Starting phenix.real_space_refine on Tue Feb 11 05:17:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7f3u_31441/02_2025/7f3u_31441.cif Found real_map, /net/cci-nas-00/data/ceres_data/7f3u_31441/02_2025/7f3u_31441.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7f3u_31441/02_2025/7f3u_31441.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7f3u_31441/02_2025/7f3u_31441.map" model { file = "/net/cci-nas-00/data/ceres_data/7f3u_31441/02_2025/7f3u_31441.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7f3u_31441/02_2025/7f3u_31441.cif" } resolution = 4.0 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 18 5.16 5 C 2716 2.51 5 N 740 2.21 5 O 800 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 4274 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2137 Classifications: {'peptide': 328} Incomplete info: {'truncation_to_alanine': 153} Link IDs: {'PTRANS': 8, 'TRANS': 319} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 653 Unresolved non-hydrogen angles: 828 Unresolved non-hydrogen dihedrals: 568 Unresolved non-hydrogen chiralities: 45 Planarities with less than four sites: {'GLN:plan1': 16, 'HIS:plan': 6, 'TYR:plan': 2, 'ASN:plan1': 6, 'TRP:plan': 5, 'ASP:plan': 5, 'PHE:plan': 18, 'GLU:plan': 12, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 397 Restraints were copied for chains: B Time building chain proxies: 3.55, per 1000 atoms: 0.83 Number of scatterers: 4274 At special positions: 0 Unit cell: (71.34, 113.98, 88.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 18 16.00 O 800 8.00 N 740 7.00 C 2716 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.18 Conformation dependent library (CDL) restraints added in 617.8 milliseconds 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1244 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 0 sheets defined 85.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 7 through 72 Proline residue: A 70 - end of helix Processing helix chain 'A' and resid 73 through 99 removed outlier: 4.186A pdb=" N ALA A 79 " --> pdb=" O GLU A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 113 Processing helix chain 'A' and resid 122 through 154 Processing helix chain 'A' and resid 157 through 186 removed outlier: 3.623A pdb=" N ASP A 161 " --> pdb=" O SER A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 209 Processing helix chain 'A' and resid 213 through 252 removed outlier: 4.526A pdb=" N ASN A 221 " --> pdb=" O GLN A 217 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N GLN A 222 " --> pdb=" O LYS A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 297 Proline residue: A 277 - end of helix Processing helix chain 'A' and resid 306 through 334 Proline residue: A 313 - end of helix Processing helix chain 'B' and resid 8 through 72 Proline residue: B 70 - end of helix Processing helix chain 'B' and resid 73 through 99 removed outlier: 4.185A pdb=" N ALA B 79 " --> pdb=" O GLU B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 113 Processing helix chain 'B' and resid 122 through 154 Processing helix chain 'B' and resid 157 through 186 removed outlier: 3.623A pdb=" N ASP B 161 " --> pdb=" O SER B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 209 Processing helix chain 'B' and resid 213 through 252 removed outlier: 4.527A pdb=" N ASN B 221 " --> pdb=" O GLN B 217 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N GLN B 222 " --> pdb=" O LYS B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 297 Proline residue: B 277 - end of helix Processing helix chain 'B' and resid 306 through 334 Proline residue: B 313 - end of helix 461 hydrogen bonds defined for protein. 1383 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: 1.30 Time building geometry restraints manager: 1.35 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: 1428 1.34 - 1.45: 646 1.45 - 1.57: 2258 1.57 - 1.69: 0 1.69 - 1.81: 24 Bond restraints: 4356 Sorted by residual: bond pdb=" CG ARG A 178 " pdb=" CD ARG A 178 " ideal model delta sigma weight residual 1.520 1.470 0.050 3.00e-02 1.11e+03 2.80e+00 bond pdb=" CG ARG B 178 " pdb=" CD ARG B 178 " ideal model delta sigma weight residual 1.520 1.470 0.050 3.00e-02 1.11e+03 2.79e+00 bond pdb=" CA VAL A 233 " pdb=" CB VAL A 233 " ideal model delta sigma weight residual 1.540 1.525 0.015 1.25e-02 6.40e+03 1.51e+00 bond pdb=" CB TRP A 170 " pdb=" CG TRP A 170 " ideal model delta sigma weight residual 1.498 1.460 0.038 3.10e-02 1.04e+03 1.49e+00 bond pdb=" CA ILE B 145 " pdb=" CB ILE B 145 " ideal model delta sigma weight residual 1.540 1.525 0.014 1.17e-02 