Starting phenix.real_space_refine on Thu Mar 6 02:03:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sk1_25169/03_2025/7sk1_25169.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sk1_25169/03_2025/7sk1_25169.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7sk1_25169/03_2025/7sk1_25169.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sk1_25169/03_2025/7sk1_25169.map" model { file = "/net/cci-nas-00/data/ceres_data/7sk1_25169/03_2025/7sk1_25169.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sk1_25169/03_2025/7sk1_25169.cif" } resolution = 3.43 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= 0.008 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 K 3 8.98 5 S 18 5.16 5 C 2880 2.51 5 N 666 2.21 5 O 724 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 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: 4291 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2122 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 7, 'TRANS': 254} Chain: "B" Number of atoms: 2122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2122 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 7, 'TRANS': 254} Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 25 Unusual residues: {' K': 3, 'C14': 1, 'OCT': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {'C14': 1, 'OCT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.51, per 1000 atoms: 0.82 Number of scatterers: 4291 At special positions: 0 Unit cell: (70.245, 56.865, 98.12, 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) K 3 19.00 S 18 16.00 O 724 8.00 N 666 7.00 C 2880 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 69 " - pdb=" SG CYS B 69 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.33 Conformation dependent library (CDL) restraints added in 496.0 milliseconds 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 972 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 0 sheets defined 85.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 21 through 68 removed outlier: 3.876A pdb=" N PHE A 25 " --> pdb=" O TRP A 21 " (cutoff:3.500A) Proline residue: A 47 - end of helix removed outlier: 4.441A pdb=" N ARG A 61 " --> pdb=" O ARG A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 89 removed outlier: 3.921A pdb=" N GLN A 77 " --> pdb=" O PRO A 73 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N PHE A 78 " --> pdb=" O GLN A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 97 removed outlier: 3.847A pdb=" N SER A 97 " --> pdb=" O LEU A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 116 Processing helix chain 'A' and resid 127 through 161 removed outlier: 3.610A pdb=" N ALA A 132 " --> pdb=" O ASP A 128 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE A 136 " --> pdb=" O ALA A 132 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE A 140 " --> pdb=" O ILE A 136 " (cutoff:3.500A) Proline residue: A 143 - end of helix removed outlier: 3.525A pdb=" N HIS A 159 " --> pdb=" O ARG A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 172 removed outlier: 3.729A pdb=" N TRP A 172 " --> pdb=" O PHE A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 196 removed outlier: 3.567A pdb=" N VAL A 192 " --> pdb=" O GLY A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 207 Processing helix chain 'A' and resid 211 through 224 Processing helix chain 'A' and resid 241 through 270 removed outlier: 4.030A pdb=" N GLU A 265 " --> pdb=" O LEU A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 281 Processing helix chain 'B' and resid 21 through 68 removed outlier: 3.875A pdb=" N PHE B 25 " --> pdb=" O TRP B 21 " (cutoff:3.500A) Proline residue: B 47 - end of helix removed outlier: 4.442A pdb=" N ARG B 61 " --> pdb=" O ARG B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 89 removed outlier: 3.920A pdb=" N GLN B 77 " --> pdb=" O PRO B 73 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N PHE B 78 " --> pdb=" O GLN B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 97 removed outlier: 3.847A pdb=" N SER B 97 " --> pdb=" O LEU B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 116 Processing helix chain 'B' and resid 127 through 161 removed outlier: 