Starting phenix.real_space_refine on Tue Jan 14 16:18:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b9r_44389/01_2025/9b9r_44389.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b9r_44389/01_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_44389/01_2025/9b9r_44389.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b9r_44389/01_2025/9b9r_44389.map" model { file = "/net/cci-nas-00/data/ceres_data/9b9r_44389/01_2025/9b9r_44389.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b9r_44389/01_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-5571/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: 3.67, per 1000 atoms: 0.53 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: 1.89 Conformation dependent library (CDL) restraints added in 609.7 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: 0.53 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: 2.36 Time building geometry restraints manager: 2.21 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: 0.000 Normalize map: mean=0, sd=1: 0.390 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: 0.130 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 18.510 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: 0.010 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.650 ------------------------------------------------------------------------------- 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 : 0.603 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: 0.2795 time to fit residues: 74.4045 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 : 0.545 ------------------------------------------------------------------------------- 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 = 0.056447 restraints weight = 48498.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.059117 restraints weight = 20004.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.060784 restraints weight = 10410.674| |-----------------------------------------------------------------------------| 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 : 0.519 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: 0.9576 (t70) cc_final: 0.9315 (t0) REVERT: A 90 MET cc_start: 0.5548 (mmm) cc_final: 0.5009 (mmm) REVERT: B 8 GLU cc_start: 0.9125 (mp0) cc_final: 0.8777 (mp0) REVERT: B 36 LYS cc_start: 0.9459 (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: 0.8310 (tmt) cc_final: 0.7607 (tmm) REVERT: B 86 THR cc_start: 0.7922 (p) cc_final: 0.7665 (p) REVERT: D 9 GLN cc_start: 0.9266 (pt0) cc_final: 0.8887 (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: 0.8891 (m-70) cc_final: 0.8563 (m-70) REVERT: D 64 MET cc_start: 0.8759 (ppp) cc_final: 0.8030 (ppp) REVERT: D 68 ASP cc_start: 0.9476 (t0) cc_final: 0.9196 (t0) REVERT: D 82 ASP cc_start: 0.9205 (m-30) cc_final: 0.8945 (m-30) outliers start: 9 outliers final: 5 residues processed: 154 average time/residue: 0.2651 time to fit residues: 51.9588 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 : 0.543 ------------------------------------------------------------------------------- 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: 7.9990 chunk 41 optimal weight: 0.3980 chunk 25 optimal weight: 6.9990 chunk 13 optimal weight: 0.6980 chunk 38 optimal weight: 0.4980 chunk 33 optimal weight: 0.2980 chunk 2 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 27 optimal weight: 4.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.3411 r_free = 0.3411 target = 0.064764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.056573 restraints weight = 49509.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.059288 restraints weight = 20763.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.061058 restraints weight = 10893.051| |-----------------------------------------------------------------------------| r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.6073 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= 0.179 Angle : 0.555 4.497 4808 Z= 0.304 Chirality : 0.037 0.190 560 Planarity : 0.003 0.020 608 Dihedral : 3.805 14.149 464 Min Nonbonded Distance : 2.328 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: 2.11 (0.37), residues: 428 helix: 1.88 (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 0.005 0.001 HIS A 48 PHE 0.016 0.001 PHE D 77 TYR 0.003 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 142 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 134 time to evaluate : 0.525 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: 0.9472 (t) cc_final: 0.9155 (t) REVERT: A 68 ASP cc_start: 0.9586 (t70) cc_final: 0.9323 (t0) REVERT: A 90 MET cc_start: 0.5552 (mmm) cc_final: 0.5026 (mmm) REVERT: B 8 GLU cc_start: 0.9244 (mp0) cc_final: 0.8832 (mp0) REVERT: B 15 ASN cc_start: 0.8911 (OUTLIER) cc_final: 0.8529 (m110) REVERT: B 