7.31e+03 1.49e+00 ... (remaining 4351 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.26: 5828 2.26 - 4.51: 126 4.51 - 6.77: 32 6.77 - 9.02: 6 9.02 - 11.28: 2 Bond angle restraints: 5994 Sorted by residual: angle pdb=" N PRO B 8 " pdb=" CA PRO B 8 " pdb=" CB PRO B 8 " ideal model delta sigma weight residual 103.39 110.08 -6.69 1.08e+00 8.57e-01 3.84e+01 angle pdb=" N PRO A 8 " pdb=" CA PRO A 8 " pdb=" CB PRO A 8 " ideal model delta sigma weight residual 103.39 110.07 -6.68 1.08e+00 8.57e-01 3.83e+01 angle pdb=" NE ARG B 178 " pdb=" CZ ARG B 178 " pdb=" NH1 ARG B 178 " ideal model delta sigma weight residual 121.50 117.42 4.08 1.00e+00 1.00e+00 1.66e+01 angle pdb=" NE ARG A 178 " pdb=" CZ ARG A 178 " pdb=" NH1 ARG A 178 " ideal model delta sigma weight residual 121.50 117.52 3.98 1.00e+00 1.00e+00 1.58e+01 angle pdb=" CB MET A 87 " pdb=" CG MET A 87 " pdb=" SD MET A 87 " ideal model delta sigma weight residual 112.70 123.98 -11.28 3.00e+00 1.11e-01 1.41e+01 ... (remaining 5989 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.29: 2272 12.29 - 24.58: 152 24.58 - 36.86: 74 36.86 - 49.15: 6 49.15 - 61.44: 6 Dihedral angle restraints: 2510 sinusoidal: 586 harmonic: 1924 Sorted by residual: dihedral pdb=" CA LEU B 154 " pdb=" C LEU B 154 " pdb=" N LEU B 155 " pdb=" CA LEU B 155 " ideal model delta harmonic sigma weight residual -180.00 -153.52 -26.48 0 5.00e+00 4.00e-02 2.80e+01 dihedral pdb=" CA LEU A 154 " pdb=" C LEU A 154 " pdb=" N LEU A 155 " pdb=" CA LEU A 155 " ideal model delta harmonic sigma weight residual -180.00 -153.53 -26.47 0 5.00e+00 4.00e-02 2.80e+01 dihedral pdb=" CA GLY A 106 " pdb=" C GLY A 106 " pdb=" N LEU A 107 " pdb=" CA LEU A 107 " ideal model delta harmonic sigma weight residual 180.00 154.77 25.23 0 5.00e+00 4.00e-02 2.55e+01 ... (remaining 2507 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 524 0.046 - 0.093: 174 0.093 - 0.139: 17 0.139 - 0.185: 7 0.185 - 0.231: 2 Chirality restraints: 724 Sorted by residual: chirality pdb=" CA PRO A 8 " pdb=" N PRO A 8 " pdb=" C PRO A 8 " pdb=" CB PRO A 8 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA PRO B 8 " pdb=" N PRO B 8 " pdb=" C PRO B 8 " pdb=" CB PRO B 8 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CG LEU B 140 " pdb=" CB LEU B 140 " pdb=" CD1 LEU B 140 " pdb=" CD2 LEU B 140 " both_signs ideal model delta sigma weight residual False -2.59 -2.75 0.16 2.00e-01 2.50e+01 6.10e-01 ... (remaining 721 not shown) Planarity restraints: 790 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 139 " 0.016 2.00e-02 2.50e+03 1.39e-02 3.84e+00 pdb=" CG TYR B 139 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR B 139 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR B 139 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR B 139 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 139 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR B 139 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 139 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 139 " -0.016 2.00e-02 2.50e+03 1.38e-02 3.79e+00 pdb=" CG TYR A 139 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR A 139 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR A 139 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR A 139 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 139 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR A 139 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 139 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 238 " 0.016 2.00e-02 2.50e+03 9.75e-03 1.90e+00 pdb=" CG TYR A 238 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR A 238 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR A 238 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR A 238 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A 238 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR A 238 " 0.007 2.00e-02 2.50e+03 pdb=" OH TYR A 238 " 0.000 2.00e-02 2.50e+03 ... (remaining 787 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.82: 1454 2.82 - 3.34: 5127 3.34 - 3.86: 7295 3.86 - 4.38: 7293 4.38 - 4.90: 11642 Nonbonded interactions: 32811 Sorted by model distance: nonbonded pdb=" ND2 ASN A 105 " pdb=" O ASN A 115 " model vdw 2.295 3.120 nonbonded pdb=" ND2 ASN B 105 " pdb=" O ASN B 115 " model vdw 2.295 3.120 nonbonded pdb=" ND2 ASN B 165 " pdb=" OG SER B 204 " model vdw 2.320 3.120 nonbonded pdb=" ND2 ASN A 165 " pdb=" OG SER A 204 " model vdw 2.321 3.120 nonbonded pdb=" O MET A 228 " pdb=" OG SER A 231 " model vdw 2.324 3.040 ... (remaining 32806 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.940 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.060 Process input model: 15.160 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 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 : 0.006 0.050 4356 Z= 0.390 Angle : 0.885 11.280 5994 Z= 0.512 Chirality : 0.045 0.231 724 Planarity : 0.004 0.029 790 Dihedral : 11.591 61.439 1266 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 21.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.59 % Favored : 91.41 % Rotamer: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % 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: 2.22 (0.33), residues: 652 helix: 2.47 (0.21), residues: 524 sheet: None (None), residues: 0 loop : -3.11 (0.53), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 210 HIS 0.009 0.003 HIS A 197 PHE 0.021 0.002 PHE A 153 TYR 0.034 0.003 TYR B 139 ARG 0.009 0.001 ARG B 152 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.479 Fit side-chains revert: symmetry clash REVERT: A 135 LYS cc_start: 0.8931 (mmmm) cc_final: 0.7947 (mmmm) REVERT: A 139 TYR cc_start: 0.7886 (m-80) cc_final: 0.7335 (m-80) REVERT: B 135 LYS cc_start: 0.8908 (mmmm) cc_final: 0.7930 (mmmm) REVERT: B 136 PHE cc_start: 0.8159 (t80) cc_final: 0.7954 (t80) REVERT: B 139 TYR cc_start: 0.7900 (m-80) cc_final: 0.7287 (m-80) outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.1436 time to fit residues: 30.4798 Evaluate side-chains 120 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 54 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 26 optimal weight: 20.0000 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 6.9990 chunk 25 optimal weight: 30.0000 chunk 50 optimal weight: 6.9990 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 58 optimal weight: 20.0000 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 ASN ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.101218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.082617 restraints weight = 15439.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.084801 restraints weight = 9364.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.086076 restraints weight = 6558.611| |-----------------------------------------------------------------------------| r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4356 Z= 0.193 Angle : 0.726 10.899 5994 Z= 0.371 Chirality : 0.040 0.143 724 Planarity : 0.003 0.024 790 Dihedral : 4.712 21.899 690 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 5.56 % Allowed : 19.79 % Favored : 74.65 % 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: 3.45 (0.34), residues: 652 helix: 3.37 (0.21), residues: 524 sheet: None (None), residues: 0 loop : -2.91 (0.53), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 210 HIS 0.002 0.001 HIS A 197 PHE 0.018 0.001 PHE A 153 TYR 0.021 0.002 TYR B 139 ARG 0.004 0.001 ARG B 90 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 162 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 135 LYS cc_start: 0.8983 (mmmm) cc_final: 0.8196 (mmmm) REVERT: A 139 TYR cc_start: 0.8036 (m-80) cc_final: 0.7433 (m-80) REVERT: A 153 PHE cc_start: 0.8428 (m-80) cc_final: 0.8104 (m-80) REVERT: B 129 TYR cc_start: 0.8273 (t80) cc_final: 0.8038 (t80) REVERT: B 135 LYS cc_start: 0.8959 (mmmm) cc_final: 0.8250 (mmmm) REVERT: B 139 TYR cc_start: 0.7942 (m-80) cc_final: 0.7377 (m-80) REVERT: B 153 PHE cc_start: 0.8385 (m-80) cc_final: 0.8091 (m-80) outliers start: 16 outliers final: 12 residues processed: 169 average time/residue: 0.1428 time to fit residues: 30.6170 Evaluate side-chains 155 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 143 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 232 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 24 optimal weight: 20.0000 chunk 47 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 53 optimal weight: 8.9990 chunk 19 optimal weight: 1.9990 chunk 12 optimal weight: 10.0000 chunk 15 optimal weight: 9.9990 chunk 60 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 chunk 50 optimal weight: 7.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN A 185 ASN B 165 ASN B 185 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.098612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.079424 restraints weight = 15803.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.081531 restraints weight = 9676.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.083000 restraints weight = 6855.523| |-----------------------------------------------------------------------------| r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4356 Z= 0.227 Angle : 0.740 8.678 5994 Z= 0.391 Chirality : 0.041 0.161 724 Planarity : 0.003 0.020 790 Dihedral : 4.621 22.226 690 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 7.99 % Allowed : 28.12 % Favored : 63.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.49 (0.34), residues: 652 helix: 3.30 (0.21), residues: 536 sheet: None (None), residues: 0 loop : -3.03 (0.55), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 210 HIS 0.004 0.002 HIS A 196 PHE 0.011 0.001 PHE A 153 TYR 0.017 0.002 TYR B 171 ARG 0.002 0.001 ARG B 178 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 146 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 139 TYR cc_start: 0.8104 (m-80) cc_final: 0.7835 (m-80) REVERT: A 153 PHE cc_start: 0.8579 (m-10) cc_final: 0.8121 (m-80) REVERT: A 175 LEU cc_start: 0.9278 (OUTLIER) cc_final: 0.9073 (tt) REVERT: A 314 PHE cc_start: 0.9105 (m-80) cc_final: 0.8734 (m-80) REVERT: B 153 PHE cc_start: 0.8545 (m-10) cc_final: 0.8093 (m-80) REVERT: B 314 PHE cc_start: 0.9113 (m-80) cc_final: 0.8743 (m-80) outliers start: 23 outliers final: 19 residues processed: 154 average time/residue: 0.1482 time to fit residues: 28.7509 Evaluate side-chains 159 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 139 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 184 ASN Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 184 ASN Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain B residue 235 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 32 optimal weight: 5.9990 chunk 5 optimal weight: 20.0000 chunk 24 optimal weight: 30.0000 chunk 25 optimal weight: 0.4980 chunk 29 optimal weight: 0.2980 chunk 52 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 chunk 6 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 62 optimal weight: 0.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 ASN A 237 GLN B 185 ASN B 237 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.101233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.082500 restraints weight = 15584.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.084611 restraints weight = 9606.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.086098 restraints weight = 6819.987| |-----------------------------------------------------------------------------| r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.3152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4356 Z= 0.178 Angle : 0.725 8.551 5994 Z= 0.364 Chirality : 0.040 0.149 724 Planarity : 0.003 0.020 790 Dihedral : 4.411 20.104 690 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 7.29 % Allowed : 29.17 % Favored : 63.54 % 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: 3.56 (0.34), residues: 652 helix: 3.33 (0.21), residues: 536 sheet: None (None), residues: 0 loop : -2.94 (0.55), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 210 HIS 0.003 0.001 HIS A 196 PHE 0.015 0.001 PHE B 219 TYR 0.017 0.001 TYR A 246 ARG 0.002 0.000 ARG B 90 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 151 time to evaluate : 0.474 Fit side-chains REVERT: A 175 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8917 (tt) REVERT: A 314 PHE cc_start: 0.9053 (m-80) cc_final: 0.8676 (m-10) outliers start: 21 outliers final: 18 residues processed: 160 average time/residue: 0.1516 time to fit residues: 30.4383 Evaluate side-chains 161 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 142 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 184 ASN Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 184 ASN Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain B residue 235 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 5 optimal weight: 20.0000 chunk 29 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 chunk 41 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 chunk 27 optimal weight: 0.0170 chunk 46 optimal weight: 6.9990 chunk 12 optimal weight: 9.9990 chunk 35 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 overall best weight: 3.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 ASN A 217 GLN B 185 ASN B 217 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.098458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.078989 restraints weight = 16108.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.081086 restraints weight = 9920.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.082507 restraints weight = 7047.694| |-----------------------------------------------------------------------------| r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4356 Z= 0.248 Angle : 0.757 8.265 5994 Z= 0.398 Chirality : 0.042 0.206 724 Planarity : 0.003 0.021 790 Dihedral : 4.568 23.979 690 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 8.68 % Allowed : 32.64 % Favored : 58.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.56 (0.34), residues: 652 helix: 3.25 (0.21), residues: 538 sheet: None (None), residues: 0 loop : -2.57 (0.57), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 210 HIS 0.004 0.002 HIS A 197 PHE 0.028 0.002 PHE A 153 TYR 0.022 0.002 TYR B 171 ARG 0.006 0.001 ARG B 178 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 139 time to evaluate : 0.468 Fit side-chains revert: symmetry clash REVERT: B 165 ASN cc_start: 0.8503 (t0) cc_final: 0.8177 (t0) outliers start: 25 outliers final: 24 residues processed: 150 average time/residue: 0.1532 time to fit residues: 28.6969 Evaluate side-chains 160 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 136 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 184 ASN Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 235 PHE Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 184 ASN Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain B residue 235 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 29 optimal weight: 0.8980 chunk 6 optimal weight: 30.0000 chunk 44 optimal weight: 5.9990 chunk 56 optimal weight: 20.0000 chunk 40 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 57 optimal weight: 0.0030 chunk 58 optimal weight: 0.8980 chunk 46 optimal weight: 4.9990 chunk 28 optimal weight: 10.0000 chunk 55 optimal weight: 1.9990 overall best weight: 0.9594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 ASN B 185 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.101293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.082491 restraints weight = 15389.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.084528 restraints weight = 9537.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.085939 restraints weight = 6798.401| |-----------------------------------------------------------------------------| r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.3294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4356 Z= 0.184 Angle : 0.753 9.420 5994 Z= 0.380 Chirality : 0.041 0.199 724 Planarity : 0.003 0.019 790 Dihedral : 4.441 23.138 690 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 7.99 % Allowed : 32.29 % Favored : 59.72 % 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: 3.47 (0.34), residues: 652 helix: 3.21 (0.21), residues: 538 sheet: None (None), residues: 0 loop : -2.74 (0.57), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 210 HIS 0.003 0.001 HIS A 197 PHE 0.028 0.001 PHE A 153 TYR 0.022 0.002 TYR B 33 ARG 0.003 0.001 ARG B 178 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 146 time to evaluate : 0.517 Fit side-chains revert: symmetry clash outliers start: 23 outliers final: 19 residues processed: 158 average time/residue: 0.1656 time to fit residues: 33.0035 Evaluate side-chains 155 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 136 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 184 ASN Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 235 PHE Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 184 ASN Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain B residue 235 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 27 optimal weight: 8.9990 chunk 31 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 1 optimal weight: 0.9990 chunk 62 optimal weight: 0.6980 chunk 11 optimal weight: 5.9990 chunk 47 optimal weight: 7.9990 chunk 19 optimal weight: 7.9990 chunk 37 optimal weight: 20.0000 chunk 43 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 ASN A 237 GLN B 185 ASN B 237 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.099902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.081062 restraints weight = 15692.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.083128 restraints weight = 9797.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.084614 restraints weight = 6998.408| |-----------------------------------------------------------------------------| r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.3326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 4356 Z= 0.212 Angle : 0.771 8.147 5994 Z= 0.399 Chirality : 0.042 0.215 724 Planarity : 0.004 0.078 790 Dihedral : 4.457 23.811 690 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 7.29 % Allowed : 35.07 % Favored : 57.64 % 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: 3.45 (0.34), residues: 652 helix: 3.17 (0.22), residues: 538 sheet: None (None), residues: 0 loop : -2.61 (0.59), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 210 HIS 0.003 0.001 HIS A 197 PHE 0.028 0.001 PHE B 153 TYR 0.014 0.001 TYR B 238 ARG 0.016 0.001 ARG B 90 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 142 time to evaluate : 0.558 Fit side-chains revert: symmetry clash outliers start: 21 outliers final: 21 residues processed: 151 average time/residue: 0.1575 time to fit residues: 29.8929 Evaluate side-chains 158 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 137 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 184 ASN Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 235 PHE Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 184 ASN Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 219 PHE Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain B residue 235 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 16 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 5 optimal weight: 20.0000 chunk 57 optimal weight: 40.0000 chunk 42 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 3 optimal weight: 10.0000 chunk 52 optimal weight: 7.9990 chunk 49 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 ASN B 185 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.100994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.082191 restraints weight = 15338.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.084059 restraints weight = 9605.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.085574 restraints weight = 7038.417| |-----------------------------------------------------------------------------| r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.3514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4356 Z= 0.200 Angle : 0.770 9.084 5994 Z= 0.394 Chirality : 0.042 0.207 724 Planarity : 0.004 0.057 790 Dihedral : 4.422 23.036 690 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 8.33 % Allowed : 35.42 % Favored : 56.25 % 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: 3.42 (0.34), residues: 652 helix: 3.16 (0.22), residues: 538 sheet: None (None), residues: 0 loop : -2.63 (0.59), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 210 HIS 0.002 0.001 HIS A 197 PHE 0.027 0.001 PHE A 153 TYR 0.014 0.001 TYR B 238 ARG 0.011 0.001 ARG B 90 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 142 time to evaluate : 0.457 Fit side-chains revert: symmetry clash REVERT: B 175 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8815 (tt) outliers start: 24 outliers final: 22 residues processed: 154 average time/residue: 0.1511 time to fit residues: 28.9690 Evaluate side-chains 160 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 137 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 184 ASN Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 235 PHE Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 184 ASN Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 219 PHE Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain B residue 235 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 17 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 26 optimal weight: 9.9990 chunk 57 optimal weight: 40.0000 chunk 32 optimal weight: 7.9990 chunk 20 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 3 optimal weight: 10.0000 chunk 43 optimal weight: 0.0970 chunk 63 optimal weight: 0.9990 chunk 39 optimal weight: 5.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 ASN B 185 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.101930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.082815 restraints weight = 15977.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.084921 restraints weight = 10129.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.086421 restraints weight = 7269.263| |-----------------------------------------------------------------------------| r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.3740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4356 Z= 0.198 Angle : 0.798 10.114 5994 Z= 0.401 Chirality : 0.043 0.242 724 Planarity : 0.003 0.042 790 Dihedral : 4.344 22.257 690 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 7.29 % Allowed : 37.85 % Favored : 54.86 % 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: 3.40 (0.34), residues: 652 helix: 3.14 (0.22), residues: 538 sheet: None (None), residues: 0 loop : -2.60 (0.58), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 210 HIS 0.002 0.001 HIS A 197 PHE 0.028 0.001 PHE A 153 TYR 0.014 0.001 TYR B 238 ARG 0.011 0.001 ARG B 90 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 150 time to evaluate : 0.479 Fit side-chains REVERT: B 175 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8752 (tt) outliers start: 21 outliers final: 20 residues processed: 158 average time/residue: 0.1538 time to fit residues: 30.4915 Evaluate side-chains 165 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 144 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 184 ASN Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 235 PHE Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 184 ASN Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain B residue 235 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 31 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 43 optimal weight: 8.9990 chunk 46 optimal weight: 0.7980 chunk 0 optimal weight: 30.0000 chunk 3 optimal weight: 9.9990 chunk 13 optimal weight: 0.9980 chunk 58 optimal weight: 20.0000 chunk 16 optimal weight: 0.7980 chunk 30 optimal weight: 0.1980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 ASN B 185 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.102327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.083426 restraints weight = 15275.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.085463 restraints weight = 9820.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.086885 restraints weight = 7056.918| |-----------------------------------------------------------------------------| r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.3833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4356 Z= 0.197 Angle : 0.798 11.649 5994 Z= 0.402 Chirality : 0.044 0.291 724 Planarity : 0.003 0.036 790 Dihedral : 4.306 22.023 690 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 7.29 % Allowed : 37.85 % Favored : 54.86 % 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: 3.23 (0.34), residues: 652 helix: 3.05 (0.22), residues: 528 sheet: None (None), residues: 0 loop : -2.32 (0.54), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 210 HIS 0.002 0.001 HIS A 197 PHE 0.028 0.002 PHE A 153 TYR 0.014 0.001 TYR B 238 ARG 0.009 0.001 ARG B 90 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 145 time to evaluate : 0.524 Fit side-chains REVERT: B 175 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8754 (tt) outliers start: 21 outliers final: 20 residues processed: 154 average time/residue: 0.1584 time to fit residues: 30.9708 Evaluate side-chains 163 residues out of total 594 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 142 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 184 ASN Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 210 TRP Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 235 PHE Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 184 ASN Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain B residue 235 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 12 optimal weight: 9.9990 chunk 17 optimal weight: 0.9990 chunk 22 optimal weight: 8.9990 chunk 31 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 37 optimal weight: 20.0000 chunk 23 optimal weight: 8.9990 chunk 13 optimal weight: 2.9990 chunk 38 optimal weight: 20.0000 chunk 21 optimal weight: 0.9980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 ASN B 185 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.101383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.082545 restraints weight = 15329.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.084645 restraints weight = 9686.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.086060 restraints weight = 6943.982| |-----------------------------------------------------------------------------| r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.3796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4356 Z= 0.205 Angle : 0.799 11.538 5994 Z= 0.404 Chirality : 0.044 0.295 724 Planarity : 0.003 0.031 790 Dihedral : 4.292 21.955 690 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 7.29 % Allowed : 38.89 % Favored : 53.82 % 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: 3.30 (0.34), residues: 652 helix: 3.07 (0.22), residues: 528 sheet: None (None), residues: 0 loop : -2.11 (0.53), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 210 HIS 0.002 0.001 HIS A 197 PHE 0.026 0.001 PHE A 153 TYR 0.014 0.001 TYR B 238 ARG 0.009 0.001 ARG B 90 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1572.03 seconds wall clock time: 28 minutes 47.08 seconds (1727.08 seconds total)