3.610A pdb=" N ALA B 132 " --> pdb=" O ASP B 128 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE B 136 " --> pdb=" O ALA B 132 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE B 140 " --> pdb=" O ILE B 136 " (cutoff:3.500A) Proline residue: B 143 - end of helix removed outlier: 3.526A pdb=" N HIS B 159 " --> pdb=" O ARG B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 172 removed outlier: 3.730A pdb=" N TRP B 172 " --> pdb=" O PHE B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 196 removed outlier: 3.566A pdb=" N VAL B 192 " --> pdb=" O GLY B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 207 Processing helix chain 'B' and resid 211 through 224 Processing helix chain 'B' and resid 241 through 270 removed outlier: 4.029A pdb=" N GLU B 265 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 281 324 hydrogen bonds defined for protein. 972 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: 1.32 Time building geometry restraints manager: 1.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1274 1.34 - 1.46: 1093 1.46 - 1.58: 2019 1.58 - 1.69: 0 1.69 - 1.81: 22 Bond restraints: 4408 Sorted by residual: bond pdb=" CB TRP B 100 " pdb=" CG TRP B 100 " ideal model delta sigma weight residual 1.498 1.439 0.059 3.10e-02 1.04e+03 3.63e+00 bond pdb=" CB TRP A 100 " pdb=" CG TRP A 100 " ideal model delta sigma weight residual 1.498 1.439 0.059 3.10e-02 1.04e+03 3.61e+00 bond pdb=" CG LEU B 115 " pdb=" CD1 LEU B 115 " ideal model delta sigma weight residual 1.521 1.465 0.056 3.30e-02 9.18e+02 2.92e+00 bond pdb=" CG LEU A 115 " pdb=" CD1 LEU A 115 " ideal model delta sigma weight residual 1.521 1.465 0.056 3.30e-02 9.18e+02 2.92e+00 bond pdb=" CG LEU A 126 " pdb=" CD1 LEU A 126 " ideal model delta sigma weight residual 1.521 1.465 0.056 3.30e-02 9.18e+02 2.91e+00 ... (remaining 4403 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.91: 5562 1.91 - 3.82: 335 3.82 - 5.73: 49 5.73 - 7.64: 16 7.64 - 9.55: 8 Bond angle restraints: 5970 Sorted by residual: angle pdb=" CA LYS B 246 " pdb=" CB LYS B 246 " pdb=" CG LYS B 246 " ideal model delta sigma weight residual 114.10 123.65 -9.55 2.00e+00 2.50e-01 2.28e+01 angle pdb=" CA LYS A 246 " pdb=" CB LYS A 246 " pdb=" CG LYS A 246 " ideal model delta sigma weight residual 114.10 123.58 -9.48 2.00e+00 2.50e-01 2.25e+01 angle pdb=" CB LYS A 246 " pdb=" CG LYS A 246 " pdb=" CD LYS A 246 " ideal model delta sigma weight residual 111.30 120.15 -8.85 2.30e+00 1.89e-01 1.48e+01 angle pdb=" CB LYS B 246 " pdb=" CG LYS B 246 " pdb=" CD LYS B 246 " ideal model delta sigma weight residual 111.30 120.09 -8.79 2.30e+00 1.89e-01 1.46e+01 angle pdb=" CG LYS A 274 " pdb=" CD LYS A 274 " pdb=" CE LYS A 274 " ideal model delta sigma weight residual 111.30 118.11 -6.81 2.30e+00 1.89e-01 8.76e+00 ... (remaining 5965 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 16.12: 2293 16.12 - 32.24: 168 32.24 - 48.35: 34 48.35 - 64.46: 2 64.46 - 80.58: 10 Dihedral angle restraints: 2507 sinusoidal: 987 harmonic: 1520 Sorted by residual: dihedral pdb=" CA LEU B 223 " pdb=" C LEU B 223 " pdb=" N SER B 224 " pdb=" CA SER B 224 " ideal model delta harmonic sigma weight residual 180.00 159.47 20.53 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" CA LEU A 223 " pdb=" C LEU A 223 " pdb=" N SER A 224 " pdb=" CA SER A 224 " ideal model delta harmonic sigma weight residual 180.00 159.50 20.50 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA ASN B 99 " pdb=" CB ASN B 99 " pdb=" CG ASN B 99 " pdb=" OD1 ASN B 99 " ideal model delta sinusoidal sigma weight residual 120.00 -173.61 -66.39 2 2.00e+01 2.50e-03 1.01e+01 ... (remaining 2504 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 428 0.046 - 0.093: 157 0.093 - 0.139: 67 0.139 - 0.185: 14 0.185 - 0.232: 2 Chirality restraints: 668 Sorted by residual: chirality pdb=" CB ILE B 221 " pdb=" CA ILE B 221 " pdb=" CG1 ILE B 221 " pdb=" CG2 ILE B 221 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CB ILE A 221 " pdb=" CA ILE A 221 " pdb=" CG1 ILE A 221 " pdb=" CG2 ILE A 221 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CA LYS B 246 " pdb=" N LYS B 246 " pdb=" C LYS B 246 " pdb=" CB