22 GLN cc_start: 0.9383 (tp40) cc_final: 0.9048 (mt0) REVERT: B 45 CYS cc_start: 0.7639 (m) cc_final: 0.5465 (m) REVERT: B 82 ASP cc_start: 0.8353 (m-30) cc_final: 0.7884 (t0) REVERT: B 83 MET cc_start: 0.8253 (tmt) cc_final: 0.7573 (tmm) REVERT: B 86 THR cc_start: 0.8155 (p) cc_final: 0.7879 (p) REVERT: C 84 MET cc_start: 0.9376 (ttp) cc_final: 0.9090 (tpp) REVERT: D 9 GLN cc_start: 0.9254 (pt0) cc_final: 0.8929 (mp10) REVERT: D 15 ASN cc_start: 0.9532 (t0) cc_final: 0.9305 (t0) REVERT: D 64 MET cc_start: 0.8870 (ppp) cc_final: 0.8169 (ppp) REVERT: D 68 ASP cc_start: 0.9441 (t0) cc_final: 0.9162 (t0) REVERT: D 82 ASP cc_start: 0.9169 (m-30) cc_final: 0.8920 (m-30) outliers start: 8 outliers final: 4 residues processed: 139 average time/residue: 0.2409 time to fit residues: 43.2316 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 : 0.646 ------------------------------------------------------------------------------- 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: 0.6980 chunk 23 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 15 optimal weight: 0.8980 chunk 3 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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 ** C 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 HIS ** C 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.061727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.053796 restraints weight = 50058.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.056414 restraints weight = 20673.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.058132 restraints weight = 10792.666| |-----------------------------------------------------------------------------| r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.7526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 3560 Z= 0.263 Angle : 0.612 5.958 4808 Z= 0.345 Chirality : 0.038 0.163 560 Planarity : 0.003 0.018 608 Dihedral : 3.869 14.843 464 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 3.12 % Allowed : 18.49 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.37), residues: 428 helix: 1.61 (0.29), residues: 288 sheet: None (None), residues: 0 loop : 0.14 (0.44), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS A 20 PHE 0.017 0.002 PHE B 3 TYR 0.009 0.002 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 134 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 122 time to evaluate : 0.533 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 8 GLU cc_start: 0.9183 (mp0) cc_final: 0.8905 (mp0) REVERT: A 70 GLU cc_start: 0.9544 (tp30) cc_final: 0.9316 (tp30) REVERT: A 90 MET cc_start: 0.5547 (mmm) cc_final: 0.5048 (mmm) REVERT: B 8 GLU cc_start: 0.9224 (mp0) cc_final: 0.8972 (mp0) REVERT: B 42 LEU cc_start: 0.9441 (mt) cc_final: 0.8836 (mt) REVERT: B 82 ASP cc_start: 0.8472 (m-30) cc_final: 0.7844 (t70) REVERT: B 83 MET cc_start: 0.8454 (tmt) cc_final: 0.7569 (tmm) REVERT: B 86 THR cc_start: 0.8246 (p) cc_final: 0.7910 (p) REVERT: C 75 GLU cc_start: 0.9358 (mp0) cc_final: 0.9108 (mp0) REVERT: D 9 GLN cc_start: 0.9271 (pt0) cc_final: 0.9043 (mp10) REVERT: D 64 MET cc_start: 0.8969 (ppp) cc_final: 0.8180 (ppp) REVERT: D 68 ASP cc_start: 0.9478 (t0) cc_final: 0.8967 (t0) REVERT: D 82 ASP cc_start: 0.9322 (m-30) cc_final: 0.9082 (m-30) outliers start: 12 outliers final: 11 residues processed: 127 average time/residue: 0.2446 time to fit residues: 39.9659 Evaluate side-chains 122 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 111 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 A residue 101 LEU 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 94 SER Chi-restraints excluded: chain D residue 98 ASP 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: 5.9990 chunk 7 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 = 0.3318 r_free = 0.3318 target = 0.061056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.053320 restraints weight = 50386.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.055920 restraints weight = 20807.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.057566 restraints weight = 10787.924| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.7935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3560 Z= 0.173 Angle : 0.554 7.043 4808 Z= 0.300 Chirality : 0.037 0.156 560 Planarity : 0.002 0.017 608 Dihedral : 3.856 14.703 464 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Rotamer: Outliers : 2.34 % Allowed : 22.66 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.37), residues: 428 helix: 1.73 (0.29), residues: 288 sheet: None (None), residues: 0 loop : 0.11 (0.44), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 20 PHE 0.009 0.001 PHE D 77 TYR 0.011 0.001 TYR D 16 ARG 0.002 0.000 ARG B 39 *********************** 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 135 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 126 time to evaluate : 0.575 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: 0.9181 (mp0) cc_final: 0.8822 (mp0) REVERT: A 70 GLU cc_start: 0.9586 (tp30) cc_final: 0.9382 (tp30) REVERT: B 8 GLU cc_start: 0.9303 (mp0) cc_final: 0.9047 (mp0) REVERT: B 15 ASN cc_start: 0.9328 (OUTLIER) cc_final: 0.8860 (m-40) REVERT: B 82 ASP cc_start: 0.8511 (m-30) cc_final: 0.7849 (t70) REVERT: B 83 MET cc_start: 0.8543 (tmt) cc_final: 0.7941 (tmm) REVERT: B 86 THR cc_start: 0.8307 (p) cc_final: 0.7930 (p) REVERT: B 91 LEU cc_start: 0.8677 (mt) cc_final: 0.8436 (mm) REVERT: C 75 GLU cc_start: 0.9366 (mp0) cc_final: 0.9142 (mp0) REVERT: D 64 MET cc_start: 0.9020 (ppp) cc_final: 0.8232 (ppp) REVERT: D 68 ASP cc_start: 0.9303 (t0) cc_final: 0.9091 (t70) REVERT: D 82 ASP cc_start: 0.9256 (m-30) cc_final: 0.9028 (m-30) REVERT: D 83 MET cc_start: 0.9424 (tmm) cc_final: 0.9152 (tmm) outliers start: 9 outliers final: 7 residues processed: 130 average time/residue: 0.2377 time to fit residues: 40.0044 Evaluate side-chains 127 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 3 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 HIS B 15 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.059409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.051698 restraints weight = 51153.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 18)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.054233 restraints weight = 20892.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.055867 restraints weight = 10764.329| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.8425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3560 Z= 0.251 Angle : 0.590 5.539 4808 Z= 0.328 Chirality : 0.037 0.148 560 Planarity : 0.003 0.017 608 Dihedral : 3.857 14.316 464 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 2.86 % Allowed : 25.00 % Favored : 72.14 % 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: 1.38 (0.37), residues: 428 helix: 1.44 (0.29), residues: 288 sheet: None (None), residues: 0 loop : -0.05 (0.43), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 20 PHE 0.012 0.002 PHE A 77 TYR 0.010 0.001 TYR D 16 ARG 0.002 0.000 ARG D 33 *********************** 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: 11 poor density : 120 time to evaluate : 0.571 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 70 GLU cc_start: 0.9606 (tp30) cc_final: 0.9404 (tp30) REVERT: B 8 GLU cc_start: 0.9240 (mp0) cc_final: 0.9013 (mp0) REVERT: B 68 ASP cc_start: 0.8407 (t0) cc_final: 0.8104 (t70) REVERT: B 82 ASP cc_start: 0.8759 (m-30) cc_final: 0.8225 (t0) REVERT: B 83 MET cc_start: 0.8691 (tmt) cc_final: 0.8164 (tmm) REVERT: B 84 MET cc_start: 0.9207 (tpp) cc_final: 0.9004 (tpp) REVERT: B 86 THR cc_start: 0.8513 (p) cc_final: 0.8209 (p) REVERT: B 91 LEU cc_start: 0.8789 (mt) cc_final: 0.8490 (mm) REVERT: D 64 MET cc_start: 0.9043 (ppp) cc_final: 0.8254 (ppp) REVERT: D 68 ASP cc_start: 0.9202 (t0) cc_final: 0.8823 (t0) REVERT: D 82 ASP cc_start: 0.9354 (m-30) cc_final: 0.9120 (m-30) REVERT: D 83 MET cc_start: 0.9487 (tmm) cc_final: 0.9162 (tmm) REVERT: D 91 LEU cc_start: 0.8876 (mt) cc_final: 0.8355 (mm) REVERT: D 110 SER cc_start: 0.9599 (p) cc_final: 0.9298 (p) outliers start: 11 outliers final: 11 residues processed: 124 average time/residue: 0.2413 time to fit residues: 38.8940 Evaluate side-chains 125 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 114 time to evaluate : 0.531 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 98 ASP 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: 4.9990 chunk 42 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 36 optimal weight: 6.9990 chunk 8 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 30 optimal weight: 0.4980 chunk 34 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.3327 r_free = 0.3327 target = 0.060939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.053267 restraints weight = 49499.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.055790 restraints weight = 19883.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.057525 restraints weight = 10263.308| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.8693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 3560 Z= 0.218 Angle : 0.619 5.727 4808 Z= 0.334 Chirality : 0.037 0.148 560 Planarity : 0.002 0.017 608 Dihedral : 3.935 16.560 464 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 2.34 % Allowed : 26.82 % Favored : 70.83 % 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: 1.42 (0.38), residues: 428 helix: 1.50 (0.30), residues: 288 sheet: None (None), residues: 0 loop : -0.11 (0.44), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 6 PHE 0.009 0.001 PHE A 77 TYR 0.008 0.001 TYR B 16 ARG 0.002 