Starting phenix.real_space_refine on Thu Mar 6 04:39:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sza_40905/03_2025/8sza_40905.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sza_40905/03_2025/8sza_40905.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8sza_40905/03_2025/8sza_40905.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sza_40905/03_2025/8sza_40905.map" model { file = "/net/cci-nas-00/data/ceres_data/8sza_40905/03_2025/8sza_40905.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sza_40905/03_2025/8sza_40905.cif" } resolution = 2.75 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= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 12 5.16 5 C 3258 2.51 5 N 726 2.21 5 O 804 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 4800 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 772 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain: "B" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 772 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain: "C" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 772 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain: "D" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 772 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain: "E" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 772 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain: "F" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 772 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'CLR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.59, per 1000 atoms: 0.96 Number of scatterers: 4800 At special positions: 0 Unit cell: (56.76, 70.62, 94.38, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 12 16.00 O 804 8.00 N 726 7.00 C 3258 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.32 Conformation dependent library (CDL) restraints added in 550.7 milliseconds 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1164 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 0 sheets defined 88.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 40 through 50 Processing helix chain 'A' and resid 54 through 71 removed outlier: 3.517A pdb=" N GLY A 71 " --> pdb=" O VAL A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 103 removed outlier: 4.120A pdb=" N LYS A 103 " --> pdb=" O ILE A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 108 removed outlier: 4.005A pdb=" N ASN A 108 " --> pdb=" O TYR A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 139 Processing helix chain 'B' and resid 40 through 50 Processing helix chain 'B' and resid 54 through 71 removed outlier: 3.572A pdb=" N GLY B 71 " --> pdb=" O VAL B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 107 removed outlier: 4.175A pdb=" N LYS B 103 " --> pdb=" O ILE B 99 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N TYR B 104 " --> pdb=" O PHE B 100 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASP B 105 " --> pdb=" O LEU B 101 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU B 106 " --> pdb=" O VAL B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 139 Processing helix chain 'C' and resid 40 through 50 removed outlier: 3.506A pdb=" N SER C 50 " --> pdb=" O SER C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 71 Processing helix chain 'C' and resid 76 through 102 Processing helix chain 'C' and resid 111 through 139 Processing helix chain 'D' and resid 40 through 50 Processing helix chain 'D' and resid 54 through 71 removed outlier: 3.744A pdb=" N MET D 58 " --> pdb=" O ILE D 54 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLY D 71 " --> pdb=" O VAL D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 107 removed outlier: 3.512A pdb=" N VAL D 102 " --> pdb=" O LEU D 98 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LYS D 103 " --> pdb=" O ILE D 99 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N TYR D 104 " --> pdb=" O PHE D 100 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU D 106 " --> pdb=" O VAL D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 139 removed outlier: 3.643A pdb=" N PHE D 135 " --> pdb=" O VAL D 