Starting phenix.real_space_refine on Fri Dec 27 05:58:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ctk_26993/12_2024/8ctk_26993.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ctk_26993/12_2024/8ctk_26993.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ctk_26993/12_2024/8ctk_26993.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ctk_26993/12_2024/8ctk_26993.map" model { file = "/net/cci-nas-00/data/ceres_data/8ctk_26993/12_2024/8ctk_26993.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ctk_26993/12_2024/8ctk_26993.cif" } resolution = 3.52 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= 0.000 sd= 0.018 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 14 5.16 5 C 2020 2.51 5 N 520 2.21 5 O 488 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 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: 3042 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1521 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 5, 'TRANS': 182} Restraints were copied for chains: B Time building chain proxies: 2.79, per 1000 atoms: 0.92 Number of scatterers: 3042 At special positions: 0 Unit cell: (74.881, 54.525, 80.697, 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 14 16.00 O 488 8.00 N 520 7.00 C 2020 6.00 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: 0.70 Conformation dependent library (CDL) restraints added in 912.9 milliseconds 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 700 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 2 sheets defined 48.7% alpha, 23.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 17 through 38 removed outlier: 3.836A pdb=" N ASN A 21 " --> pdb=" O LEU A 17 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU A 35 " --> pdb=" O TRP A 31 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLN A 36 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N PHE A 37 " --> pdb=" O CYS A 33 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA A 38 " --> pdb=" O LEU A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 56 Processing helix chain 'A' and resid 56 through 71 removed outlier: 4.123A pdb=" N TYR A 71 " --> pdb=" O LEU A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 107 removed outlier: 3.853A pdb=" N GLY A 78 " --> pdb=" O ASN A 74 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ARG A 105 " --> pdb=" O ARG A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 113 removed outlier: 3.733A pdb=" N ASN A 113 " --> pdb=" O TRP A 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 38 removed outlier: 3.622A pdb=" N LEU B 35 " --> pdb=" O TRP B 31 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLN B 36 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N PHE B 37 " --> pdb=" O CYS B 33 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA B 38 " --> pdb=" O LEU B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 56 Processing helix chain 'B' and resid 56 through 71 removed outlier: 4.123A pdb=" N TYR B 71 " --> pdb=" O LEU B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 107 removed outlier: 3.852A pdb=" N GLY B 78 " --> pdb=" O ASN B 74 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ARG B 105 " --> pdb=" O ARG B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 113 removed outlier: 3.732A pdb=" N ASN B 113 " --> pdb=" O TRP B 110 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 128 through 132 removed outlier: 7.079A pdb=" N GLU A 167 " --> pdb=" O PRO A 123 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N LEU A 176 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ILE A 201 " --> pdb=" O LEU A 176 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N TYR A 178 " --> pdb=" O TYR A 199 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N ALA A 195 " --> pdb=" O GLY A 182 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N SER A 184 " --> pdb=" O PHE A 193 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N PHE A 193 " --> pdb=" O SER A 184 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N LEU A 149 " --> pdb=" O LEU A 156 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 128 through 132 removed outlier: 7.079A pdb=" N GLU B 167 " --> pdb=" O PRO B 123 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N LEU B 176 " --> pdb=" O ILE B 201 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ILE B 201 " --> pdb=" O LEU B 176 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N TYR B 178 " --> pdb=" O TYR B 199 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N ALA B 195 " --> pdb=" O GLY B 182 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N SER B 184 " --> pdb=" O PHE B 193 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N PHE B 193 " --> pdb=" O SER B 184 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N LEU B 149 " --> pdb=" O LEU B 156 " (cutoff:3.500A) 186 hydrogen bonds defined for protein. 