0.000 ARG D 39 *********************** 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 127 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 118 time to evaluate : 0.703 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: 0.8884 (ptp) cc_final: 0.8679 (pmm) REVERT: B 8 GLU cc_start: 0.9242 (mp0) cc_final: 0.9025 (mp0) REVERT: B 82 ASP cc_start: 0.8760 (m-30) cc_final: 0.8243 (t0) REVERT: B 83 MET cc_start: 0.8752 (tmt) cc_final: 0.8253 (tmm) REVERT: B 86 THR cc_start: 0.8582 (p) cc_final: 0.8286 (p) REVERT: B 97 MET cc_start: 0.9169 (tpp) cc_final: 0.8944 (mmt) REVERT: D 64 MET cc_start: 0.9050 (ppp) cc_final: 0.8274 (ppp) REVERT: D 82 ASP cc_start: 0.9336 (m-30) cc_final: 0.9096 (m-30) REVERT: D 83 MET cc_start: 0.9484 (tmm) cc_final: 0.9136 (tmm) REVERT: D 110 SER cc_start: 0.9594 (p) cc_final: 0.9290 (p) outliers start: 9 outliers final: 8 residues processed: 121 average time/residue: 0.2821 time to fit residues: 44.3402 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 : 0.741 ------------------------------------------------------------------------------- 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 80 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 17 optimal weight: 4.9990 chunk 31 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 41 optimal weight: 0.6980 chunk 6 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 chunk 38 optimal weight: 0.3980 chunk 28 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 15 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.061676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.053872 restraints weight = 49173.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.056446 restraints weight = 19980.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.058106 restraints weight = 10269.488| |-----------------------------------------------------------------------------| r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.8895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3560 Z= 0.197 Angle : 0.625 7.194 4808 Z= 0.331 Chirality : 0.038 0.145 560 Planarity : 0.002 0.017 608 Dihedral : 3.931 13.530 464 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % 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: 1.71 (0.39), residues: 428 helix: 1.77 (0.31), residues: 284 sheet: None (None), residues: 0 loop : -0.06 (0.43), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 6 PHE 0.011 0.001 PHE A 7 TYR 0.016 0.001 TYR D 16 ARG 0.002 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: 7 poor density : 116 time to evaluate : 0.519 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 97 MET cc_start: 0.8904 (ptp) cc_final: 0.8598 (pmm) REVERT: B 8 GLU cc_start: 0.9244 (mp0) cc_final: 0.8993 (mp0) REVERT: B 82 ASP cc_start: 0.8766 (m-30) cc_final: 0.8232 (t0) REVERT: B 83 MET cc_start: 0.8758 (tmt) cc_final: 0.8247 (tmm) REVERT: B 86 THR cc_start: 0.8556 (p) cc_final: 0.8245 (p) REVERT: B 97 MET cc_start: 0.9166 (tpp) cc_final: 0.8935 (mmt) REVERT: D 64 MET cc_start: 0.9046 (ppp) cc_final: 0.8280 (ppp) REVERT: D 82 ASP cc_start: 0.9279 (m-30) cc_final: 0.9071 (m-30) REVERT: D 83 MET cc_start: 0.9484 (tmm) cc_final: 0.9116 (tmm) REVERT: D 110 SER cc_start: 0.9583 (p) cc_final: 0.9278 (p) outliers start: 7 outliers final: 7 residues processed: 119 average time/residue: 0.2438 time to fit residues: 37.6894 Evaluate side-chains 122 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 115 time to evaluate : 0.566 ------------------------------------------------------------------------------- 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 D residue 84 MET Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 94 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 2 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 5 optimal weight: 0.9980 chunk 16 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 41 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 20 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 = 0.3277 r_free = 0.3277 target = 0.059125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.051517 restraints weight = 51259.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.053972 restraints weight = 21181.