Starting phenix.real_space_refine on Thu Mar 6 01:05:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uc3_42114/03_2025/8uc3_42114.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uc3_42114/03_2025/8uc3_42114.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8uc3_42114/03_2025/8uc3_42114.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uc3_42114/03_2025/8uc3_42114.map" model { file = "/net/cci-nas-00/data/ceres_data/8uc3_42114/03_2025/8uc3_42114.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uc3_42114/03_2025/8uc3_42114.cif" } resolution = 2.78 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= 0.039 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 28 5.16 5 C 2700 2.51 5 N 766 2.21 5 O 808 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 4304 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1365 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 13, 'TRANS': 166} Chain: "C" Number of atoms: 756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 756 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 6, 'TRANS': 91} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'FMN': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: D, B Time building chain proxies: 3.89, per 1000 atoms: 0.90 Number of scatterers: 4304 At special positions: 0 Unit cell: (84.87, 75.5343, 78.9291, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 28 16.00 P 2 15.00 O 808 8.00 N 766 7.00 C 2700 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.29 Conformation dependent library (CDL) restraints added in 519.0 milliseconds 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1044 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 2 sheets defined 58.3% alpha, 8.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 16 through 24 Processing helix chain 'A' and resid 36 through 48 Processing helix chain 'A' and resid 52 through 56 Processing helix chain 'A' and resid 66 through 76 removed outlier: 3.801A pdb=" N ARG A 71 " --> pdb=" O PRO A 67 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N PHE A 76 " --> pdb=" O ARG A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 97 No H-bonds generated for 'chain 'A' and resid 95 through 97' Processing helix chain 'A' and resid 101 through 130 removed outlier: 3.733A pdb=" N THR A 111 " --> pdb=" O LYS A 107 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER A 112 " --> pdb=" O ILE A 108 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS A 113 " --> pdb=" O TYR A 109 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N MET A 118 " --> pdb=" O LEU A 114 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA A 119 " --> pdb=" O CYS A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 150 removed outlier: 3.503A pdb=" N VAL A 145 " --> pdb=" O ARG A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 181 removed outlier: 3.855A pdb=" N VAL A 181 " --> pdb=" O ALA A 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 177 through 181' Processing helix chain 'D' and resid 9 through 29 Processing helix chain 'D' and resid 37 through 55 removed outlier: 3.505A pdb=" N GLU D 55 " --> pdb=" O GLN D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 76 removed outlier: 3.732A pdb=" N ARG D 67 " --> pdb=" O LEU D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 99 Processing helix chain 'D' and resid 100 through 103 Processing helix chain 'C' and resid 9 through 29 Processing helix chain 'C' and resid 37 through 55 removed outlier: 3.505A pdb=" N GLU C 55 " --> pdb=" O GLN C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 76 removed outlier: 3.733A pdb=" N ARG C 67 " --> pdb=" O LEU C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 99 Processing helix chain 'C' and resid 100 through 103 Processing helix chain 'B' and resid 16 through 24 Processing helix chain 'B' and resid 36 through 48 Processing helix chain 'B' and resid 52 through 56 Processing helix chain 'B' and resid 66 through 76 removed outlier: 3.801A pdb=" N ARG B 71 " --> pdb=" O PRO B 67 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N PHE B 76 " --> pdb=" O ARG B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 97 No H-bonds