_final: 0.7579 (t) REVERT: A 66 MET cc_start: 0.7692 (tpp) cc_final: 0.7447 (mpp) REVERT: A 103 PHE cc_start: 0.8383 (t80) cc_final: 0.8107 (t80) REVERT: B 19 LEU cc_start: 0.8283 (tp) cc_final: 0.7786 (tt) REVERT: B 27 ILE cc_start: 0.7551 (OUTLIER) cc_final: 0.7187 (mm) REVERT: B 71 TRP cc_start: 0.8368 (t60) cc_final: 0.7976 (t-100) REVERT: B 83 GLU cc_start: 0.6600 (OUTLIER) cc_final: 0.5982 (mt-10) outliers start: 15 outliers final: 12 residues processed: 158 average time/residue: 0.1309 time to fit residues: 26.4218 Evaluate side-chains 164 residues out of total 446 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 150 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain h residue 30 ASN Chi-restraints excluded: chain h residue 69 THR Chi-restraints excluded: chain h residue 96 CYS Chi-restraints excluded: chain l residue 33 ASN Chi-restraints excluded: chain l residue 75 SER Chi-restraints excluded: chain l residue 94 MET Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 66 MET Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 108 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 41 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 7 optimal weight: 6.9990 chunk 35 optimal weight: 0.3980 chunk 2 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 46 optimal weight: 4.9990 chunk 27 optimal weight: 0.0370 chunk 34 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 32 optimal weight: 0.0770 overall best weight: 0.4616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.128490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.111066 restraints weight = 8129.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.115187 restraints weight = 4403.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.118002 restraints weight = 2752.289| |-----------------------------------------------------------------------------| r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.4912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 4177 Z= 0.159 Angle : 0.734 14.286 5694 Z= 0.333 Chirality : 0.046 0.412 624 Planarity : 0.004 0.039 731 Dihedral : 5.474 57.547 569 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.81 % Allowed : 29.37 % Favored : 66.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 1.78 (0.39), residues: 508 helix: 2.43 (0.39), residues: 177 sheet: 0.35 (0.53), residues: 103 loop : 0.71 (0.44), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP h 36 HIS 0.004 0.001 HIS B 104 PHE 0.011 0.001 PHE l 67 TYR 0.019 0.001 TYR B 118 ARG 0.019 0.001 ARG h 87 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1328.25 seconds wall clock time: 25 minutes 3.19 seconds (1503.19 seconds total)