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.055638 restraints weight = 11027.474| |-----------------------------------------------------------------------------| r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.9415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 3560 Z= 0.324 Angle : 0.677 8.034 4808 Z= 0.377 Chirality : 0.038 0.136 560 Planarity : 0.003 0.017 608 Dihedral : 4.037 16.490 464 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 3.39 % Allowed : 26.82 % 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: 1.06 (0.37), residues: 428 helix: 1.23 (0.30), residues: 284 sheet: None (None), residues: 0 loop : -0.23 (0.43), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS C 20 PHE 0.015 0.002 PHE A 77 TYR 0.008 0.001 TYR D 16 ARG 0.003 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: 13 poor density : 106 time to evaluate : 0.551 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: B 82 ASP cc_start: 0.8827 (m-30) cc_final: 0.8340 (t70) REVERT: B 83 MET cc_start: 0.9018 (tmt) cc_final: 0.8811 (tmm) REVERT: D 64 MET cc_start: 0.9074 (ppp) cc_final: 0.8346 (ppp) REVERT: D 82 ASP cc_start: 0.9380 (m-30) cc_final: 0.9163 (m-30) REVERT: D 83 MET cc_start: 0.9505 (tmm) cc_final: 0.9138 (tmm) outliers start: 13 outliers final: 13 residues processed: 110 average time/residue: 0.2557 time to fit residues: 36.5889 Evaluate side-chains 119 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 106 time to evaluate : 0.520 ------------------------------------------------------------------------------- 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 2 ASP Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain D residue 25 ASP 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 98 ASP Chi-restraints excluded: chain D residue 100 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 4 optimal weight: 2.9990 chunk 16 optimal weight: 0.0670 chunk 5 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 overall best weight: 0.7718 ------------------------------------------------------------------------------- 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 = 0.3317 r_free = 0.3317 target = 0.060566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.052305 restraints weight = 50517.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.054921 restraints weight = 20985.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.056623 restraints weight = 10962.583| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.9440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 3560 Z= 0.215 Angle : 0.651 6.846 4808 Z= 0.348 Chirality : 0.037 0.143 560 Planarity : 0.002 0.016 608 Dihedral : 4.057 17.051 464 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % 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: 1.32 (0.38), residues: 428 helix: 1.42 (0.30), residues: 284 sheet: None (None), residues: 0 loop : -0.09 (0.45), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 6 PHE 0.009 0.001 PHE C 7 TYR 0.014 0.001 TYR D 16 ARG 0.002 0.000 ARG D 18 ********************** 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 118 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 111 time to evaluate : 0.598 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: 0.8851 (ptp) cc_final: 0.8630 (pmm) REVERT: B 82 ASP cc_start: 0.8757 (m-30) cc_final: 0.8182 (t70) REVERT: B 83 MET cc_start: 0.9001 (tmt) cc_final: 0.8789 (tmm) REVERT: D 9 GLN cc_start: 0.9223 (pt0) cc_final: 0.8899 (pt0) REVERT: D 64 MET cc_start: 0.9115 (ppp) cc_final: 0.8379 (ppp) REVERT: D 82 ASP cc_start: 0.9366 (m-30) cc_final: 0.9143 (m-30) REVERT: D 83 MET cc_start: 0.9510 (tmm) cc_final: 0.9096 (tmm) outliers start: 7 outliers final: 5 residues processed: 112 average time/residue: 0.2476 time to fit residues: 35.8461 Evaluate side-chains 116 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 111 time to evaluate : 0.621 ------------------------------------------------------------------------------- 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 D residue 84 MET Chi-restraints excluded: chain D residue 94 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 21 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 16 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3310 r_free = 0.3310 target = 0.060169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.052437 restraints weight = 49367.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.054944 restraints weight = 20189.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.056570 restraints weight = 10420.333| |-----------------------------------------------------------------------------| r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.9634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 3560 Z= 0.203 Angle : 0.636 6.684 4808 Z= 0.342 Chirality : 0.037 0.144 560 Planarity : 0.002 0.015 608 Dihedral : 3.916 13.732 464 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.30 % Allowed : 28.12 % Favored : 70.57 % 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: 1.42 (0.39), residues: 428 helix: 1.48 (0.30), residues: 284 sheet: None (None), residues: 0 loop : -0.03 (0.46), residues: 144 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 0.007 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: 2999.60 seconds wall clock time: 53 minutes 45.55 seconds (3225.55 seconds total)