generated for 'chain 'B' and resid 95 through 97' Processing helix chain 'B' and resid 101 through 130 removed outlier: 3.733A pdb=" N THR B 111 " --> pdb=" O LYS B 107 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N SER B 112 " --> pdb=" O ILE B 108 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS B 113 " --> pdb=" O TYR B 109 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N MET B 118 " --> pdb=" O LEU B 114 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA B 119 " --> pdb=" O CYS B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 150 removed outlier: 3.504A pdb=" N VAL B 145 " --> pdb=" O ARG B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 181 removed outlier: 3.855A pdb=" N VAL B 181 " --> pdb=" O ALA B 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 177 through 181' Processing sheet with id=AA1, first strand: chain 'A' and resid 133 through 134 removed outlier: 6.078A pdb=" N VAL A 92 " --> pdb=" O PRO A 157 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 182 through 184 removed outlier: 6.903A pdb=" N ASN A 183 " --> pdb=" O VAL B 63 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N VAL B 92 " --> pdb=" O PRO B 157 " (cutoff:3.500A) 234 hydrogen bonds defined for protein. 672 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: 1.02 Time building geometry restraints manager: 1.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1176 1.33 - 1.45: 646 1.45 - 1.57: 2514 1.57 - 1.69: 2 1.69 - 1.81: 46 Bond restraints: 4384 Sorted by residual: bond pdb=" N VAL B 182 " pdb=" CA VAL B 182 " ideal model delta sigma weight residual 1.458 1.500 -0.041 1.19e-02 7.06e+03 1.21e+01 bond pdb=" N VAL A 182 " pdb=" CA VAL A 182 " ideal model delta sigma weight residual 1.458 1.499 -0.041 1.19e-02 7.06e+03 1.20e+01 bond pdb=" N THR B 23 " pdb=" CA THR B 23 " ideal model delta sigma weight residual 1.458 1.499 -0.041 1.33e-02 5.65e+03 9.73e+00 bond pdb=" N THR A 23 " pdb=" CA THR A 23 " ideal model delta sigma weight residual 1.458 1.499 -0.041 1.33e-02 5.65e+03 9.64e+00 bond pdb=" N ARG B 24 " pdb=" CA ARG B 24 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.30e-02 5.92e+03 8.57e+00 ... (remaining 4379 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.54: 5543 1.54 - 3.07: 360 3.07 - 4.61: 49 4.61 - 6.15: 14 6.15 - 7.68: 4 Bond angle restraints: 5970 Sorted by residual: angle pdb=" N THR B 23 " pdb=" CA THR B 23 " pdb=" C THR B 23 " ideal model delta sigma weight residual 112.54 118.53 -5.99 1.22e+00 6.72e-01 2.41e+01 angle pdb=" N THR A 23 " pdb=" CA THR A 23 " pdb=" C THR A 23 " ideal model delta sigma weight residual 112.54 118.49 -5.95 1.22e+00 6.72e-01 2.38e+01 angle pdb=" N ARG B 66 " pdb=" CA ARG B 66 " pdb=" C ARG B 66 " ideal model delta sigma weight residual 109.64 103.67 5.97 1.27e+00 6.20e-01 2.21e+01 angle pdb=" N ARG A 66 " pdb=" CA ARG A 66 " pdb=" C ARG A 66 " ideal model delta sigma weight residual 109.64 103.68 5.96 1.27e+00 6.20e-01 2.20e+01 angle pdb=" CA GLU A 180 " pdb=" C GLU A 180 " pdb=" O GLU A 180 " ideal model delta sigma weight residual 120.55 116.93 3.62 1.06e+00 8.90e-01 1.17e+01 ... (remaining 5965 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.90: 2345 16.90 - 33.79: 223 33.79 - 50.69: 96 50.69 - 67.58: 12 67.58 - 84.48: 8 Dihedral angle restraints: 2684 sinusoidal: 1076 harmonic: 1608 Sorted by residual: dihedral pdb=" CG ARG A 74 " pdb=" CD ARG A 74 " pdb=" NE ARG A 74 " pdb=" CZ ARG A 74 " ideal model delta sinusoidal sigma weight residual -180.00 -135.17 -44.83 2 1.50e+01 4.44e-03 1.06e+01 dihedral pdb=" CG ARG B 74 " pdb=" CD ARG B 74 " pdb=" NE ARG B 74 " pdb=" CZ ARG B 74 " ideal model delta sinusoidal sigma weight residual 180.00 -135.19 -44.81 2 1.50e+01 4.44e-03 1.06e+01 dihedral pdb=" CA ARG A 56 " pdb=" CB ARG A 56 " pdb=" CG ARG A 56 " pdb=" CD ARG A 56 " ideal model delta sinusoidal sigma weight residual -180.00 -125.98 -54.02 3 1.50e+01 4.44e-03 9.25e+00 ... (remaining 2681 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 534 0.050 - 0.100: 107 0.100 - 0.149: 45 0.149 - 0.199: 0 0.199 - 0.249: 2 Chirality restraints: 688 Sorted by residual: chirality pdb=" CA VAL A 64 " pdb=" N VAL A 64 " pdb=" C VAL A 64 " pdb=" CB VAL A 64 " both_signs ideal model delta sigma weight residual False 2.44 2.69 -0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CA VAL B 64 " pdb=" N VAL B 64 " pdb=" C VAL B 64 " pdb=" CB VAL B 64 " both_signs ideal model delta sigma weight residual False 2.44 2.69 -0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CG LEU A 100 " pdb=" CB LEU A 100 " pdb=" CD1 LEU A 100 " pdb=" CD2 LEU A 100 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.50e-01 ... (remaining 685 not shown) Planarity restraints: 772 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 179 " -0.019 2.00e-02 2.50e+03 3.73e-02 1.39e+01 pdb=" C ASN A 179 " 0.064 2.00e-02 2.50e+03 pdb=" O ASN A 179 " -0.024 2.00e-02 2.50e+03 pdb=" N GLU A 180 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 179 " 0.018 2.00e-02 2.50e+03 3.71e-02 1.37e+01 pdb=" C ASN B 179 " -0.064 2.00e-02 2.50e+03 pdb=" O ASN B 179 " 0.024 2.00e-02 2.50e+03 pdb=" N GLU B 180 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 161 " 0.036 5.00e-02 4.00e+02 5.44e-02 4.74e+00 pdb=" N PRO B 162 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO B 162 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 162 " 0.030 5.00e-02 4.00e+02 ... (remaining 769 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 74 2.67 - 3.23: 4019 3.23 - 3.79: 6215 3.79 - 4.34: 8917 4.34 - 4.90: 14548 Nonbonded interactions: 33773 Sorted by model distance: nonbonded pdb=" OE2 GLU D 32 " pdb=" NH2 ARG B 141 " model vdw 2.115 3.120 nonbonded pdb=" OD1 ASP C 44 " pdb=" NH1 ARG C 47 " model vdw 2.321 3.120 nonbonded pdb=" OD1 ASP D 44 " pdb=" NH1 ARG D 47 " model vdw 2.321 3.120 nonbonded pdb=" NH2 ARG C 62 " pdb=" OE2 GLU C 101 " model vdw 2.343 3.120 nonbonded pdb=" NH2 ARG D 62 " pdb=" OE2 GLU D 101 " model vdw 2.343 3.120 ... (remaining 33768 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: 0.02 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.320 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 15.650 Find NCS groups from input model: 0.090 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:13.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6948 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 : 0.005 0.041 4384 Z= 0.302 Angle : 0.848 7.683 5970 Z= 0.548 Chirality : 0.049 0.249 688 Planarity : 0.006 0.054 772 Dihedral : 16.433 84.478 1640 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.78 % Allowed : 22.67 % Favored : 75.56 % 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: 0.37 (0.36), residues: 548 helix: 0.58 (0.32), residues: 272 sheet: 2.34 (0.74), residues: 44 loop : -0.48 (0.42), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 187 HIS 0.002 0.001 HIS B 154 PHE 0.005 0.001 PHE B 86 TYR 0.009 0.001 TYR B 109 ARG 0.004 0.001 ARG C 69 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 83 time to evaluate : 0.440 Fit side-chains REVERT: C 62 ARG cc_start: 0.6692 (ttm170) cc_final: 0.6217 (mtp180) REVERT: C 94 GLN cc_start: 0.7342 (mt0) cc_final: 0.7056 (mt0) REVERT: B 118 MET cc_start: 0.7280 (mtt) cc_final: 0.6907 (mtt) outliers start: 8 outliers final: 2 residues processed: 89 average time/residue: 1.2414 time to fit residues: 114.1959 Evaluate side-chains 70 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 68 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 183 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 49 optimal weight: 0.0030 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 183 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.190991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.152328 restraints weight = 4822.286| |-----------------------------------------------------------------------------| r_work (start): 0.3891 rms_B_bonded: 2.07 r_work: 0.3806 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3692 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4384 Z= 0.212 Angle : 0.615 6.527 5970 Z= 0.321 Chirality : 0.042 0.139 688 Planarity : 0.006 0.053 772 Dihedral : 6.757 56.445 629 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 6.00 % Allowed : 20.44 % Favored : 73.56 % 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: 1.00 (0.37), residues: 548 helix: 1.17 (0.31), residues: 294 sheet: 2.05 (0.75), residues: 54 loop : -0.41 (0.46), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 18 HIS 0.003 0.001 HIS A 154 PHE 0.006 0.001 PHE A 86 TYR 0.012 0.002 TYR D 22 ARG 0.003 0.001 ARG C 62 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 66 time to evaluate : 0.478 Fit side-chains REVERT: A 22 LYS cc_start: 0.6488 (mtmt) cc_final: 0.6286 (mptt) REVERT: D 33 GLU cc_start: 0.8249 (mt-10) cc_final: 0.7940 (mt-10) REVERT: C 40 TYR cc_start: 0.7192 (m-80) cc_final: 0.6975 (m-80) REVERT: C 97 ASP cc_start: 0.7297 (m-30) cc_final: 0.6719 (t0) REVERT: B 108 ILE cc_start: 0.7886 (pt) cc_final: 0.7657 (pp) REVERT: B 174 GLN cc_start: 0.7252 (tp40) cc_final: 0.7030 (tp40) outliers start: 27 outliers final: 11 residues processed: 80 average time/residue: 1.0803 time to fit residues: 90.1768 Evaluate side-chains 74 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 183 ASN Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 173 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 17 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 4 optimal weight: 0.6980 chunk 8 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 183 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.182866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.142321 restraints weight = 4691.218| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 2.08 r_work: 0.3664 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3546 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4384 Z= 0.245 Angle : 0.621 11.149 5970 Z= 0.314 Chirality : 0.042 0.139 688 Planarity : 0.006 0.056 772 Dihedral : 6.520 57.242 629 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 4.67 % Allowed : 20.22 % Favored : 75.11 % 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: 1.23 (0.37), residues: 548 helix: 1.52 (0.30), residues: 288 sheet: 2.05 (0.77), residues: 54 loop : -0.50 (0.45), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 18 HIS 0.003 0.001 HIS A 128 PHE 0.009 0.001 PHE A 86 TYR 0.013 0.002 TYR D 22 ARG 0.003 0.000 ARG A 28 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 68 time to evaluate : 0.441 Fit side-chains REVERT: A 22 LYS cc_start: 0.6415 (mtmt) cc_final: 0.6143 (mttp) REVERT: A 56 ARG cc_start: 0.6599 (mtt180) cc_final: 0.6355 (mtm-85) REVERT: D 33 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7872 (mt-10) REVERT: C 40 TYR cc_start: 0.6995 (m-80) cc_final: 0.6617 (m-80) REVERT: B 174 GLN cc_start: 0.7330 (tp40) cc_final: 0.7073 (tp40) outliers start: 21 outliers final: 10 residues processed: 79 average time/residue: 1.5585 time to fit residues: 127.3815 Evaluate side-chains 74 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 183 ASN Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 173 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 2 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.181160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.140125 restraints weight = 4761.822| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 2.10 r_work: 0.3636 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3519 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.3143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4384 Z= 0.265 Angle : 0.630 6.677 5970 Z= 0.320 Chirality : 0.043 0.141 688 Planarity : 0.006 0.060 772 Dihedral : 6.454 53.124 628 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 5.78 % Allowed : 18.89 % Favored : 75.33 % 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: 1.13 (0.37), residues: 548 helix: 1.47 (0.30), residues: 284 sheet: 1.79 (0.77), residues: 54 loop : -0.49 (0.45), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 18 HIS 0.002 0.001 HIS A 128 PHE 0.009 0.001 PHE A 86 TYR 0.012 0.002 TYR C 22 ARG 0.009 0.001 ARG A 165 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 64 time to evaluate : 0.583 Fit side-chains REVERT: A 22 LYS cc_start: 0.6254 (mtmt) cc_final: 0.6042 (mtmm) REVERT: A 56 ARG cc_start: 0.6667 (mtt180) cc_final: 0.6375 (mtm-85) REVERT: A 62 MET cc_start: 0.8155 (OUTLIER) cc_final: 0.7752 (ttp) REVERT: A 109 TYR cc_start: 0.7768 (t80) cc_final: 