LYS B 246 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.36e-01 ... (remaining 665 not shown) Planarity restraints: 728 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 48 " -0.028 2.00e-02 2.50e+03 2.95e-02 1.74e+01 pdb=" CG TYR A 48 " 0.072 2.00e-02 2.50e+03 pdb=" CD1 TYR A 48 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR A 48 " -0.016 2.00e-02 2.50e+03 pdb=" CE1 TYR A 48 " -0.021 2.00e-02 2.50e+03 pdb=" CE2 TYR A 48 " -0.013 2.00e-02 2.50e+03 pdb=" CZ TYR A 48 " 0.007 2.00e-02 2.50e+03 pdb=" OH TYR A 48 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 48 " -0.028 2.00e-02 2.50e+03 2.91e-02 1.70e+01 pdb=" CG TYR B 48 " 0.071 2.00e-02 2.50e+03 pdb=" CD1 TYR B 48 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR B 48 " -0.016 2.00e-02 2.50e+03 pdb=" CE1 TYR B 48 " -0.020 2.00e-02 2.50e+03 pdb=" CE2 TYR B 48 " -0.013 2.00e-02 2.50e+03 pdb=" CZ TYR B 48 " 0.007 2.00e-02 2.50e+03 pdb=" OH TYR B 48 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 156 " -0.014 2.00e-02 2.50e+03 2.70e-02 7.29e+00 pdb=" C VAL A 156 " 0.047 2.00e-02 2.50e+03 pdb=" O VAL A 156 " -0.017 2.00e-02 2.50e+03 pdb=" N THR A 157 " -0.016 2.00e-02 2.50e+03 ... (remaining 725 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.83: 1366 2.83 - 3.41: 5281 3.41 - 3.99: 7840 3.99 - 4.56: 11142 4.56 - 5.14: 15919 Nonbonded interactions: 41548 Sorted by model distance: nonbonded pdb=" OD1 ASP A 128 " pdb=" N GLY A 129 " model vdw 2.254 3.120 nonbonded pdb=" OD1 ASP B 128 " pdb=" N GLY B 129 " model vdw 2.254 3.120 nonbonded pdb=" O ASN B 99 " pdb=" ND2 ASN B 99 " model vdw 2.286 3.120 nonbonded pdb=" O ASN A 99 " pdb=" ND2 ASN A 99 " model vdw 2.287 3.120 nonbonded pdb=" OH TYR A 120 " pdb=" OG SER A 222 " model vdw 2.358 3.040 ... (remaining 41543 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' and resid 20 through 281) selection = (chain 'B' and resid 20 through 281) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.500 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7043 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 : 0.009 0.059 4408 Z= 0.550 Angle : 1.065 9.548 5970 Z= 0.564 Chirality : 0.058 0.232 668 Planarity : 0.006 0.035 728 Dihedral : 12.815 80.576 1532 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 1.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.43 % Allowed : 0.43 % Favored : 99.13 % 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: 1.09 (0.37), residues: 520 helix: 1.51 (0.25), residues: 402 sheet: None (None), residues: 0 loop : -2.07 (0.61), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP A 210 HIS 0.007 0.003 HIS B 159 PHE 0.030 0.004 PHE B 174 TYR 0.072 0.004 TYR A 48 ARG 0.003 0.001 ARG B 57 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 83 time to evaluate : 0.435 Fit side-chains REVERT: B 247 ILE cc_start: 0.8402 (tt) cc_final: 0.8197 (tt) outliers start: 2 outliers final: 0 residues processed: 83 average time/residue: 0.1807 time to fit residues: 18.6867 Evaluate side-chains 73 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 43 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 chunk 47 optimal weight: 6.9990 chunk 14 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.157132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.136085 restraints weight = 5860.703| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 2.31 r_work: 0.3531 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4408 Z= 0.259 Angle : 0.661 5.860 5970 Z= 0.358 Chirality : 0.042 0.174 668 Planarity : 0.004 0.031 728 Dihedral : 5.108 56.731 602 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.30 % Allowed : 10.00 % Favored : 88.70 % 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: 1.34 (0.37), residues: 520 helix: 1.60 (0.24), residues: 422 sheet: None (None), residues: 0 loop : -2.28 (0.66), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 210 HIS 0.006 0.002 HIS A 169 PHE 0.024 0.002 PHE A 280 TYR 0.014 0.002 TYR A 137 ARG 0.002 0.001 ARG A 81 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 93 time to evaluate : 0.482 Fit side-chains REVERT: A 102 TRP cc_start: 0.8074 (m100) cc_final: 0.7870 (m100) REVERT: A 239 GLN cc_start: 0.6605 (tt0) cc_final: 0.6120 (mt0) REVERT: A 243 GLU cc_start: 0.7048 (pm20) cc_final: 0.6730 (pt0) REVERT: B 102 TRP cc_start: 0.8125 (m100) cc_final: 0.7828 (m100) REVERT: B 243 GLU cc_start: 0.7159 (pm20) cc_final: 0.6779 (pt0) outliers start: 6 outliers final: 4 residues processed: 99 average time/residue: 0.1839 time to fit residues: 22.4358 Evaluate side-chains 80 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 76 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 222 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 35 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 13 optimal weight: 0.4980 chunk 20 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 31 optimal weight: 0.3980 chunk 40 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.160445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.138766 restraints weight = 5669.894| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 2.29 r_work: 0.3523 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7097 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4408 Z= 0.210 Angle : 0.603 6.236 5970 Z= 0.323 Chirality : 0.041 0.175 668 Planarity : 0.004 0.039 728 Dihedral : 5.041 56.850 602 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.91 % Allowed : 12.83 % Favored : 83.26 % 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: 1.58 (0.37), residues: 520 helix: 1.79 (0.24), residues: 422 sheet: None (None), residues: 0 loop : -2.33 (0.65), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 210 HIS 0.005 0.001 HIS A 169 PHE 0.019 0.002 PHE B 280 TYR 0.012 0.001 TYR A 137 ARG 0.006 0.001 ARG A 155 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 89 time to evaluate : 0.474 Fit side-chains REVERT: B 243 GLU cc_start: 0.7258 (pm20) cc_final: 0.6895 (pt0) outliers start: 18 outliers final: 9 residues processed: 104 average time/residue: 0.1569 time to fit residues: 20.9103 Evaluate side-chains 86 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 77 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 222 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 46 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 50 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 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 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.151701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.128265 restraints weight = 6251.622| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 2.64 r_work: 0.3454 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7019 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4408 Z= 0.209 Angle : 0.578 6.701 5970 Z= 0.307 Chirality : 0.039 0.156 668 Planarity : 0.004 0.032 728 Dihedral : 5.011 57.935 602 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.26 % Allowed : 17.61 % Favored : 79.13 % 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: 1.76 (0.37), residues: 520 helix: 1.95 (0.24), residues: 422 sheet: None (None), residues: 0 loop : -2.47 (0.63), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 172 HIS 0.004 0.001 HIS A 169 PHE 0.019 0.002 PHE B 276 TYR 0.010 0.001 TYR B 88 ARG 0.003 0.000 ARG A 155 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 85 time to evaluate : 0.508 Fit side-chains revert: symmetry clash REVERT: A 67 HIS cc_start: 0.6653 (OUTLIER) cc_final: 0.6412 (m-70) REVERT: A 71 SER cc_start: 0.7894 (m) cc_final: 0.7257 (t) REVERT: A 174 PHE cc_start: 0.7730 (p90) cc_final: 0.7502 (p90) REVERT: B 279 MET cc_start: 0.6605 (ppp) cc_final: 0.5256 (ttp) outliers start: 15 outliers final: 10 residues processed: 96 average time/residue: 0.1921 time to fit residues: 22.5794 Evaluate side-chains 87 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain A residue 67 HIS Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 273 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 30 optimal weight: 0.6980 chunk 40 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 99 ASN ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.149693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.126195 restraints weight = 6244.578| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 2.61 r_work: 0.3443 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7046 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4408 Z= 0.205 Angle : 0.600 8.236 5970 Z= 0.316 Chirality : 0.039 0.135 668 Planarity : 0.004 0.046 728 Dihedral : 5.017 57.991 602 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.91 % Allowed : 18.70 % Favored : 77.39 % 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: 1.82 (0.37), residues: 520 helix: 1.96 (0.24), residues: 422 sheet: None (None), residues: 0 loop : -2.29 (0.65), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 210 HIS 0.003 0.001 HIS A 169 PHE 0.021 0.002 PHE B 276 TYR 0.010 0.001 TYR B 88 ARG 0.006 0.001 ARG B 57 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 80 time to evaluate : 0.458 Fit side-chains revert: symmetry clash REVERT: A 71 SER cc_start: 0.7914 (m) cc_final: 0.7304 (t) REVERT: A 279 MET cc_start: 0.6831 (ppp) cc_final: 0.5699 (ttp) REVERT: B 77 GLN cc_start: 0.7785 (pp30) cc_final: 0.7516 (pp30) REVERT: B 279 MET cc_start: 0.6372 (ppp) cc_final: 0.5135 (ttp) outliers start: 18 outliers final: 14 residues processed: 92 average time/residue: 0.1836 time to fit residues: 20.9833 Evaluate side-chains 89 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 273 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 39 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.149026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.125607 restraints weight = 6144.647| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 2.58 r_work: 0.3436 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7072 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4408 Z= 0.225 Angle : 0.590 6.317 5970 Z= 0.313 Chirality : 0.039 0.140 668 Planarity : 0.004 0.050 728 Dihedral : 5.060 57.911 602 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.91 % Allowed : 18.48 % Favored : 77.61 % 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: 1.84 (0.37), residues: 520 helix: 1.98 (0.24), residues: 422 sheet: None (None), residues: 0 loop : -2.28 (0.64), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 172 HIS 0.002 0.001 HIS A 169 PHE 0.025 0.002 PHE A 276 TYR 0.014 0.001 TYR A 88 ARG 0.006 0.001 ARG A 155 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 88 time to evaluate : 0.500 Fit side-chains revert: symmetry clash REVERT: A 71 SER cc_start: 0.7926 (m) cc_final: 0.7367 (t) REVERT: A 167 TYR cc_start: 0.7312 (OUTLIER) cc_final: 0.6315 (m-10) REVERT: A 239 GLN cc_start: 0.6427 (tt0) cc_final: 0.6083 (mt0) REVERT: A 279 MET cc_start: 0.6822 (ppp) cc_final: 0.5623 (ttp) REVERT: B 254 LEU cc_start: 0.7910 (OUTLIER) cc_final: 0.7655 (tt) REVERT: B 279 MET cc_start: 0.6366 (ppp) cc_final: 0.5145 (ttp) outliers start: 18 outliers final: 15 residues processed: 99 average time/residue: 0.2290 time to fit residues: 29.1749 Evaluate side-chains 95 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 78 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 167 TYR Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 273 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 26 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 99 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.150304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.126458 restraints weight = 6253.663| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 2.62 r_work: 0.3435 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 moved from start: 0.3452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4408 Z= 0.206 Angle : 0.582 6.242 5970 Z= 0.310 Chirality : 0.039 0.135 668 Planarity : 0.004 0.047 728 Dihedral : 5.018 57.976 602 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 4.13 % Allowed : 20.22 % Favored : 75.65 % 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: 1.85 (0.37), residues: 520 helix: 1.99 (0.24), residues: 422 sheet: None (None), residues: 0 loop : -2.31 (0.64), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 172 HIS 0.002 0.001 HIS B 159 PHE 0.024 0.002 PHE B 220 TYR 0.011 0.001 TYR A 88 ARG 0.006 0.001 ARG A 155 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 80 time to