522 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.79 Time building geometry restraints manager: 0.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 924 1.34 - 1.46: 773 1.46 - 1.58: 1409 1.58 - 1.69: 0 1.69 - 1.81: 20 Bond restraints: 3126 Sorted by residual: bond pdb=" CB ASP B 190 " pdb=" CG ASP B 190 " ideal model delta sigma weight residual 1.516 1.542 -0.026 2.50e-02 1.60e+03 1.08e+00 bond pdb=" CB ASP A 190 " pdb=" CG ASP A 190 " ideal model delta sigma weight residual 1.516 1.542 -0.026 2.50e-02 1.60e+03 1.07e+00 bond pdb=" C TRP A 58 " pdb=" N PRO A 59 " ideal model delta sigma weight residual 1.335 1.346 -0.011 1.28e-02 6.10e+03 7.29e-01 bond pdb=" C TRP B 58 " pdb=" N PRO B 59 " ideal model delta sigma weight residual 1.335 1.345 -0.010 1.28e-02 6.10e+03 6.67e-01 bond pdb=" CB ASP A 160 " pdb=" CG ASP A 160 " ideal model delta sigma weight residual 1.516 1.536 -0.020 2.50e-02 1.60e+03 6.36e-01 ... (remaining 3121 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 4112 1.61 - 3.22: 114 3.22 - 4.82: 14 4.82 - 6.43: 12 6.43 - 8.04: 2 Bond angle restraints: 4254 Sorted by residual: angle pdb=" N ILE B 73 " pdb=" CA ILE B 73 " pdb=" C ILE B 73 " ideal model delta sigma weight residual 111.62 107.80 3.82 7.90e-01 1.60e+00 2.34e+01 angle pdb=" N ILE A 73 " pdb=" CA ILE A 73 " pdb=" C ILE A 73 " ideal model delta sigma weight residual 111.62 107.82 3.80 7.90e-01 1.60e+00 2.31e+01 angle pdb=" CA MET B 91 " pdb=" CB MET B 91 " pdb=" CG MET B 91 " ideal model delta sigma weight residual 114.10 119.39 -5.29 2.00e+00 2.50e-01 7.00e+00 angle pdb=" CA MET A 91 " pdb=" CB MET A 91 " pdb=" CG MET A 91 " ideal model delta sigma weight residual 114.10 119.35 -5.25 2.00e+00 2.50e-01 6.90e+00 angle pdb=" CA LEU A 56 " pdb=" CB LEU A 56 " pdb=" CG LEU A 56 " ideal model delta sigma weight residual 116.30 124.34 -8.04 3.50e+00 8.16e-02 5.28e+00 ... (remaining 4249 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.01: 1512 13.01 - 26.02: 170 26.02 - 39.03: 78 39.03 - 52.03: 22 52.03 - 65.04: 6 Dihedral angle restraints: 1788 sinusoidal: 696 harmonic: 1092 Sorted by residual: dihedral pdb=" CG ARG A 198 " pdb=" CD ARG A 198 " pdb=" NE ARG A 198 " pdb=" CZ ARG A 198 " ideal model delta sinusoidal sigma weight residual 180.00 135.44 44.56 2 1.50e+01 4.44e-03 1.05e+01 dihedral pdb=" CG ARG B 198 " pdb=" CD ARG B 198 " pdb=" NE ARG B 198 " pdb=" CZ ARG B 198 " ideal model delta sinusoidal sigma weight residual 180.00 135.49 44.51 2 1.50e+01 4.44e-03 1.05e+01 dihedral pdb=" N MET A 84 " pdb=" CA MET A 84 " pdb=" CB MET A 84 " pdb=" CG MET A 84 " ideal model delta sinusoidal sigma weight residual -60.00 -113.00 53.00 3 1.50e+01 4.44e-03 9.17e+00 ... (remaining 1785 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 354 0.045 - 0.090: 99 0.090 - 0.134: 30 0.134 - 0.179: 1 0.179 - 0.224: 2 Chirality restraints: 486 Sorted by residual: chirality pdb=" CA ILE A 118 " pdb=" N ILE A 118 " pdb=" C ILE A 118 " pdb=" CB ILE A 118 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CA ILE B 118 " pdb=" N ILE B 118 " pdb=" C ILE B 118 " pdb=" CB ILE B 118 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA VAL A 143 " pdb=" N VAL A 143 " pdb=" C VAL A 143 " pdb=" CB VAL A 143 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.75e-01 ... (remaining 483 not shown) Planarity restraints: 512 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 31 " 0.025 2.00e-02 2.50e+03 1.49e-02 5.55e+00 pdb=" CG TRP A 31 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 TRP A 31 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TRP A 31 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP A 31 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 31 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 31 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 31 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 31 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 31 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 31 " -0.025 2.00e-02 2.50e+03 1.48e-02 5.44e+00 pdb=" CG TRP B 31 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TRP B 31 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TRP B 31 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP B 31 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 31 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 31 " 0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 31 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 31 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP B 31 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 193 " -0.012 2.00e-02 2.50e+03 1.35e-02 3.19e+00 pdb=" CG PHE A 193 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 PHE A 193 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE A 193 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE A 193 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 193 " -0.015 2.00e-02 2.50e+03 pdb=" CZ PHE A 193 " 0.005 2.00e-02 2.50e+03 ... (remaining 509 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 1035 2.86 - 3.37: 2693 3.37 - 3.88: 4899 3.88 - 4.39: 5175 4.39 - 4.90: 8964 Nonbonded interactions: 22766 Sorted by model distance: nonbonded pdb=" O PRO A 132 " pdb=" NE2 HIS A 154 " model vdw 2.347 3.120 nonbonded pdb=" O PRO B 132 " pdb=" NE2 HIS B 154 " model vdw 2.348 3.120 nonbonded pdb=" O VAL A 187 " pdb=" OG SER A 191 " model vdw 2.395 3.040 nonbonded pdb=" O VAL B 187 " pdb=" OG SER B 191 " model vdw 2.395 3.040 nonbonded pdb=" N GLU B 137 " pdb=" OE1 GLU B 137 " model vdw 2.407 3.120 ... (remaining 22761 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' } 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: 0.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 12.150 Find NCS groups from input model: 0.070 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: 0.000 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: 16.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6845 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 0.035 3126 Z= 0.214 Angle : 0.691 8.040 4254 Z= 0.364 Chirality : 0.047 0.224 486 Planarity : 0.005 0.043 512 Dihedral : 14.365 65.043 1088 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 0.00 % Allowed : 20.25 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.43), residues: 372 helix: 0.55 (0.41), residues: 164 sheet: -0.63 (0.60), residues: 78 loop : -2.38 (0.48), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 31 HIS 0.001 0.000 HIS B 125 PHE 0.027 0.002 PHE A 193 TYR 0.007 0.001 TYR A 47 ARG 0.003 0.000 ARG B 158 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.319 Fit side-chains REVERT: A 166 LYS cc_start: 0.7853 (tptp) cc_final: 0.7258 (mmpt) REVERT: B 166 LYS cc_start: 0.7666 (tptp) cc_final: 0.7067 (mmpt) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.1105 time to fit residues: 7.6332 Evaluate side-chains 49 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 30 optimal weight: 0.3980 chunk 27 optimal weight: 0.8980 chunk 15 optimal weight: 0.4980 chunk 9 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 32 optimal weight: 0.4980 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 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6936 moved from start: 0.1144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3126 Z= 0.201 Angle : 0.533 6.627 4254 Z= 0.276 Chirality : 0.043 0.185 486 Planarity : 0.004 0.033 512 Dihedral : 3.605 11.700 420 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.27 % Allowed : 21.84 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.43), residues: 372 helix: 0.86 (0.41), residues: 166 sheet: -0.85 (0.58), residues: 78 loop : -2.28 (0.49), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 31 HIS 0.003 0.001 HIS B 154 PHE 0.016 0.002 PHE B 193 TYR 0.007 0.001 TYR B 196 ARG 0.002 0.000 ARG A 200 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 53 time to evaluate : 0.315 Fit side-chains revert: symmetry clash REVERT: A 166 LYS cc_start: 0.7783 (tptp) cc_final: 0.7228 (mmpt) REVERT: B 77 THR cc_start: 0.7573 (p) cc_final: 0.7259 (t) REVERT: B 166 LYS cc_start: 0.7682 (tptp) cc_final: 0.7101 (mmpt) outliers start: 4 outliers final: 4 residues processed: 53 average time/residue: 0.1043 time to fit residues: 7.3307 Evaluate side-chains 56 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 52 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 109 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 18 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 