0.7507 (t80) REVERT: A 147 SER cc_start: 0.7203 (t) cc_final: 0.6837 (p) REVERT: A 156 GLU cc_start: 0.7457 (tt0) cc_final: 0.7189 (pt0) REVERT: D 33 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7680 (mt-10) REVERT: C 40 TYR cc_start: 0.7011 (m-80) cc_final: 0.6243 (m-80) REVERT: B 170 LEU cc_start: 0.8088 (OUTLIER) cc_final: 0.7705 (mt) REVERT: B 174 GLN cc_start: 0.7361 (tp40) cc_final: 0.5789 (pm20) outliers start: 26 outliers final: 13 residues processed: 75 average time/residue: 1.5648 time to fit residues: 121.5493 Evaluate side-chains 80 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 64 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 91 CYS Chi-restraints excluded: chain A residue 183 ASN Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 87 ILE Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 91 CYS Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 173 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 25 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 53 optimal weight: 0.0070 chunk 6 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.184230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.143375 restraints weight = 4793.472| |-----------------------------------------------------------------------------| r_work (start): 0.3781 rms_B_bonded: 2.12 r_work: 0.3680 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3563 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 moved from start: 0.3340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4384 Z= 0.187 Angle : 0.551 5.823 5970 Z= 0.282 Chirality : 0.040 0.133 688 Planarity : 0.006 0.059 772 Dihedral : 5.999 49.412 628 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 4.00 % Allowed : 20.00 % Favored : 76.00 % 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: 1.52 (0.38), residues: 548 helix: 1.70 (0.30), residues: 292 sheet: 1.78 (0.78), residues: 54 loop : -0.19 (0.48), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 18 HIS 0.003 0.001 HIS A 154 PHE 0.009 0.001 PHE A 86 TYR 0.008 0.001 TYR D 22 ARG 0.015 0.000 ARG A 165 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 68 time to evaluate : 0.460 Fit side-chains REVERT: A 18 TRP cc_start: 0.6048 (OUTLIER) cc_final: 0.5488 (m-90) REVERT: A 22 LYS cc_start: 0.6204 (mtmt) cc_final: 0.5894 (mttt) REVERT: A 56 ARG cc_start: 0.6680 (mtt180) cc_final: 0.6403 (mtm-85) REVERT: A 62 MET cc_start: 0.8075 (OUTLIER) cc_final: 0.7718 (ttp) REVERT: A 147 SER cc_start: 0.7179 (t) cc_final: 0.6823 (p) REVERT: D 33 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7729 (mt-10) REVERT: C 40 TYR cc_start: 0.6909 (m-80) cc_final: 0.6201 (m-80) REVERT: B 45 GLU cc_start: 0.7439 (OUTLIER) cc_final: 0.7189 (tt0) REVERT: B 174 GLN cc_start: 0.7397 (tp40) cc_final: 0.5821 (pm20) outliers start: 18 outliers final: 9 residues processed: 77 average time/residue: 1.2529 time to fit residues: 99.9564 Evaluate side-chains 75 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 TRP Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 91 CYS Chi-restraints excluded: chain A residue 183 ASN Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 173 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 47 optimal weight: 1.9990 chunk 52 optimal weight: 0.0870 chunk 23 optimal weight: 9.9990 chunk 11 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 35 optimal weight: 0.8980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.178106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.136779 restraints weight = 4788.283| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 2.22 r_work: 0.3568 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3450 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7028 moved from start: 0.3481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4384 Z= 0.197 Angle : 0.559 6.066 5970 Z= 0.285 Chirality : 0.040 0.137 688 Planarity : 0.006 0.068 772 Dihedral : 5.877 49.510 628 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 4.22 % Allowed : 20.00 % Favored : 75.78 % 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: 1.57 (0.37), residues: 548 helix: 1.80 (0.30), residues: 290 sheet: 1.84 (0.78), residues: 