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 50 Processing helix chain 'E' and resid 54 through 71 removed outlier: 3.660A pdb=" N GLY E 71 " --> pdb=" O VAL E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 103 removed outlier: 4.151A pdb=" N LYS E 103 " --> pdb=" O ILE E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 108 removed outlier: 3.667A pdb=" N ASN E 108 " --> pdb=" O TYR E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 139 Processing helix chain 'F' and resid 40 through 50 Processing helix chain 'F' and resid 54 through 71 removed outlier: 3.500A pdb=" N GLY F 71 " --> pdb=" O VAL F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 76 through 102 Processing helix chain 'F' and resid 111 through 139 410 hydrogen bonds defined for protein. 1230 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.64 Time building geometry restraints manager: 1.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1416 1.35 - 1.46: 1057 1.46 - 1.58: 2405 1.58 - 1.70: 0 1.70 - 1.82: 24 Bond restraints: 4902 Sorted by residual: bond pdb=" CB GLU A 69 " pdb=" CG GLU A 69 " ideal model delta sigma weight residual 1.520 1.563 -0.043 3.00e-02 1.11e+03 2.06e+00 bond pdb=" CA PHE C 74 " pdb=" CB PHE C 74 " ideal model delta sigma weight residual 1.528 1.507 0.021 1.58e-02 4.01e+03 1.70e+00 bond pdb=" CD2 HIS F 112 " pdb=" NE2 HIS F 112 " ideal model delta sigma weight residual 1.374 1.360 0.014 1.10e-02 8.26e+03 1.61e+00 bond pdb=" CA HIS F 112 " pdb=" CB HIS F 112 " ideal model delta sigma weight residual 1.528 1.510 0.019 1.59e-02 3.96e+03 1.39e+00 bond pdb=" CG HIS F 112 " pdb=" ND1 HIS F 112 " ideal model delta sigma weight residual 1.378 1.390 -0.012 1.10e-02 8.26e+03 1.28e+00 ... (remaining 4897 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.15: 6596 2.15 - 4.31: 81 4.31 - 6.46: 25 6.46 - 8.61: 3 8.61 - 10.77: 3 Bond angle restraints: 6708 Sorted by residual: angle pdb=" CB MET A 51 " pdb=" CG MET A 51 " pdb=" SD MET A 51 " ideal model delta sigma weight residual 112.70 123.47 -10.77 3.00e+00 1.11e-01 1.29e+01 angle pdb=" CA MET A 58 " pdb=" CB MET A 58 " pdb=" CG MET A 58 " ideal model delta sigma weight residual 114.10 120.87 -6.77 2.00e+00 2.50e-01 1.14e+01 angle pdb=" CA GLU A 69 " pdb=" CB GLU A 69 " pdb=" CG GLU A 69 " ideal model delta sigma weight residual 114.10 120.83 -6.73 2.00e+00 2.50e-01 1.13e+01 angle pdb=" C TYR D 77 " pdb=" N VAL D 78 " pdb=" CA VAL D 78 " ideal model delta sigma weight residual 120.33 122.84 -2.51 8.00e-01 1.56e+00 9.83e+00 angle pdb=" CB GLU A 69 " pdb=" CG GLU A 69 " pdb=" CD GLU A 69 " ideal model delta sigma weight residual 112.60 117.81 -5.21 1.70e+00 3.46e-01 9.41e+00 ... (remaining 6703 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.55: 2792 16.55 - 33.09: 284 33.09 - 49.64: 88 49.64 - 66.19: 27 66.19 - 82.73: 1 Dihedral angle restraints: 3192 sinusoidal: 1410 harmonic: 1782 Sorted by residual: dihedral pdb=" CG LYS B 65 " pdb=" CD LYS B 65 " pdb=" CE LYS B 65 " pdb=" NZ LYS B 65 " ideal model delta sinusoidal sigma weight residual -60.00 -2.88 -57.12 3 1.50e+01 4.44e-03 9.43e+00 dihedral pdb=" CG LYS B 103 " pdb=" CD LYS B 103 " pdb=" CE LYS B 103 " pdb=" NZ LYS B 103 " ideal model delta sinusoidal sigma weight residual 180.00 122.94 57.06 3 1.50e+01 4.44e-03 9.43e+00 dihedral pdb=" N MET E 51 " pdb=" CA MET E 51 " pdb=" CB MET E 51 " pdb=" CG MET E 51 " ideal model delta sinusoidal sigma weight residual -180.00 -123.30 -56.70 3 1.50e+01 4.44e-03 9.41e+00 ... (remaining 3189 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.021: 454 0.021 - 0.042: 244 0.042 - 0.063: 109 0.063 - 0.084: 45 0.084 - 0.104: 18 Chirality restraints: 870 Sorted by residual: chirality pdb=" CB VAL A 67 " pdb=" CA VAL A 67 " pdb=" CG1 VAL A 67 " pdb=" CG2 VAL A 67 " both_signs ideal model delta sigma weight residual False -2.63 -2.52 -0.10 2.00e-01 2.50e+01 2.73e-01 chirality pdb=" CA PRO F 79 " pdb=" N PRO F 79 " pdb=" C PRO F 79 " pdb=" CB PRO F 79 " both_signs ideal model delta sigma weight residual False 2.72 2.62 0.10 2.00e-01 2.50e+01 2.48e-01 chirality pdb=" CA PRO C 79 " pdb=" N PRO C 79 " pdb=" C PRO C 79 " pdb=" CB