evaluate : 0.886 Fit side-chains revert: symmetry clash REVERT: A 163 ARG cc_start: 0.5249 (ttt180) cc_final: 0.4687 (ttt180) REVERT: A 167 TYR cc_start: 0.7301 (OUTLIER) cc_final: 0.6310 (m-10) REVERT: A 239 GLN cc_start: 0.6399 (tt0) cc_final: 0.6017 (mt0) REVERT: A 279 MET cc_start: 0.6612 (ppp) cc_final: 0.5536 (ttp) REVERT: B 254 LEU cc_start: 0.7951 (OUTLIER) cc_final: 0.7708 (tt) REVERT: B 279 MET cc_start: 0.6022 (ppp) cc_final: 0.4903 (ttp) outliers start: 19 outliers final: 12 residues processed: 93 average time/residue: 0.3784 time to fit residues: 46.0828 Evaluate side-chains 90 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 76 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 167 TYR Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 273 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 39 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 33 optimal weight: 0.0050 chunk 6 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 21 optimal weight: 0.1980 chunk 48 optimal weight: 0.9990 chunk 12 optimal weight: 0.4980 chunk 2 optimal weight: 0.4980 chunk 41 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 overall best weight: 0.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 99 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.152824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.129388 restraints weight = 6041.455| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 2.61 r_work: 0.3461 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7020 moved from start: 0.3533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4408 Z= 0.166 Angle : 0.565 6.262 5970 Z= 0.304 Chirality : 0.038 0.132 668 Planarity : 0.004 0.051 728 Dihedral : 4.952 58.599 602 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 3.48 % Allowed : 21.74 % Favored : 74.78 % 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: 1.90 (0.37), residues: 520 helix: 2.04 (0.24), residues: 422 sheet: None (None), residues: 0 loop : -2.37 (0.62), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 100 HIS 0.002 0.001 HIS B 169 PHE 0.031 0.002 PHE B 276 TYR 0.011 0.001 TYR A 88 ARG 0.007 0.001 ARG A 155 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 82 time to evaluate : 0.584 Fit side-chains revert: symmetry clash REVERT: A 163 ARG cc_start: 0.5203 (ttt180) cc_final: 0.4640 (ttt180) REVERT: A 167 TYR cc_start: 0.7400 (OUTLIER) cc_final: 0.6394 (m-10) REVERT: A 239 GLN cc_start: 0.6367 (tt0) cc_final: 0.6023 (mt0) REVERT: A 279 MET cc_start: 0.6498 (ppp) cc_final: 0.5658 (ttp) REVERT: B 254 LEU cc_start: 0.7896 (OUTLIER) cc_final: 0.7678 (tt) REVERT: B 279 MET cc_start: 0.6006 (ppp) cc_final: 0.4948 (ttp) outliers start: 16 outliers final: 10 residues processed: 93 average time/residue: 0.3319 time to fit residues: 37.8993 Evaluate side-chains 86 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 74 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 167 TYR Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 273 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 31 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 17 optimal weight: 0.1980 chunk 24 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 38 optimal weight: 0.4980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.149980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.126471 restraints weight = 6294.549| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 2.67 r_work: 0.3449 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 moved from start: 0.3574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4408 Z= 0.195 Angle : 0.594 7.077 5970 Z= 0.314 Chirality : 0.039 0.130 668 Planarity : 0.005 0.061 728 Dihedral : 4.956 58.546 602 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 3.04 % Allowed : 23.26 % Favored : 73.70 % 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: 1.90 (0.37), residues: 520 helix: 2.03 (0.25), residues: 422 sheet: None (None), residues: 0 loop : -2.31 (0.63), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 100 HIS 0.002 0.001 HIS B 169 PHE 0.033 0.002 PHE B 276 TYR 0.011 0.001 TYR A 88 ARG 0.008 0.001 ARG B 155 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 