52 loop : -0.23 (0.48), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 18 HIS 0.003 0.001 HIS A 154 PHE 0.010 0.001 PHE A 86 TYR 0.009 0.001 TYR D 22 ARG 0.016 0.001 ARG A 165 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 61 time to evaluate : 0.650 Fit side-chains REVERT: A 18 TRP cc_start: 0.5897 (OUTLIER) cc_final: 0.5379 (m-90) REVERT: A 22 LYS cc_start: 0.5960 (mtmt) cc_final: 0.5567 (mttt) REVERT: A 56 ARG cc_start: 0.6527 (mmt180) cc_final: 0.6210 (mtm-85) REVERT: A 62 MET cc_start: 0.7903 (OUTLIER) cc_final: 0.7579 (ttp) REVERT: A 147 SER cc_start: 0.6988 (t) cc_final: 0.6642 (p) REVERT: D 33 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.7650 (mt-10) REVERT: C 40 TYR cc_start: 0.6731 (m-80) cc_final: 0.5978 (m-80) REVERT: B 45 GLU cc_start: 0.7112 (OUTLIER) cc_final: 0.6857 (tt0) REVERT: B 174 GLN cc_start: 0.7364 (tp40) cc_final: 0.5818 (pm20) outliers start: 19 outliers final: 12 residues processed: 73 average time/residue: 1.3301 time to fit residues: 100.5099 Evaluate side-chains 77 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 61 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 TRP Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 91 CYS Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 183 ASN Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 91 CYS Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 173 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 12 optimal weight: 0.7980 chunk 32 optimal weight: 7.9990 chunk 47 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 chunk 46 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 39 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.175409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.132767 restraints weight = 4810.859| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 2.28 r_work: 0.3452 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3329 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6969 moved from start: 0.3573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4384 Z= 0.205 Angle : 0.567 6.192 5970 Z= 0.289 Chirality : 0.040 0.137 688 Planarity : 0.006 0.074 772 Dihedral : 5.721 49.499 628 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 4.44 % Allowed : 20.67 % Favored : 74.89 % 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: 1.57 (0.37), residues: 548 helix: 1.82 (0.30), residues: 290 sheet: 1.72 (0.78), residues: 52 loop : -0.23 (0.48), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 18 HIS 0.003 0.001 HIS A 154 PHE 0.010 0.001 PHE A 86 TYR 0.010 0.001 TYR C 22 ARG 0.016 0.001 ARG A 165 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 65 time to evaluate : 0.494 Fit side-chains REVERT: A 18 TRP cc_start: 0.5806 (OUTLIER) cc_final: 0.5330 (m-90) REVERT: A 22 LYS cc_start: 0.5839 (mtmt) cc_final: 0.5457 (mttt) REVERT: A 56 ARG cc_start: 0.6554 (mmt180) cc_final: 0.6190 (mtm-85) REVERT: A 62 MET cc_start: 0.7854 (OUTLIER) cc_final: 0.7523 (ttp) REVERT: A 109 TYR cc_start: 0.7366 (t80) cc_final: 0.7123 (t80) REVERT: A 147 SER cc_start: 0.7005 (t) cc_final: 0.6667 (p) REVERT: D 33 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7569 (mt-10) REVERT: C 36 ASP cc_start: 0.8127 (t0) cc_final: 0.6660 (t0) REVERT: C 40 TYR cc_start: 0.6652 (m-80) cc_final: 0.5751 (m-80) REVERT: B 45 GLU cc_start: 0.6941 (OUTLIER) cc_final: 0.6704 (tt0) REVERT: B 174 GLN cc_start: 0.7380 (tp40) cc_final: 0.5721 (pm20) outliers start: 20 outliers final: 13 residues processed: 77 average time/residue: 1.3296 time to fit residues: 105.8988 Evaluate side-chains 79 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 62 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 TRP Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 91 CYS Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 91 CYS Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 173 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 50 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 chunk 38 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 23 optimal weight: 10.0000 chunk 35 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 GLN A 183 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.174821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.132447 restraints weight = 4706.227| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 2.26 r_work: 0.3449 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3325 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6985 moved from start: 0.3632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4384 Z= 0.218 Angle : 0.585 6.426 5970 Z= 0.298 Chirality : 0.041 0.140 688 Planarity : 0.006 0.081 772 Dihedral : 5.588 50.338 626 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 4.44 % Allowed : 20.67 % Favored : 74.89 % 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: 1.52 (0.37), residues: 548 helix: 1.84 (0.30), residues: 288 sheet: 1.41 (0.78), residues: 54 loop : -0.25 (0.48), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 18 HIS 0.002 0.001 HIS A 154 PHE 0.010 0.001 PHE A 86 TYR 0.009 0.001 TYR D 22 ARG 0.019 0.001 ARG A 165 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 62 time to evaluate : 0.483 Fit side-chains REVERT: A 18 TRP cc_start: 0.5826 (OUTLIER) cc_final: 0.5336 (m-90) REVERT: A 22 LYS cc_start: 0.5784 (mtmt) cc_final: 0.5435 (mttt) REVERT: A 56 ARG cc_start: 0.6551 (mmt180) cc_final: 0.6224 (mtm-85) REVERT: A 62 MET cc_start: 0.7864 (OUTLIER) cc_final: 0.7541 (ttp) REVERT: A 147 SER cc_start: 0.7026 (t) cc_final: 0.6689 (p) REVERT: D 33 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7584 (mt-10) REVERT: D 72 GLU cc_start: 0.7083 (tm-30) cc_final: 0.5852 (mt-10) REVERT: C 36 ASP cc_start: 0.8140 (t0) cc_final: 0.6717 (t0) REVERT: C 40 TYR cc_start: 0.6683 (m-80) cc_final: 0.5825 (m-80) REVERT: B 45 GLU cc_start: 0.6970 (OUTLIER) cc_final: 0.6763 (tt0) REVERT: B 174 GLN cc_start: 0.7440 (tp40) cc_final: 0.5757 (pm20) outliers start: 20 outliers final: 13 residues processed: 73 average time/residue: 1.3064 time to fit residues: 98.7764 Evaluate side-chains 80 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 63 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 TRP Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 91 CYS Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 91 CYS Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 173 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 21 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 45 optimal weight: 0.0980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.173571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.131269 restraints weight = 4817.753| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 2.27 r_work: 0.3426 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7012 moved from start: 0.3732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4384 Z= 0.241 Angle : 0.610 7.018 5970 Z= 0.311 Chirality : 0.041 0.143 688 Planarity : 0.006 0.086 772 Dihedral : 5.704 51.928 626 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 4.00 % Allowed : 20.67 % Favored : 75.33 % 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: 1.40 (0.37), residues: 548 helix: 1.72 (0.30), residues: 288 sheet: 1.41 (0.78), residues: 54 loop : -0.29 (0.48), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 18 HIS 0.002 0.001 HIS B 128 PHE 0.010 0.001 PHE A 86 TYR 0.009 0.002 TYR D 22 ARG 0.020 0.001 ARG A 165 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 65 time to evaluate : 0.484 Fit side-chains REVERT: A 18 TRP cc_start: 0.5877 (OUTLIER) cc_final: 0.5375 (m-90) REVERT: A 22 LYS cc_start: 0.6035 (mtmt) cc_final: 0.5646 (mttt) REVERT: A 56 ARG cc_start: 0.6614 (mmt180) cc_final: 0.6276 (mtm-85) REVERT: A 62 MET cc_start: 0.7890 (OUTLIER) cc_final: 0.7547 (ttp) REVERT: A 147 SER cc_start: 0.7106 (t) cc_final: 0.6753 (p) REVERT: D 33 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7602 (mt-10) REVERT: D 90 ASP cc_start: 0.6108 (t70) cc_final: 0.5681 (t0) REVERT: C 36 ASP cc_start: 0.8144 (t0) cc_final: 0.6745 (t0) REVERT: C 40 TYR cc_start: 0.6665 (m-80) cc_final: 0.5827 (m-80) REVERT: B 45 GLU cc_start: 0.6956 (OUTLIER) cc_final: 0.6751 (tt0) REVERT: B 174 GLN cc_start: 0.7417 (tp40) cc_final: 0.5707 (pm20) outliers start: 18 outliers final: 12 residues processed: 74 average time/residue: 