PRO C 79 " both_signs ideal model delta sigma weight residual False 2.72 2.62 0.10 2.00e-01 2.50e+01 2.42e-01 ... (remaining 867 not shown) Planarity restraints: 780 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 127 " -0.013 2.00e-02 2.50e+03 1.72e-02 5.18e+00 pdb=" CG PHE A 127 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 PHE A 127 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE A 127 " -0.015 2.00e-02 2.50e+03 pdb=" CE1 PHE A 127 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 127 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 127 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 69 " -0.010 2.00e-02 2.50e+03 2.12e-02 4.50e+00 pdb=" CD GLU A 69 " 0.037 2.00e-02 2.50e+03 pdb=" OE1 GLU A 69 " -0.013 2.00e-02 2.50e+03 pdb=" OE2 GLU A 69 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP F 53 " -0.006 2.00e-02 2.50e+03 1.29e-02 1.66e+00 pdb=" CG ASP F 53 " 0.022 2.00e-02 2.50e+03 pdb=" OD1 ASP F 53 " -0.008 2.00e-02 2.50e+03 pdb=" OD2 ASP F 53 " -0.008 2.00e-02 2.50e+03 ... (remaining 777 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 184 2.73 - 3.27: 5207 3.27 - 3.81: 7791 3.81 - 4.36: 8925 4.36 - 4.90: 15072 Nonbonded interactions: 37179 Sorted by model distance: nonbonded pdb=" O MET D 58 " pdb=" OG SER D 62 " model vdw 2.185 3.040 nonbonded pdb=" OH TYR F 104 " pdb=" O1 CLR F 201 " model vdw 2.196 3.040 nonbonded pdb=" O MET E 58 " pdb=" OG SER E 62 " model vdw 2.225 3.040 nonbonded pdb=" OD1 ASN D 120 " pdb=" NZ LYS E 103 " model vdw 2.351 3.120 nonbonded pdb=" O MET F 58 " pdb=" OG SER F 62 " model vdw 2.414 3.040 ... (remaining 37174 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 39 through 139) selection = (chain 'C' and resid 39 through 139) selection = (chain 'D' and resid 39 through 139) selection = (chain 'E' and resid 39 through 139) selection = (chain 'F' and resid 39 through 139) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 404.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 17.640 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.060 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:19.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 441.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 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 : 0.003 0.043 4902 Z= 0.203 Angle : 0.652 10.766 6708 Z= 0.325 Chirality : 0.033 0.104 870 Planarity : 0.002 0.022 780 Dihedral : 15.140 82.732 2028 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Rotamer: Outliers : 0.98 % Allowed : 20.98 % Favored : 78.04 % 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: 2.12 (0.35), residues: 594 helix: 1.96 (0.23), residues: 492 sheet: None (None), residues: 0 loop : -1.39 (0.67), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 112 PHE 0.039 0.001 PHE A 127 TYR 0.009 0.001 TYR B 77 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 87 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 44 LYS cc_start: 0.6964 (mmtt) cc_final: 0.5977 (tmtt) outliers start: 5 outliers final: 5 residues processed: 90 average time/residue: 0.9404 time to fit residues: 89.2746 Evaluate side-chains 89 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 84 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 54 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 0.5980 chunk 45 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 30 optimal weight: 10.0000 chunk 24 optimal weight: 0.8980 chunk 47 optimal weight: 0.4980 chunk 18 optimal weight: 0.8980 chunk 28 optimal weight: 0.5980 chunk 35 optimal weight: 0.6980 chunk 54 optimal weight: 0.3980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4567 r_free = 0.4567 target = 0.188543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.158426 restraints weight = 6479.830| |-----------------------------------------------------------------------------| r_work (start): 0.4257 rms_B_bonded: 2.50 r_work: 0.4146 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.4146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4902 Z= 0.189 Angle : 0.550 6.863 6708 Z= 0.278 Chirality : 0.036 0.136 870 Planarity : 0.003 0.017 780 Dihedral : 9.507 50.538 1017 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Rotamer: Outliers : 1.57 % Allowed : 19.80 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.17 (0.35), residues: 594 helix: 2.62 (0.23), residues: 504 sheet: None (None), residues: 0 loop : -1.13 (0.76), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 112 PHE 0.019 0.001 PHE F 127 TYR 0.011 0.001 TYR D 41 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 98 time to evaluate : 0.499 Fit side-chains REVERT: A 58 MET cc_start: 0.8063 (mpt) cc_final: 0.7782 (mpt) REVERT: A 104 TYR cc_start: 0.8026 (OUTLIER) cc_final: 0.6348 (t80) REVERT: B 58 MET cc_start: 0.7478 (mtp) cc_final: 0.7216 (mtm) REVERT: D 44 LYS cc_start: 0.7004 (mmtt) cc_final: 0.6026 (tmtt) outliers start: 8 outliers final: 4 residues processed: 101 average time/residue: 0.6845 time to fit residues: 73.7876 Evaluate side-chains 93 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 88 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 104 TYR Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain D residue 102 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 5 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 chunk 27 optimal weight: 0.1980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4555 r_free = 0.4555 target = 0.187721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.157661 restraints weight = 6497.975| |-----------------------------------------------------------------------------| r_work (start): 0.4241 rms_B_bonded: 2.48 r_work: 0.4131 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.4131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4902 Z= 0.188 Angle : 0.523 6.886 6708 Z= 0.260 Chirality : 0.036 0.119 870 Planarity : 0.002 0.015 780 Dihedral : 9.222 49.724 1008 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Rotamer: Outliers : 2.55 % Allowed : 19.61 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.30 (0.36), residues: 594 helix: 2.69 (0.23), residues: 504 sheet: None (None), residues: 0 loop : -0.99 (0.77), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS F 112 PHE 0.021 0.002 PHE C 127 TYR 0.015 0.001 TYR B 77 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 0.481 Fit side-chains revert: symmetry clash REVERT: A 58 MET cc_start: 0.8002 (mpt) cc_final: 0.7381 (mpt) REVERT: A 104 TYR cc_start: 0.8018 (OUTLIER) cc_final: 0.6401 (t80) REVERT: B 58 MET cc_start: 0.7589 (mtp) cc_final: 0.7311 (mtm) REVERT: C 70 GLN cc_start: 0.8401 (tt0) cc_final: 0.8121 (tp-100) REVERT: D 44 LYS cc_start: 0.7038 (mmtt) cc_final: 0.5957 (tmtt) REVERT: D 88 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.7713 (mt) REVERT: D 101 LEU cc_start: 0.7999 (OUTLIER) cc_final: 0.7656 (tt) REVERT: E 88 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7883 (tm) outliers start: 13 outliers final: 7 residues processed: 102 average time/residue: 0.7365 time to fit residues: 79.8508 Evaluate side-chains 99 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 104 TYR Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain E residue 88 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 32 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 59 optimal weight: 0.0000 chunk 9 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 21 optimal weight: 0.0970 chunk 13 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 chunk 57 optimal weight: 0.7980 overall best weight: 0.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 119 ASN ** B 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4559 r_free = 0.4559 target = 0.188428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.158415 restraints weight = 6523.604| |-----------------------------------------------------------------------------| r_work (start): 0.4250 rms_B_bonded: 2.49 r_work: 0.4139 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.4139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4902 Z= 0.166 Angle : 0.503 6.937 6708 Z= 0.249 Chirality : 0.035 0.115 870 Planarity : 0.002 0.014 780 Dihedral : 9.095 49.190 1008 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 2.35 % Allowed : 21.18 % