Starting phenix.real_space_refine on Wed Mar 12 00:38:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b9r_44389/03_2025/9b9r_44389.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b9r_44389/03_2025/9b9r_44389.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b9r_44389/03_2025/9b9r_44389.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b9r_44389/03_2025/9b9r_44389.map" model { file = "/net/cci-nas-00/data/ceres_data/9b9r_44389/03_2025/9b9r_44389.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b9r_44389/03_2025/9b9r_44389.cif" } resolution = 3.7 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= 0.001 sd= 0.017 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 S 36 5.16 5 C 2220 2.51 5 N 612 2.21 5 O 624 1.98 5 H 3436 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 6928 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 1732 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 1, 'TRANS': 109} Chain breaks: 1 Chain: "B" Number of atoms: 1732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 1732 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 1, 'TRANS': 109} Chain breaks: 1 Chain: "C" Number of atoms: 1732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 1732 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 1, 'TRANS': 109} Chain breaks: 1 Chain: "D" Number of atoms: 1732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 1732 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 1, 'TRANS': 109} Chain breaks: 1 Time building chain proxies: 3.75, per 1000 atoms: 0.54 Number of scatterers: 6928 At special positions: 0 Unit cell: (95.85, 71.55, 87.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 36 16.00 O 624 8.00 N 612 7.00 C 2220 6.00 H 3436 1.00 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: 1.56 Conformation dependent library (CDL) restraints added in 562.2 milliseconds 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 856 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 4 sheets defined 66.9% alpha, 9.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'A' and resid 5 through 21 Processing helix chain 'A' and resid 38 through 46 Processing helix chain 'A' and resid 46 through 53 Processing helix chain 'A' and resid 73 through 87 removed outlier: 3.550A pdb=" N TYR A 85 " --> pdb=" O ILE A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 106 Processing helix chain 'A' and resid 108 through 119 Processing helix chain 'B' and resid 5 through 21 Processing helix chain 'B' and resid 38 through 46 Processing helix chain 'B' and resid 46 through 54 Processing helix chain 'B' and resid 73 through 87 Processing helix chain 'B' and resid 95 through 106 Processing helix chain 'B' and resid 108 through 120 Processing helix chain 'C' and resid 5 through 21 Processing helix chain 'C' and resid 38 through 46 Processing helix chain 'C' and resid 46 through 54 Processing helix chain 'C' and resid 73 through 87 Processing helix chain 'C' and resid 95 through 106 Processing helix chain 'C' and resid 108 through 120 Processing helix chain 'D' and resid 5 through 21 Processing helix chain 'D' and resid 38 through 46 Processing helix chain 'D' and resid 46 through 53 Processing helix chain 'D' and resid 73 through 87 Processing helix chain 'D' and resid 95 through 106 Processing helix chain 'D' and resid 108 through 120 Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 37 Processing sheet with id=AA2, first strand: chain 'B' and resid 33 through 37 Processing sheet with id=AA3, first strand: chain 'C' and resid 33 through 37 Processing sheet with id=AA4, first strand: chain 'D' and resid 33 through 37 233 hydrogen bonds defined for protein. 675 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: 2.22 Time building geometry restraints manager: 1.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 3420 1.03 - 1.23: 16 1.23 - 1.42: 1532 1.42 - 1.62: 1972 1.62 - 1.81: 56 Bond restraints: 6996 Sorted by residual: bond pdb=" CA VAL A 111 " pdb=" C VAL A 111 " ideal model delta sigma weight residual 1.524 1.512 0.012 1.39e-02 5.18e+03 7.43e-01 bond pdb=" N VAL A 99 " pdb=" CA VAL A 99 " ideal model delta sigma weight residual 1.459 1.448 0.011 1.30e-02 5.92e+03 7.19e-01 bond pdb=" CA VAL C 41 " pdb=" C VAL C 41 " ideal model delta sigma weight residual 1.524 1.513 0.011 1.33e-02 5.65e+03 6.66e-01 bond pdb=" CA VAL B 111 " pdb=" C VAL B 111 " ideal model delta sigma weight residual 1.524 1.513 0.011 1.39e-02 5.18e+03 6.37e-01 bond pdb=" CA ASP A 98 " pdb=" C ASP A 98 " ideal model delta sigma weight residual 1.524 1.513 0.010 1.32e-02 5.74e+03 6.31e-01 ... (remaining 6991 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 12264 1.56 - 3.13: 275 3.13 - 4.69: 14 4.69 - 6.25: 6 6.25 - 7.82: 1 Bond angle restraints: 12560 Sorted by residual: angle pdb=" N VAL A 99 " pdb=" CA VAL A 99 " pdb=" C VAL A 99 " ideal model delta sigma weight residual 111.09 106.37 4.72 1.25e+00 6.40e-01 1.43e+01 angle pdb=" N GLY C 92 " pdb=" CA GLY C 92 " pdb=" C GLY C 92 " ideal model delta sigma weight residual 113.18 105.36 7.82 2.37e+00 1.78e-01 1.09e+01 angle pdb=" C ASP D 25 " pdb=" N CYS D 26 " pdb=" CA CYS D 26 " ideal model delta sigma weight residual 121.75 116.88 4.87 1.73e+00 3.34e-01 7.92e+00 angle pdb=" N GLY D 31 " pdb=" CA GLY D 31 " pdb=" C GLY D 31 " ideal model delta sigma weight residual 111.02 105.82 5.20 1.86e+00 2.89e-01 7.81e+00 angle pdb=" N GLY B 31 " pdb=" CA GLY B 31 " pdb=" C GLY B 31 " ideal model delta sigma weight residual 111.02 105.89 5.13 1.86e+00 2.89e-01 7.60e+00 ... (remaining 12555 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.01: 3072 13.01 - 26.01: 171 26.01 - 39.02: 24 39.02 - 52.02: 29 52.02 - 65.03: 8 Dihedral angle restraints: 3304 sinusoidal: 1716 harmonic: 1588 Sorted by residual: dihedral pdb=" CA ASP C 68 " pdb=" CB ASP C 68 " pdb=" CG ASP C 68 " pdb=" OD1 ASP C 68 " ideal model delta sinusoidal sigma weight residual -30.00 -83.44 53.44 1 2.00e+01 2.50e-03 9.70e+00 dihedral pdb=" CA ASP A 68 " pdb=" CB ASP A 68 " pdb=" CG ASP A 68 " pdb=" OD1 ASP A 68 " ideal model delta sinusoidal sigma weight residual -30.00 -80.96 50.96 1 2.00e+01 2.50e-03 8.88e+00 dihedral pdb=" CB MET B 97 " pdb=" CG MET B 97 " pdb=" SD MET B 97 " pdb=" CE MET B 97 " ideal model delta sinusoidal sigma weight residual -60.00 -109.23 49.23 3 1.50e+01 4.44e-03 8.75e+00 ... (remaining 3301 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 402 0.033 - 0.066: 91 0.066 - 0.099: 53 0.099 - 0.132: 7 0.132 - 0.165: 7 Chirality restraints: 560 Sorted by residual: chirality pdb=" CA ILE D 28 " pdb=" N ILE D 28 " pdb=" C ILE D 28 " pdb=" CB ILE D 28 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.83e-01 chirality pdb=" CA ILE B 28 " pdb=" N ILE B 28 " pdb=" C ILE B 28 " pdb=" CB ILE B 28 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.89e-01 chirality pdb=" CA ILE A 28 " pdb=" N ILE A 28 " pdb=" C ILE A 28 " pdb=" CB ILE A 28 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.85e-01 ... (remaining 557 not shown) Planarity restraints: 1040 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER C 40 " -0.018 2.00e-02 2.50e+03 3.67e-02 1.35e+01 pdb=" C SER C 40 " 0.064 2.00e-02 2.50e+03 pdb=" O SER C 40 " -0.024 2.00e-02 2.50e+03 pdb=" N VAL C 41 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 97 " -0.013 2.00e-02 2.50e+03 2.64e-02 6.95e+00 pdb=" C MET A 97 " 0.046 2.00e-02 2.50e+03 pdb=" O MET A 97 " -0.017 2.00e-02 2.50e+03 pdb=" N ASP A 98 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 110 " 0.011 2.00e-02 2.50e+03 2.28e-02 5.18e+00 pdb=" C SER B 110 " -0.039 2.00e-02 2.50e+03 pdb=" O SER B 110 " 0.015 2.00e-02 2.50e+03 pdb=" N VAL B 111 " 0.013 2.00e-02 2.50e+03 ... (remaining 1037 not shown) Histogram of nonbonded interaction distances: 1.50 - 2.12: 113 2.12 - 2.74: 12115 2.74 - 3.36: 19705 3.36 - 3.98: 24861 3.98 - 4.60: 39064 Nonbonded interactions: 95858 Sorted by model distance: nonbonded pdb=" HG SER B 46 " pdb=" O LEU B 106 " model vdw 1.498 2.450 nonbonded pdb=" HG SER A 46 " pdb=" O LEU A 106 " model vdw 1.573 2.450 nonbonded pdb=" O ASP D 82 " pdb=" HG1 THR D 86 " model vdw 1.587 2.450 nonbonded pdb=" O ASP B 82 " pdb=" HG1 THR B 86 " model vdw 1.606 2.450 nonbonded pdb=" O ASP A 82 " pdb=" HG1 THR A 86 " model vdw 1.667 2.450 ... (remaining 95853 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 0.520 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: 0.160 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 18.180 Find NCS groups from input model: 0.160 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 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 : 0.002 0.020 3560 Z= 0.148 Angle : 0.680 7.817 4808 Z= 0.458 Chirality : 0.039 0.165 560 Planarity : 0.005 0.037 608 Dihedral : 11.042 65.027 1244 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.33), residues: 428 helix: 0.35 (0.25), residues: 284 sheet: None (None), residues: 0 loop : 0.72 (0.43), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS B 6 PHE 0.014 0.002 PHE D 11 TYR 0.017 0.003 TYR A 85 ARG 0.007 0.001 ARG B 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 214 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 ASP cc_start: 0.9283 (t70) cc_final: 0.8848 (t0) REVERT: A 112 VAL cc_start: 0.9567 (t) cc_final: 0.9362 (m) REVERT: B 35 PHE cc_start: 0.8604 (m-80) cc_final: 0.7837 (m-80) REVERT: B 82 ASP cc_start: 0.8346 (m-30) cc_final: 0.7854 (t0) REVERT: C 41 VAL cc_start: 0.9239 (t) cc_final: 0.8863 (m) REVERT: C 45 CYS cc_start: 0.7349 (m) cc_final: 0.7067 (m) REVERT: C 111 VAL cc_start: 0.9186 (t) cc_final: 0.8956 (t) REVERT: D 15 ASN cc_start: 0.9305 (t0) cc_final: 0.9025 (t0) REVERT: D 16 TYR cc_start: 0.8588 (t80) cc_final: 0.8329 (t80) REVERT: D 20 HIS cc_start: 0.8943 (m-70) cc_final: 0.8520 (m-70) REVERT: D 30 VAL cc_start: 0.8675 (t) cc_final: 0.8400 (p) REVERT: D 68 ASP cc_start: 0.9508 (t0) cc_final: 0.9217 (t0) REVERT: D 82 ASP cc_start: 0.9171 (m-30) cc_final: 0.8967 (m-30) outliers start: 0 outliers final: 0 residues processed: 214 average time/residue: 0.2680 time to fit residues: 71.3670 Evaluate side-chains 141 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 37 optimal weight: 3.9990 chunk 33 optimal weight: 0.4980 chunk 18 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 17 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 13 optimal weight: 0.3980 chunk 20 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS B 15 ASN B 20 HIS ** B 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.064346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.056448 restraints weight = 48499.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.059124 restraints weight = 20004.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.060787 restraints weight = 10398.406| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.5221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3560 Z= 0.200 Angle : 0.588 4.929 4808 Z= 0.330 Chirality : 0.039 0.170 560 Planarity : 0.003 0.026 608 Dihedral : 3.815 15.227 464 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Rotamer: Outliers : 2.34 % Allowed : 16.67 % Favored : 80.99 % 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: 2.07 (0.37), residues: 428 helix: 1.75 (0.28), residues: 288 sheet: None (None), residues: 0 loop : 0.75 (0.45), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 20 PHE 0.017 0.002 PHE D 77 TYR 0.007 0.001 TYR C 16 ARG 0.002 0.000 ARG D 50 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 146 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 GLU cc_start: 0.9189 (mp0) cc_final: 0.8786 (mp0) REVERT: A 68 ASP cc_start: 0.9575 (t70) cc_final: 0.9315 (t0) REVERT: A 90 MET cc_start: 0.5549 (mmm) cc_final: 0.5011 (mmm) REVERT: B 8 GLU cc_start: 0.9124 (mp0) cc_final: 0.8775 (mp0) REVERT: B 36 LYS cc_start: 0.9458 (mttt) cc_final: 0.9190 (mmmm) REVERT: B 82 ASP cc_start: 0.8322 (m-30) cc_final: 0.7853 (t0) REVERT: B 83 MET cc_start: 0.8307 (tmt) cc_final: 0.7605 (tmm) REVERT: B 86 THR cc_start: 0.7921 (p) cc_final: 0.7664 (p) REVERT: D 9 GLN cc_start: 0.9266 (pt0) cc_final: 0.8886 (mp10) REVERT: D 15 ASN cc_start: 0.9496 (t0) cc_final: 0.9275 (t0) REVERT: D 16 TYR cc_start: 0.8888 (t80) cc_final: 0.8653 (t80) REVERT: D 20 HIS cc_start: 0.8893 (m-70) cc_final: 0.8563 (m-70) REVERT: D 64 MET cc_start: 0.8758 (ppp) cc_final: 0.8030 (ppp) REVERT: D 68 ASP cc_start: 0.9474 (t0) cc_final: 0.9195 (t0) REVERT: D 82 ASP cc_start: 0.9204 (m-30) cc_final: 0.8945 (m-30) outliers start: 9 outliers final: 5 residues processed: 154 average time/residue: 0.2497 time to fit residues: 48.8113 Evaluate side-chains 136 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 131 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 HIS Chi-restraints excluded: chain B residue 15 ASN Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 87 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 1 optimal weight: 2.9990 chunk 14 optimal weight: 8.9990 chunk 41 optimal weight: 0.0870 chunk 25 optimal weight: 6.9990 chunk 13 optimal weight: 0.6980 chunk 38 optimal weight: 0.0010 chunk 33 optimal weight: 0.3980 chunk 2 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 overall best weight: 0.6366 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS C 34 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.064327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.056269 restraints weight = 49186.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.058938 restraints weight = 20248.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.060681 restraints weight = 10519.938| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.6092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3560 Z= 0.180 Angle : 0.555 4.470 4808 Z= 0.305 Chirality : 0.037 0.190 560 Planarity : 0.003 0.019 608 Dihedral : 3.803 14.118 464 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 2.08 % Allowed : 20.05 % Favored : 77.86 % 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: 2.09 (0.37), residues: 428 helix: 1.87 (0.29), residues: 288 sheet: None (None), residues: 0 loop : 0.51 (0.44), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS A 34 PHE 0.016 0.001 PHE D 77 TYR 0.004 0.001 TYR B 85 ARG 0.002 0.000 ARG D 50 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 135 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 CYS cc_start: 0.9462 (t) cc_final: 0.9163 (t) REVERT: A 68 ASP cc_start: 0.9588 (t70) cc_final: 0.9327 (t0) REVERT: A 90 MET cc_start: 0.5552 (mmm) cc_final: 0.5024 (mmm) REVERT: B 8 GLU cc_start: 0.9257 (mp0) cc_final: 0.8847 (mp0) REVERT: B 15 ASN cc_start: 0.8948 (OUTLIER) cc_final: 0.8572 (m110) REVERT: B 22 GLN cc_start: 0.9399 (tp40) cc_final: 0.9041 (mt0) REVERT: B 45 CYS cc_start: 0.7646 (m) cc_final: 0.5504 (m) REVERT: B 82 ASP cc_start: 0.8354 (m-30) cc_final: 0.7883 (t0) REVERT: B 83 MET cc_start: 0.8317 (tmt) cc_final: 0.7642 (tmm) REVERT: B 86 THR cc_start: 0.8168 (p) cc_final: 0.7885 (p) REVERT: C 84 MET cc_start: 0.9398 (ttp) cc_final: 0.9135 (tpp) REVERT: D 9 GLN cc_start: 0.9269 (pt0) cc_final: 0.8932 (mp10) REVERT: D 15 ASN cc_start: 0.9521 (t0) cc_final: 0.9305 (t0) REVERT: D 64 MET cc_start: 0.8880 (ppp) cc_final: 0.8170 (ppp) REVERT: D 68 ASP cc_start: 0.9458 (t0) cc_final: 0.9176 (t0) REVERT: D 82 ASP cc_start: 0.9180 (m-30) cc_final: 0.8939 (m-30) outliers start: 8 outliers final: 4 residues processed: 140 average time/residue: 0.2327 time to fit residues: 42.0230 Evaluate side-chains 133 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 128 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain B residue 15 ASN Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 94 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 14 optimal weight: 7.9990 chunk 16 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 28 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 15 optimal weight: 0.9980 chunk 3 optimal weight: 5.9990 chunk 6 optimal weight: 0.0870 overall best weight: 1.3362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 105 HIS ** 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 = 0.3375 r_free = 0.3375 target = 0.063021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.055076 restraints weight = 49209.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.057721 restraints weight = 20094.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.059439 restraints weight = 10413.436| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.7125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3560 Z= 0.205 Angle : 0.564 5.785 4808 Z= 0.312 Chirality : 0.037 0.168 560 Planarity : 0.003 0.016 608 Dihedral : 3.770 13.157 464 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Rotamer: Outliers : 2.34 % Allowed : 18.75 % 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: 1.89 (0.37), residues: 428 helix: 1.77 (0.29), residues: 288 sheet: None (None), residues: 0 loop : 0.29 (0.44), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 20 PHE 0.011 0.002 PHE D 77 TYR 0.009 0.001 TYR D 16 ARG 0.002 0.000 ARG D 50 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 126 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 GLU cc_start: 0.9153 (mp0) cc_final: 0.8863 (mp0) REVERT: A 68 ASP cc_start: 0.9575 (t70) cc_final: 0.9375 (t0) REVERT: A 70 GLU cc_start: 0.9513 (tp30) cc_final: 0.9276 (tp30) REVERT: A 90 MET cc_start: 0.6256 (mmm) cc_final: 0.5793 (mmm) REVERT: B 8 GLU cc_start: 0.9262 (mp0) cc_final: 0.8960 (mp0) REVERT: B 42 LEU cc_start: 0.9414 (mt) cc_final: 0.8802 (mt) REVERT: B 82 ASP cc_start: 0.8296 (m-30) cc_final: 0.7735 (t70) REVERT: B 83 MET cc_start: 0.8315 (tmt) cc_final: 0.7476 (tmm) REVERT: B 86 THR cc_start: 0.8072 (p) cc_final: 0.7788 (p) REVERT: C 75 GLU cc_start: 0.9326 (mp0) cc_final: 0.9048 (mp0) REVERT: C 90 MET cc_start: 0.6937 (mmp) cc_final: 0.6619 (mmm) REVERT: D 9 GLN cc_start: 0.9289 (pt0) cc_final: 0.8982 (mp10) REVERT: D 15 ASN cc_start: 0.9526 (t0) cc_final: 0.9298 (t0) REVERT: D 64 MET cc_start: 0.8925 (ppp) cc_final: 0.8148 (ppp) REVERT: D 68 ASP cc_start: 0.9453 (t0) cc_final: 0.8948 (t0) REVERT: D 82 ASP cc_start: 0.9235 (m-30) cc_final: 0.9011 (m-30) outliers start: 9 outliers final: 8 residues processed: 129 average time/residue: 0.2248 time to fit residues: 37.6876 Evaluate side-chains 122 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 114 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 100 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 36 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 10 optimal weight: 0.3980 chunk 4 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 15 ASN B 17 GLN C 107 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.062013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.054300 restraints weight = 50260.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.056934 restraints weight = 20883.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.058679 restraints weight = 10799.313| |-----------------------------------------------------------------------------| r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.7588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3560 Z= 0.170 Angle : 0.550 6.955 4808 Z= 0.296 Chirality : 0.037 0.163 560 Planarity : 0.002 0.016 608 Dihedral : 3.732 13.266 464 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Rotamer: Outliers : 2.34 % Allowed : 21.61 % Favored : 76.04 % 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: 2.00 (0.38), residues: 428 helix: 1.88 (0.30), residues: 288 sheet: None (None), residues: 0 loop : 0.27 (0.44), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 6 PHE 0.010 0.001 PHE D 77 TYR 0.013 0.001 TYR D 16 ARG 0.004 0.000 ARG B 50 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 129 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 GLU cc_start: 0.9160 (mp0) cc_final: 0.8803 (mp0) REVERT: A 90 MET cc_start: 0.6254 (mmm) cc_final: 0.5800 (mmm) REVERT: B 8 GLU cc_start: 0.9268 (mp0) cc_final: 0.9035 (mp0) REVERT: B 82 ASP cc_start: 0.8372 (m-30) cc_final: 0.7775 (t70) REVERT: B 83 MET cc_start: 0.8444 (tmt) cc_final: 0.7928 (tmm) REVERT: B 86 THR cc_start: 0.8187 (p) cc_final: 0.7850 (p) REVERT: B 91 LEU cc_start: 0.8589 (mt) cc_final: 0.8384 (mm) REVERT: C 75 GLU cc_start: 0.9336 (mp0) cc_final: 0.9120 (mp0) REVERT: D 9 GLN cc_start: 0.9268 (pt0) cc_final: 0.9017 (mp10) REVERT: D 15 ASN cc_start: 0.9537 (t0) cc_final: 0.9321 (t0) REVERT: D 64 MET cc_start: 0.8970 (ppp) cc_final: 0.8202 (ppp) REVERT: D 68 ASP cc_start: 0.9303 (t0) cc_final: 0.8956 (t0) REVERT: D 82 ASP cc_start: 0.9237 (m-30) cc_final: 0.9006 (m-30) REVERT: D 83 MET cc_start: 0.9390 (tmm) cc_final: 0.9126 (tmm) outliers start: 9 outliers final: 7 residues processed: 134 average time/residue: 0.2331 time to fit residues: 40.3282 Evaluate side-chains 125 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 118 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain B residue 15 ASN Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 100 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 3 optimal weight: 4.9990 chunk 21 optimal weight: 0.7980 chunk 27 optimal weight: 6.9990 chunk 29 optimal weight: 4.9990 chunk 18 optimal weight: 0.4980 chunk 7 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 41 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.062121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.053896 restraints weight = 49939.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.056603 restraints weight = 20850.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.058350 restraints weight = 10856.417| |-----------------------------------------------------------------------------| r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.7858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 3560 Z= 0.162 Angle : 0.553 5.322 4808 Z= 0.295 Chirality : 0.037 0.155 560 Planarity : 0.002 0.017 608 Dihedral : 3.718 14.632 464 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Rotamer: Outliers : 2.34 % Allowed : 24.74 % Favored : 72.92 % 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: 1.97 (0.38), residues: 428 helix: 1.88 (0.30), residues: 288 sheet: None (None), residues: 0 loop : 0.21 (0.43), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 20 PHE 0.008 0.001 PHE A 77 TYR 0.010 0.001 TYR D 16 ARG 0.002 0.000 ARG D 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 122 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.6249 (mmm) cc_final: 0.5786 (mmm) REVERT: B 8 GLU cc_start: 0.9296 (mp0) cc_final: 0.9043 (mp0) REVERT: B 82 ASP cc_start: 0.8427 (m-30) cc_final: 0.7915 (t0) REVERT: B 83 MET cc_start: 0.8518 (tmt) cc_final: 0.8003 (tmm) REVERT: B 86 THR cc_start: 0.8327 (p) cc_final: 0.7979 (p) REVERT: B 91 LEU cc_start: 0.8615 (mt) cc_final: 0.8403 (mm) REVERT: D 15 ASN cc_start: 0.9533 (t0) cc_final: 0.9318 (t0) REVERT: D 64 MET cc_start: 0.9041 (ppp) cc_final: 0.8253 (ppp) REVERT: D 68 ASP cc_start: 0.9228 (t0) cc_final: 0.8884 (t0) REVERT: D 82 ASP cc_start: 0.9254 (m-30) cc_final: 0.9029 (m-30) REVERT: D 83 MET cc_start: 0.9448 (tmm) cc_final: 0.9136 (tmm) outliers start: 9 outliers final: 9 residues processed: 126 average time/residue: 0.2242 time to fit residues: 36.7967 Evaluate side-chains 128 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 119 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain B residue 15 ASN Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 100 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 18 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 30 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 14 optimal weight: 6.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 HIS B 17 GLN B 107 HIS C 105 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.059928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.052233 restraints weight = 52253.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.054852 restraints weight = 21894.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.056517 restraints weight = 11303.413| |-----------------------------------------------------------------------------| r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.8499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 3560 Z= 0.243 Angle : 0.626 5.958 4808 Z= 0.351 Chirality : 0.037 0.143 560 Planarity : 0.003 0.014 608 Dihedral : 3.784 14.333 464 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 2.34 % Allowed : 27.60 % Favored : 70.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.38), residues: 428 helix: 1.57 (0.30), residues: 288 sheet: None (None), residues: 0 loop : 0.06 (0.44), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.002 HIS D 6 PHE 0.013 0.002 PHE A 77 TYR 0.011 0.001 TYR D 16 ARG 0.003 0.000 ARG A 50 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 116 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 GLU cc_start: 0.9134 (mp0) cc_final: 0.8929 (mp0) REVERT: B 8 GLU cc_start: 0.9212 (mp0) cc_final: 0.8989 (mp0) REVERT: B 70 GLU cc_start: 0.9471 (mp0) cc_final: 0.9194 (pm20) REVERT: B 82 ASP cc_start: 0.8758 (m-30) cc_final: 0.8147 (t70) REVERT: B 83 MET cc_start: 0.8642 (tmt) cc_final: 0.8116 (tmm) REVERT: B 86 THR cc_start: 0.8469 (p) cc_final: 0.8101 (p) REVERT: D 64 MET cc_start: 0.9012 (ppp) cc_final: 0.8273 (ppp) REVERT: D 68 ASP cc_start: 0.9299 (t0) cc_final: 0.9051 (t70) REVERT: D 82 ASP cc_start: 0.9340 (m-30) cc_final: 0.9102 (m-30) REVERT: D 83 MET cc_start: 0.9471 (tmm) cc_final: 0.9143 (tmm) REVERT: D 110 SER cc_start: 0.9583 (p) cc_final: 0.9268 (p) outliers start: 9 outliers final: 9 residues processed: 118 average time/residue: 0.2280 time to fit residues: 35.1434 Evaluate side-chains 120 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 111 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 100 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 17 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 15 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.059789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.052117 restraints weight = 51892.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.054686 restraints weight = 21038.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.056332 restraints weight = 10776.408| |-----------------------------------------------------------------------------| r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.8825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3560 Z= 0.198 Angle : 0.597 6.276 4808 Z= 0.323 Chirality : 0.037 0.148 560 Planarity : 0.002 0.015 608 Dihedral : 3.830 13.853 464 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 2.08 % Allowed : 28.12 % Favored : 69.79 % 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: 1.64 (0.38), residues: 428 helix: 1.64 (0.30), residues: 288 sheet: None (None), residues: 0 loop : 0.03 (0.44), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 6 PHE 0.008 0.001 PHE A 77 TYR 0.006 0.001 TYR D 16 ARG 0.001 0.000 ARG D 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 115 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 MET cc_start: 0.8863 (ptp) cc_final: 0.8568 (pmm) REVERT: B 8 GLU cc_start: 0.9262 (mp0) cc_final: 0.9035 (mp0) REVERT: B 70 GLU cc_start: 0.9450 (mp0) cc_final: 0.9248 (pm20) REVERT: B 82 ASP cc_start: 0.8771 (m-30) cc_final: 0.8251 (t70) REVERT: B 83 MET cc_start: 0.8805 (tmt) cc_final: 0.8286 (tmm) REVERT: B 86 THR cc_start: 0.8614 (p) cc_final: 0.8337 (p) REVERT: D 64 MET cc_start: 0.9033 (ppp) cc_final: 0.8264 (ppp) REVERT: D 68 ASP cc_start: 0.9329 (t0) cc_final: 0.9023 (t0) REVERT: D 82 ASP cc_start: 0.9359 (m-30) cc_final: 0.9129 (m-30) REVERT: D 83 MET cc_start: 0.9514 (tmm) cc_final: 0.9148 (tmm) REVERT: D 110 SER cc_start: 0.9574 (p) cc_final: 0.9269 (p) outliers start: 8 outliers final: 8 residues processed: 118 average time/residue: 0.2311 time to fit residues: 35.5095 Evaluate side-chains 120 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 112 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain B residue 15 ASN Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain D residue 87 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 2 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 19 optimal weight: 0.2980 chunk 36 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 34 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 overall best weight: 1.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.060452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.052452 restraints weight = 52792.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.055090 restraints weight = 21973.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.056817 restraints weight = 11506.101| |-----------------------------------------------------------------------------| r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.8833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3560 Z= 0.225 Angle : 1.221 59.192 4808 Z= 0.724 Chirality : 0.037 0.145 560 Planarity : 0.002 0.013 608 Dihedral : 3.827 13.827 464 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 1.82 % Allowed : 28.39 % Favored : 69.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.38), residues: 428 helix: 1.59 (0.30), residues: 288 sheet: None (None), residues: 0 loop : 0.03 (0.44), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 6 PHE 0.008 0.001 PHE A 77 TYR 0.008 0.001 TYR D 16 ARG 0.002 0.000 ARG A 50 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 112 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 MET cc_start: 0.8894 (ptp) cc_final: 0.8616 (pmm) REVERT: B 8 GLU cc_start: 0.9251 (mp0) cc_final: 0.9029 (mp0) REVERT: B 70 GLU cc_start: 0.9456 (mp0) cc_final: 0.9249 (pm20) REVERT: B 82 ASP cc_start: 0.8773 (m-30) cc_final: 0.8251 (t70) REVERT: B 83 MET cc_start: 0.8810 (tmt) cc_final: 0.8284 (tmm) REVERT: B 86 THR cc_start: 0.8621 (p) cc_final: 0.8343 (p) REVERT: D 64 MET cc_start: 0.9045 (ppp) cc_final: 0.8268 (ppp) REVERT: D 68 ASP cc_start: 0.9327 (t0) cc_final: 0.9020 (t0) REVERT: D 82 ASP cc_start: 0.9364 (m-30) cc_final: 0.9133 (m-30) REVERT: D 83 MET cc_start: 0.9517 (tmm) cc_final: 0.9145 (tmm) REVERT: D 110 SER cc_start: 0.9580 (p) cc_final: 0.9272 (p) outliers start: 7 outliers final: 7 residues processed: 114 average time/residue: 0.2299 time to fit residues: 34.0764 Evaluate side-chains 119 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 112 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain D residue 87 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 4 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 12 optimal weight: 50.0000 chunk 11 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 8 optimal weight: 4.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.060521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.052508 restraints weight = 53423.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.055168 restraints weight = 22075.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.056815 restraints weight = 11488.699| |-----------------------------------------------------------------------------| r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.8858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3560 Z= 0.226 Angle : 1.218 59.025 4808 Z= 0.723 Chirality : 0.037 0.143 560 Planarity : 0.002 0.013 608 Dihedral : 3.827 13.844 464 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 1.82 % Allowed : 28.39 % Favored : 69.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.38), residues: 428 helix: 1.59 (0.30), residues: 288 sheet: None (None), residues: 0 loop : 0.03 (0.44), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 6 PHE 0.008 0.001 PHE A 77 TYR 0.007 0.001 TYR D 16 ARG 0.002 0.000 ARG A 50 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 856 Ramachandran restraints generated. 428 Oldfield, 0 Emsley, 428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 112 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 MET cc_start: 0.8896 (ptp) cc_final: 0.8617 (pmm) REVERT: B 8 GLU cc_start: 0.9256 (mp0) cc_final: 0.9031 (mp0) REVERT: B 70 GLU cc_start: 0.9457 (mp0) cc_final: 0.9248 (pm20) REVERT: B 82 ASP cc_start: 0.8773 (m-30) cc_final: 0.8249 (t70) REVERT: B 83 MET cc_start: 0.8811 (tmt) cc_final: 0.8283 (tmm) REVERT: B 86 THR cc_start: 0.8621 (p) cc_final: 0.8343 (p) REVERT: D 64 MET cc_start: 0.9046 (ppp) cc_final: 0.8268 (ppp) REVERT: D 68 ASP cc_start: 0.9323 (t0) cc_final: 0.9016 (t0) REVERT: D 82 ASP cc_start: 0.9363 (m-30) cc_final: 0.9131 (m-30) REVERT: D 83 MET cc_start: 0.9516 (tmm) cc_final: 0.9144 (tmm) REVERT: D 110 SER cc_start: 0.9579 (p) cc_final: 0.9272 (p) outliers start: 7 outliers final: 7 residues processed: 114 average time/residue: 0.2318 time to fit residues: 34.4291 Evaluate side-chains 119 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 112 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain D residue 87 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 21 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 12 optimal weight: 50.0000 chunk 25 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.060528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.052536 restraints weight = 52940.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.055186 restraints weight = 21982.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.056906 restraints weight = 11449.439| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.8858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3560 Z= 0.226 Angle : 1.218 59.025 4808 Z= 0.723 Chirality : 0.037 0.143 560 Planarity : 0.002 0.013 608 Dihedral : 3.827 13.844 464 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 1.82 % Allowed : 28.39 % Favored : 69.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.38), residues: 428 helix: 1.59 (0.30), residues: 288 sheet: None (None), residues: 0 loop : 0.03 (0.44), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 6 PHE 0.008 0.001 PHE A 77 TYR 0.007 0.001 TYR D 16 ARG 0.002 0.000 ARG A 50 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2880.58 seconds wall clock time: 49 minutes 53.13 seconds (2993.13 seconds total)