1.2083 time to fit residues: 92.7382 Evaluate side-chains 79 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 63 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 TRP Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 91 CYS Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 91 CYS Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 173 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 4 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 chunk 3 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.174632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.132266 restraints weight = 4669.045| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 2.25 r_work: 0.3446 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3320 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6983 moved from start: 0.3807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4384 Z= 0.210 Angle : 0.591 7.104 5970 Z= 0.301 Chirality : 0.040 0.132 688 Planarity : 0.006 0.088 772 Dihedral : 5.566 50.021 626 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.78 % Allowed : 20.44 % Favored : 75.78 % 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: 1.53 (0.37), residues: 548 helix: 1.84 (0.30), residues: 288 sheet: 1.54 (0.77), residues: 52 loop : -0.27 (0.48), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 18 HIS 0.002 0.001 HIS A 154 PHE 0.010 0.001 PHE A 86 TYR 0.009 0.001 TYR A 109 ARG 0.020 0.001 ARG A 165 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 61 time to evaluate : 0.479 Fit side-chains REVERT: A 18 TRP cc_start: 0.5840 (OUTLIER) cc_final: 0.5336 (m-90) REVERT: A 22 LYS cc_start: 0.5818 (mtmt) cc_final: 0.5448 (mttt) REVERT: A 56 ARG cc_start: 0.6629 (mmt180) cc_final: 0.6263 (mtm-85) REVERT: A 62 MET cc_start: 0.7855 (OUTLIER) cc_final: 0.7518 (ttp) REVERT: A 147 SER cc_start: 0.7083 (t) cc_final: 0.6732 (p) REVERT: D 33 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7550 (mt-10) REVERT: D 97 ASP cc_start: 0.7262 (m-30) cc_final: 0.6390 (m-30) REVERT: C 36 ASP cc_start: 0.8111 (t0) cc_final: 0.6753 (t0) REVERT: C 40 TYR cc_start: 0.6598 (m-80) cc_final: 0.5767 (m-80) REVERT: C 95 MET cc_start: 0.5128 (mmm) cc_final: 0.4068 (tpt) REVERT: B 45 GLU cc_start: 0.6895 (OUTLIER) cc_final: 0.6692 (tt0) REVERT: B 174 GLN cc_start: 0.7394 (tp40) cc_final: 0.5689 (pm20) outliers start: 17 outliers final: 11 residues processed: 71 average time/residue: 1.3103 time to fit residues: 96.6562 Evaluate side-chains 76 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 61 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 TRP Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 91 CYS Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 91 CYS Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 173 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 53 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 17 optimal weight: 0.0870 chunk 15 optimal weight: 0.0870 chunk 4 optimal weight: 0.9980 chunk 18 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 overall best weight: 0.8340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.173879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.131412 restraints weight = 4719.703| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 2.27 r_work: 0.3438 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3313 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6998 moved from start: 0.3849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4384 Z= 0.227 Angle : 0.602 7.054 5970 Z= 0.306 Chirality : 0.041 0.134 688 Planarity : 0.006 0.089 772 Dihedral : 5.619 51.032 626 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.78 % Allowed : 20.89 % Favored : 75.33 % 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: 1.47 (0.37), residues: 548 helix: 1.81 (0.30), residues: 288 sheet: 1.24 (0.77), residues: 54 loop : -0.25 (0.48), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 18 HIS 0.002 0.001 HIS B 128 PHE 0.010 0.001 PHE A 86 TYR 0.008 0.001 TYR C 22 ARG 0.020 0.001 ARG A 165 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3950.52 seconds wall clock time: 69 minutes 36.17 seconds (4176.17 seconds total)