32 optimal weight: 0.0020 chunk 35 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 24 optimal weight: 5.9990 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6983 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 3126 Z= 0.206 Angle : 0.526 5.723 4254 Z= 0.270 Chirality : 0.043 0.168 486 Planarity : 0.004 0.033 512 Dihedral : 3.495 11.507 420 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.22 % Allowed : 20.25 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.43), residues: 372 helix: 1.05 (0.40), residues: 166 sheet: -1.00 (0.57), residues: 78 loop : -2.31 (0.49), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 31 HIS 0.002 0.001 HIS A 154 PHE 0.012 0.002 PHE A 193 TYR 0.006 0.001 TYR A 196 ARG 0.001 0.000 ARG A 200 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 51 time to evaluate : 0.331 Fit side-chains revert: symmetry clash REVERT: A 77 THR cc_start: 0.7810 (p) cc_final: 0.7547 (t) REVERT: A 166 LYS cc_start: 0.7797 (tptp) cc_final: 0.7268 (mmpt) REVERT: B 166 LYS cc_start: 0.7729 (tptp) cc_final: 0.7182 (mmpt) outliers start: 7 outliers final: 4 residues processed: 53 average time/residue: 0.1113 time to fit residues: 7.8377 Evaluate side-chains 53 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 PHE Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 108 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 16 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 34 optimal weight: 3.9990 chunk 17 optimal weight: 0.5980 chunk 31 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7039 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 3126 Z= 0.238 Angle : 0.538 5.964 4254 Z= 0.277 Chirality : 0.043 0.162 486 Planarity : 0.004 0.031 512 Dihedral : 3.519 10.427 420 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 3.16 % Allowed : 19.30 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.42), residues: 372 helix: 1.12 (0.40), residues: 166 sheet: -1.14 (0.56), residues: 78 loop : -2.34 (0.48), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 58 HIS 0.002 0.001 HIS A 154 PHE 0.013 0.002 PHE A 193 TYR 0.008 0.001 TYR B 95 ARG 0.001 0.000 ARG A 200 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 52 time to evaluate : 0.306 Fit side-chains revert: symmetry clash REVERT: A 166 LYS cc_start: 0.7825 (tptp) cc_final: 0.7314 (mmpt) REVERT: B 166 LYS cc_start: 0.7719 (tptp) cc_final: 0.7220 (mmpt) outliers start: 10 outliers final: 6 residues processed: 56 average time/residue: 0.1308 time to fit residues: 9.6965 Evaluate side-chains 56 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain B residue 96 PHE Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 109 MET Chi-restraints excluded: chain B residue 145 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 0 optimal weight: 5.9990 chunk 25 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 6 optimal weight: 9.9990 chunk 20 optimal weight: 5.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 3126 Z= 0.286 Angle : 0.562 5.648 4254 Z= 0.289 Chirality : 0.044 0.160 486 Planarity : 0.004 0.031 512 Dihedral : 3.631 10.360 420 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 4.43 % Allowed : 19.62 % Favored : 75.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.42), residues: 372 helix: 1.31 (0.41), residues: 164 sheet: -1.31 (0.54), residues: 78 loop : -2.45 (0.47), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 58 HIS 0.003 0.001 HIS A 154 PHE 0.014 0.002 PHE A 193 TYR 0.010 0.002 TYR B 179 ARG 0.002 0.000 ARG B 200 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 46 time to evaluate : 0.344 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 7 residues processed: 54 average time/residue: 0.0897 time to fit residues: 6.7429 Evaluate side-chains 53 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 46 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain B residue 96 PHE Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 109 MET Chi-restraints excluded: chain B residue 145 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 8 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 28 optimal weight: 0.5980 chunk 16 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 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 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 3126 Z= 0.226 Angle : 0.525 5.091 4254 Z= 0.272 Chirality : 0.043 0.150 486 Planarity : 0.004 0.030 512 Dihedral : 3.521 10.158 420 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.80 % Allowed : 19.62 % Favored : 76.