Starting phenix.real_space_refine on Tue Feb 11 06:34:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sk1_25169/02_2025/7sk1_25169.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sk1_25169/02_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_25169/02_2025/7sk1_25169.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sk1_25169/02_2025/7sk1_25169.map" model { file = "/net/cci-nas-00/data/ceres_data/7sk1_25169/02_2025/7sk1_25169.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sk1_25169/02_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-5592/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: 3.61, per 1000 atoms: 0.84 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: 1.36 Conformation dependent library (CDL) restraints added in 591.0 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: 0.35 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: 1.16 Time building geometry restraints manager: 1.50 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: 0.590 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.990 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:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.050 ------------------------------------------------------------------------------- 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 : 0.472 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: 0.1746 time to fit residues: 18.0192 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 : 0.465 ------------------------------------------------------------------------------- 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 = 35)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.136082 restraints weight = 5860.703| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 2.31 r_work: 0.3535 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 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 : 0.463 Fit side-chains REVERT: A 102 TRP cc_start: 0.8073 (m100) cc_final: 0.7871 (m100) REVERT: A 239 GLN cc_start: 0.6602 (tt0) cc_final: 0.6122 (mt0) REVERT: A 243 GLU cc_start: 0.7044 (pm20) cc_final: 0.6726 (pt0) REVERT: B 102 TRP cc_start: 0.8124 (m100) cc_final: 0.7826 (m100) REVERT: B 243 GLU cc_start: 0.7161 (pm20) cc_final: 0.6781 (pt0) outliers start: 6 outliers final: 4 residues processed: 99 average time/residue: 0.1843 time to fit residues: 22.5079 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 : 0.514 ------------------------------------------------------------------------------- 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: 1.9990 chunk 33 optimal weight: 0.5980 chunk 42 optimal weight: 0.8980 chunk 13 optimal weight: 0.4980 chunk 20 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 21 optimal weight: 0.2980 chunk 17 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3903 r_free = 0.3903 target = 0.157477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.135634 restraints weight = 5714.869| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 2.31 r_work: 0.3521 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4408 Z= 0.202 Angle : 0.600 6.719 5970 Z= 0.321 Chirality : 0.041 0.175 668 Planarity : 0.004 0.036 728 Dihedral : 5.006 56.935 602 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 4.13 % Allowed : 12.61 % 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: 1.60 (0.37), residues: 520 helix: 1.80 (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 0.020 0.002 PHE B 280 TYR 0.012 0.001 TYR B 88 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 111 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 92 time to evaluate : 0.476 Fit side-chains REVERT: B 243 GLU cc_start: 0.7257 (pm20) cc_final: 0.6895 (pt0) REVERT: B 273 LEU cc_start: 0.8297 (tp) cc_final: 0.8018 (mm) outliers start: 19 outliers final: 9 residues processed: 108 average time/residue: 0.1730 time to fit residues: 23.1883 Evaluate side-chains 85 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 0.483 ------------------------------------------------------------------------------- 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: 0.5980 chunk 24 optimal weight: 0.2980 chunk 50 optimal weight: 0.8980 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: 1.9990 chunk 2 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3855 r_free = 0.3855 target = 0.153030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.129553 restraints weight = 6259.807| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 2.64 r_work: 0.3472 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7001 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4408 Z= 0.187 Angle : 0.575 6.941 5970 Z= 0.304 Chirality : 0.038 0.151 668 Planarity : 0.004 0.034 728 Dihedral : 4.962 58.431 602 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.17 % Allowed : 18.91 % Favored : 78.91 % 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: 1.80 (0.37), residues: 520 helix: 1.98 (0.24), residues: 422 sheet: None (None), residues: 0 loop : -2.44 (0.63), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 210 HIS 0.004 0.001 HIS A 169 PHE 0.019 0.001 PHE B 276 TYR 0.011 0.001 TYR B 88 ARG 0.007 0.001 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 97 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 0.450 Fit side-chains REVERT: A 71 SER cc_start: 0.7845 (m) cc_final: 0.7253 (t) REVERT: A 239 GLN cc_start: 0.6322 (tt0) cc_final: 0.5987 (mt0) REVERT: A 279 MET cc_start: 0.6550 (ppp) cc_final: 0.5317 (ttp) REVERT: A 280 PHE cc_start: 0.7929 (t80) cc_final: 0.7639 (t80) REVERT: B 77 GLN cc_start: 0.7713 (pp30) cc_final: 0.7447 (pp30) REVERT: B 279 MET cc_start: 0.6506 (ppp) cc_final: 0.5217 (ttp) outliers start: 10 outliers final: 5 residues processed: 96 average time/residue: 0.2010 time to fit residues: 23.6177 Evaluate side-chains 82 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 77 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU 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 222 SER 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: 0.9980 chunk 3 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.150262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.126729 restraints weight = 6286.048| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 2.64 r_work: 0.3430 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 moved from start: 0.3211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 4408 Z= 0.230 Angle : 0.618 8.896 5970 Z= 0.327 Chirality : 0.040 0.140 668 Planarity : 0.005 0.046 728 Dihedral : 5.053 57.934 602 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.61 % Allowed : 20.00 % 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: 1.81 (0.37), residues: 520 helix: 1.95 (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 0.022 0.002 PHE B 174 TYR 0.011 0.001 TYR A 88 ARG 0.009 0.001 ARG B 162 *********************** 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 96 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 0.596 Fit side-chains REVERT: A 71 SER cc_start: 0.7923 (m) cc_final: 0.7360 (t) REVERT: A 279 MET cc_start: 0.6298 (ppp) cc_final: 0.5243 (ttp) REVERT: B 279 MET cc_start: 0.6350 (ppp) cc_final: 0.5119 (ttp) REVERT: B 280 PHE cc_start: 0.7785 (t80) cc_final: 0.7552 (t80) outliers start: 12 outliers final: 9 residues processed: 91 average time/residue: 0.2268 time to fit residues: 25.9954 Evaluate side-chains 84 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 75 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 153 VAL Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 222 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 39 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 7 optimal weight: 0.0870 chunk 0 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.149728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.126015 restraints weight = 6239.969| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 2.62 r_work: 0.3438 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7050 moved from start: 0.3470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4408 Z= 0.210 Angle : 0.591 6.749 5970 Z= 0.315 Chirality : 0.039 0.134 668 Planarity : 0.004 0.045 728 Dihedral : 5.027 58.076 602 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 3.70 % Allowed : 20.65 % 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: 1.80 (0.37), residues: 520 helix: 1.95 (0.24), residues: 422 sheet: None (None), residues: 0 loop : -2.30 (0.64), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 172 HIS 0.002 0.001 HIS B 159 PHE 0.021 0.002 PHE A 276 TYR 0.021 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 101 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 0.477 Fit side-chains REVERT: A 66 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7915 (pm20) REVERT: A 163 ARG cc_start: 0.5219 (ttt180) cc_final: 0.4663 (ttt180) REVERT: A 167 TYR cc_start: 0.7296 (OUTLIER) cc_final: 0.6316 (m-10) REVERT: A 239 GLN cc_start: 0.6301 (tt0) cc_final: 0.5981 (mt0) REVERT: A 279 MET cc_start: 0.5936 (ppp) cc_final: 0.5173 (ttp) REVERT: B 254 LEU cc_start: 0.7952 (OUTLIER) cc_final: 0.7705 (tt) REVERT: B 279 MET cc_start: 0.6082 (ppp) cc_final: 0.4970 (ttp) REVERT: B 280 PHE cc_start: 0.7795 (t80) cc_final: 0.7524 (t80) outliers start: 17 outliers final: 10 residues processed: 96 average time/residue: 0.1743 time to fit residues: 20.7246 Evaluate side-chains 88 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 0.614 ------------------------------------------------------------------------------- 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 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 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: 1.9990 chunk 41 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.149217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.125599 restraints weight = 6251.125| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 2.60 r_work: 0.3416 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7086 moved from start: 0.3482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4408 Z= 0.244 Angle : 0.607 6.669 5970 Z= 0.322 Chirality : 0.040 0.135 668 Planarity : 0.004 0.047 728 Dihedral : 5.106 57.401 602 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 4.78 % Allowed : 20.22 % Favored : 75.00 % 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: 1.75 (0.37), residues: 520 helix: 1.91 (0.24), residues: 422 sheet: None (None), residues: 0 loop : -2.27 (0.65), 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 271 PHE 0.029 0.002 PHE B 276 TYR 0.016 0.001 TYR A 88 ARG 0.006 0.001 ARG B 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 100 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 78 time to evaluate : 0.477 Fit side-chains REVERT: A 66 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7926 (pm20) REVERT: A 163 ARG cc_start: 0.5324 (ttt180) cc_final: 0.4766 (ttt180) REVERT: A 167 TYR cc_start: 0.7352 (OUTLIER) cc_final: 0.6322 (m-10) REVERT: A 254 LEU cc_start: 0.7958 (OUTLIER) cc_final: 0.7705 (tt) REVERT: A 279 MET cc_start: 0.5838 (ppp) cc_final: 0.5144 (ttp) REVERT: B 254 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7711 (tt) REVERT: B 279 MET cc_start: 0.6094 (ppp) cc_final: 0.4953 (ttp) REVERT: B 280 PHE cc_start: 0.7912 (t80) cc_final: 0.7660 (t80) outliers start: 22 outliers final: 15 residues processed: 93 average time/residue: 0.1753 time to fit residues: 20.5084 Evaluate side-chains 95 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 76 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 39 VAL 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 167 TYR Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 254 LEU 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 158 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 39 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 21 optimal weight: 0.1980 chunk 48 optimal weight: 0.7980 chunk 12 optimal weight: 0.4980 chunk 2 optimal weight: 0.4980 chunk 41 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN B 99 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.151054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.127577 restraints weight = 6033.495| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 2.57 r_work: 0.3444 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7042 moved from start: 0.3624 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= 0.185 Angle : 0.593 6.245 5970 Z= 0.315 Chirality : 0.039 0.130 668 Planarity : 0.004 0.055 728 Dihedral : 5.029 57.918 602 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 4.35 % Allowed : 21.96 % 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: 1.74 (0.37), residues: 520 helix: 1.92 (0.25), residues: 422 sheet: None (None), residues: 0 loop : -2.42 (0.63), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 100 HIS 0.002 0.001 HIS A 67 PHE 0.019 0.001 PHE A 174 TYR 0.016 0.001 TYR A 88 ARG 0.007 0.001 ARG B 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 100 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 80 time to evaluate : 0.377 Fit side-chains REVERT: A 66 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7910 (pm20) REVERT: A 163 ARG cc_start: 0.5288 (ttt180) cc_final: 0.4719 (ttt180) REVERT: A 167 TYR cc_start: 0.7319 (OUTLIER) cc_final: 0.6284 (m-10) REVERT: A 239 GLN cc_start: 0.6362 (tt0) cc_final: 0.6030 (mt0) REVERT: A 254 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7731 (tt) REVERT: A 279 MET cc_start: 0.5685 (ppp) cc_final: 0.4957 (ttp) REVERT: B 254 LEU cc_start: 0.7913 (OUTLIER) cc_final: 0.7690 (tt) REVERT: B 279 MET cc_start: 0.5872 (ppp) cc_final: 0.4938 (ttp) outliers start: 20 outliers final: 11 residues processed: 95 average time/residue: 0.1812 time to fit residues: 21.2143 Evaluate side-chains 90 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 75 time to evaluate : 0.454 ------------------------------------------------------------------------------- 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 94 SER Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 158 VAL 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 254 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 31 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 17 optimal weight: 0.4980 chunk 24 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.150882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.127102 restraints weight = 6376.717| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 2.65 r_work: 0.3432 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 moved from start: 0.3685 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= 0.216 Angle : 0.612 6.426 5970 Z= 0.327 Chirality : 0.039 0.131 668 Planarity : 0.004 0.058 728 Dihedral : 5.022 57.582 602 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 4.35 % Allowed : 22.39 % Favored : 73.26 % 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: 1.74 (0.37), residues: 520 helix: 1.91 (0.25), residues: 422 sheet: None (None), residues: 0 loop : -2.34 (0.64), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 100 HIS 0.003 0.001 HIS A 67 PHE 0.024 0.002 PHE B 220 TYR 0.015 0.001 TYR A 88 ARG 0.007 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 97 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 77 time to evaluate : 0.539 Fit side-chains REVERT: A 66 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7898 (pm20) REVERT: A 167 TYR cc_start: 0.7402 (OUTLIER) cc_final: 0.6390 (m-10) REVERT: A 254 LEU cc_start: 0.7972 (OUTLIER) cc_final: 0.7754 (tt) REVERT: A 279 MET cc_start: 0.5773 (ppp) cc_final: 0.5031 (ttp) REVERT: B 167 TYR cc_start: 0.7228 (OUTLIER) cc_final: 0.6430 (m-10) REVERT: B 254 LEU cc_start: 0.7942 (OUTLIER) cc_final: 0.7714 (tt) REVERT: B 279 MET cc_start: 0.5798 (ppp) cc_final: 0.4917 (ttp) outliers start: 20 outliers final: 12 residues processed: 89 average time/residue: 0.1629 time to fit residues: 18.3353 Evaluate side-chains 93 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 76 time to evaluate : 0.517 ------------------------------------------------------------------------------- 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 94 SER Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 158 VAL 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 254 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 167 TYR 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: 0.6980 chunk 4 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 33 optimal weight: 0.4980 chunk 0 optimal weight: 4.9990 chunk 44 optimal weight: 0.7980 chunk 31 optimal weight: 0.1980 chunk 19 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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** B 99 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.151509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.127901 restraints weight = 6141.526| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 2.60 r_work: 0.3449 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 moved from start: 0.3684 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= 0.190 Angle : 0.607 7.325 5970 Z= 0.326 Chirality : 0.039 0.129 668 Planarity : 0.004 0.062 728 Dihedral : 5.019 57.812 602 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 4.35 % Allowed : 22.61 % Favored : 73.04 % 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: 1.68 (0.37), residues: 520 helix: 1.88 (0.25), residues: 422 sheet: None (None), residues: 0 loop : -2.41 (0.61), 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 67 PHE 0.018 0.001 PHE A 174 TYR 0.015 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 99 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 79 time to evaluate : 0.436 Fit side-chains REVERT: A 66 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7893 (pm20) REVERT: A 167 TYR cc_start: 0.7400 (OUTLIER) cc_final: 0.6370 (m-10) REVERT: A 239 GLN cc_start: 0.6365 (tt0) cc_final: 0.6026 (mt0) REVERT: A 254 LEU cc_start: 0.7947 (OUTLIER) cc_final: 0.7746 (tt) REVERT: A 279 MET cc_start: 0.5750 (ppp) cc_final: 0.5021 (ttp) REVERT: B 144 PHE cc_start: 0.8531 (t80) cc_final: 0.8296 (t80) REVERT: B 155 ARG cc_start: 0.8611 (ttm-80) cc_final: 0.8397 (ttm-80) REVERT: B 167 TYR cc_start: 0.7235 (OUTLIER) cc_final: 0.7002 (m-10) REVERT: B 171 ARG cc_start: 0.6302 (mtm180) cc_final: 0.5593 (mtt180) REVERT: B 254 LEU cc_start: 0.7962 (OUTLIER) cc_final: 0.7743 (tt) REVERT: B 279 MET cc_start: 0.5742 (ppp) cc_final: 0.4960 (ttp) outliers start: 20 outliers final: 13 residues processed: 92 average time/residue: 0.1947 time to fit residues: 22.3771 Evaluate side-chains 91 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 73 time to evaluate : 0.510 ------------------------------------------------------------------------------- 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 94 SER Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 158 VAL 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 254 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 167 TYR 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 14 optimal weight: 0.1980 chunk 48 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 15 optimal weight: 0.3980 chunk 10 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3830 r_free = 0.3830 target = 0.150823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.127516 restraints weight = 6204.517| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 2.63 r_work: 0.3438 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7056 moved from start: 0.3744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.113 4408 Z= 0.391 Angle : 1.542 59.175 5970 Z= 0.955 Chirality : 0.052 0.677 668 Planarity : 0.005 0.060 728 Dihedral : 5.348 57.815 602 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.62 % Favored : 95.19 % Rotamer: Outliers : 4.13 % Allowed : 23.26 % Favored : 72.61 % Cbeta Deviations : 0.41 % 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: 1.66 (0.37), residues: 520 helix: 1.88 (0.25), residues: 422 sheet: None (None), residues: 0 loop : -2.48 (0.61), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 210 HIS 0.003 0.001 HIS A 67 PHE 0.018 0.001 PHE A 174 TYR 0.013 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: 1952.95 seconds wall clock time: 35 minutes 37.82 seconds (2137.82 seconds total)