0.498 Fit side-chains revert: symmetry clash REVERT: A 163 ARG cc_start: 0.5264 (ttt180) cc_final: 0.4701 (ttt180) REVERT: A 167 TYR cc_start: 0.7405 (OUTLIER) cc_final: 0.6388 (m-10) REVERT: A 279 MET cc_start: 0.6529 (ppp) cc_final: 0.5667 (ttp) REVERT: B 254 LEU cc_start: 0.7939 (OUTLIER) cc_final: 0.7735 (tt) REVERT: B 279 MET cc_start: 0.5934 (ppp) cc_final: 0.4967 (ttp) outliers start: 14 outliers final: 9 residues processed: 85 average time/residue: 0.2868 time to fit residues: 29.7930 Evaluate side-chains 87 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 167 TYR Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 273 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 28 optimal weight: 0.7980 chunk 4 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 chunk 31 optimal weight: 0.0770 chunk 19 optimal weight: 0.3980 chunk 10 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.152824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.129215 restraints weight = 6059.534| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 2.62 r_work: 0.3461 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7025 moved from start: 0.3598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4408 Z= 0.178 Angle : 0.572 6.244 5970 Z= 0.311 Chirality : 0.038 0.128 668 Planarity : 0.004 0.057 728 Dihedral : 4.923 58.858 602 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 3.70 % Allowed : 22.83 % Favored : 73.48 % 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: 1.86 (0.37), residues: 520 helix: 2.02 (0.25), residues: 422 sheet: None (None), residues: 0 loop : -2.39 (0.61), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 210 HIS 0.006 0.001 HIS A 67 PHE 0.036 0.001 PHE B 276 TYR 0.011 0.001 TYR A 88 ARG 0.008 0.001 ARG B 155 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1040 Ramachandran restraints generated. 520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 78 time to evaluate : 0.487 Fit side-chains REVERT: A 163 ARG cc_start: 0.5241 (ttt180) cc_final: 0.4658 (ttt180) REVERT: A 167 TYR cc_start: 0.7402 (OUTLIER) cc_final: 0.6402 (m-10) REVERT: A 239 GLN cc_start: 0.6267 (tt0) cc_final: 0.5935 (mt0) REVERT: A 279 MET cc_start: 0.6346 (ppp) cc_final: 0.5468 (ttp) REVERT: B 155 ARG cc_start: 0.8626 (ttm-80) cc_final: 0.8411 (ttm-80) REVERT: B 279 MET cc_start: 0.5949 (ppp) cc_final: 0.4943 (ttp) outliers start: 17 outliers final: 10 residues processed: 87 average time/residue: 0.1739 time to fit residues: 18.9873 Evaluate side-chains 85 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 167 TYR Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 222 SER Chi-restraints excluded: chain B residue 273 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 14 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 36 optimal weight: 0.0670 chunk 15 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 chunk 27 optimal weight: 0.9990 chunk 21 optimal weight: 0.0060 chunk 26 optimal weight: 0.7980 chunk 22 optimal weight: 0.5980 overall best weight: 0.4134 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.152569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.129559 restraints weight = 6200.134| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 2.60 r_work: 0.3467 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7027 moved from start: 0.3733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.134 4408 Z= 0.383 Angle : 1.195 59.140 5970 Z= 0.727 Chirality : 0.049 0.805 668 Planarity : 0.005 0.056 728 Dihedral : 5.183 58.873 602 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.62 % Favored : 95.19 % Rotamer: Outliers : 3.04 % Allowed : 23.70 % Favored : 73.26 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: 1.83 (0.37), residues: 520 helix: 2.00 (0.25), residues: 422 sheet: None (None), residues: 0 loop : -2.46 (0.61), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 210 HIS 0.006 0.001 HIS A 67 PHE 0.031 0.002 PHE B 276 TYR 0.010 0.001 TYR A 88 ARG 0.006 0.001 ARG B 155 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2294.47 seconds wall clock time: 42 minutes 37.06 seconds (2557.06 seconds total)