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.43), residues: 372 helix: 1.31 (0.41), residues: 168 sheet: -1.12 (0.56), residues: 78 loop : -2.32 (0.48), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 58 HIS 0.002 0.001 HIS B 154 PHE 0.019 0.002 PHE A 193 TYR 0.007 0.001 TYR B 179 ARG 0.001 0.000 ARG A 200 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 45 time to evaluate : 0.351 Fit side-chains revert: symmetry clash REVERT: B 84 MET cc_start: 0.5444 (OUTLIER) cc_final: 0.5205 (ttt) outliers start: 12 outliers final: 10 residues processed: 52 average time/residue: 0.0869 time to fit residues: 6.2834 Evaluate side-chains 56 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 45 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 PHE Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 96 PHE Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 109 MET Chi-restraints excluded: chain B residue 120 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 19 optimal weight: 1.9990 chunk 29 optimal weight: 0.0970 chunk 34 optimal weight: 0.1980 chunk 21 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 6 optimal weight: 8.9990 chunk 22 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7049 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 3126 Z= 0.200 Angle : 0.525 6.834 4254 Z= 0.270 Chirality : 0.042 0.144 486 Planarity : 0.004 0.031 512 Dihedral : 3.420 10.246 420 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 4.43 % Allowed : 19.30 % Favored : 76.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.44), residues: 372 helix: 1.39 (0.41), residues: 168 sheet: -1.03 (0.57), residues: 78 loop : -2.27 (0.49), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 58 HIS 0.002 0.001 HIS B 154 PHE 0.017 0.002 PHE A 193 TYR 0.007 0.001 TYR A 95 ARG 0.001 0.000 ARG B 200 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 47 time to evaluate : 0.322 Fit side-chains revert: symmetry clash REVERT: A 166 LYS cc_start: 0.7809 (tptp) cc_final: 0.7342 (mmpt) REVERT: B 84 MET cc_start: 0.5384 (OUTLIER) cc_final: 0.5160 (ttt) outliers start: 14 outliers final: 11 residues processed: 55 average time/residue: 0.0965 time to fit residues: 7.2006 Evaluate side-chains 58 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 46 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 96 PHE Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 96 PHE Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 109 MET Chi-restraints excluded: chain B residue 120 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 17 optimal weight: 0.2980 chunk 3 optimal weight: 0.7980 chunk 27 optimal weight: 0.1980 chunk 31 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 32 optimal weight: 0.0070 chunk 19 optimal weight: 3.9990 chunk 14 optimal weight: 0.1980 chunk 25 optimal weight: 0.3980 chunk 9 optimal weight: 0.4980 overall best weight: 0.2198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6977 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 3126 Z= 0.141 Angle : 0.509 7.315 4254 Z= 0.259 Chirality : 0.041 0.138 486 Planarity : 0.004 0.031 512 Dihedral : 3.293 10.499 420 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.80 % Allowed : 20.25 % Favored : 75.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.45), residues: 372 helix: 1.89 (0.41), residues: 156 sheet: -0.85 (0.59), residues: 78 loop : -1.71 (0.53), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 58 HIS 0.001 0.000 HIS B 154 PHE 0.013 0.001 PHE A 193 TYR 0.004 0.001 TYR A 95 ARG 0.001 0.000 ARG B 150 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 48 time to evaluate : 0.338 Fit side-chains revert: symmetry clash REVERT: A 166 LYS cc_start: 0.7733 (tptp) cc_final: 0.7265 (mmpt) REVERT: B 84 MET cc_start: 0.5412 (OUTLIER) cc_final: 0.5201 (ttt) REVERT: B 166 LYS cc_start: 0.7719 (tptp) cc_final: 0.7251 (mmpt) outliers start: 12 outliers final: 9 residues processed: 54 average time/residue: 0.1029 time to fit residues: 7.4076 Evaluate side-chains 57 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 96 PHE Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 96 PHE Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 109 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 29 optimal weight: 1.9990 chunk 30 optimal weight: 0.0030 chunk 32 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 34 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7029 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 3126 Z= 0.197 Angle : 0.567 7.128 4254 Z= 0.278 Chirality : 0.042 0.141 486 Planarity : 0.004 0.031 512 Dihedral : 3.334 9.964 420 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 4.11 % Allowed : 20.57 % Favored : 75.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.45), residues: 372 helix: 1.96 (0.42), residues: 156 sheet: -0.91 (0.58), residues: 78 loop : -1.75 (0.52), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 58 HIS 0.001 0.001 HIS B 154 PHE 0.013 0.001 PHE A 193 TYR 0.006 0.001 TYR A 95 ARG 0.001 0.000 ARG A 200 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 49 time to evaluate : 0.343 Fit side-chains revert: symmetry clash REVERT: A 166 LYS cc_start: 0.7760 (tptp) cc_final: 0.7304 (mmpt) REVERT: B 166 LYS cc_start: 0.7733 (tptp) cc_final: 0.7284 (mmpt) outliers start: 13 outliers final: 12 residues processed: 56 average time/residue: 0.1076 time to fit residues: 8.0139 Evaluate side-chains 60 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 48 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 96 PHE Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain A residue 113 ASN Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain B residue 96 PHE Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 109 MET Chi-restraints excluded: chain B residue 120 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 2 optimal weight: 6.9990 chunk 22 optimal weight: 0.7980 chunk 17 optimal weight: 0.3980 chunk 30 optimal weight: 0.3980 chunk 8 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7030 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 3126 Z= 0.200 Angle : 0.575 7.144 4254 Z= 0.282 Chirality : 0.042 0.143 486 Planarity : 0.004 0.033 512 Dihedral : 3.329 9.892 420 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 4.11 % Allowed : 21.20 % Favored : 74.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.45), residues: 372 helix: 1.84 (0.41), residues: 158 sheet: -0.91 (0.58), residues: 78 loop : -1.73 (0.53), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 31 HIS 0.002 0.001 HIS B 154 PHE 0.013 0.001 PHE A 193 TYR 0.005 0.001 TYR B 47 ARG 0.001 0.000 ARG A 200 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 47 time to evaluate : 0.326 Fit side-chains revert: symmetry clash REVERT: A 166 LYS cc_start: 0.7754 (tptp) cc_final: 0.7310 (mmpt) REVERT: B 166 LYS cc_start: 0.7725 (tptp) cc_final: 0.7283 (mmpt) outliers start: 13 outliers final: 12 residues processed: 54 average time/residue: 0.1003 time to fit residues: 7.2007 Evaluate side-chains 59 residues out of total 316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 47 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 96 PHE Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain A residue 113 ASN Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain B residue 96 PHE Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 109 MET Chi-restraints excluded: chain B residue 120 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 3 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 20 optimal weight: 8.9990 chunk 32 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.213613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.175839 restraints weight = 3721.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.179733 restraints weight = 2567.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.182265 restraints weight = 2002.395| |-----------------------------------------------------------------------------| r_work (final): 0.4173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7065 moved from start: 0.3016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 3126 Z= 0.237 Angle : 0.630 9.430 4254 Z= 0.304 Chirality : 0.043 0.147 486 Planarity : 0.004 0.036 512 Dihedral : 3.390 9.921 420 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.48 % Allowed : 22.15 % Favored : 74.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.44), residues: 372 helix: 1.74 (0.41), residues: 158 sheet: -1.00 (0.57), residues: 78 loop : -1.77 (0.52), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 31 HIS 0.002 0.001 HIS B 154 PHE 0.014 0.002 PHE A 193 TYR 0.007 0.001 TYR A 179 ARG 0.001 0.000 ARG A 200 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1070.96 seconds wall clock time: 20 minutes 20.71 seconds (1220.71 seconds total)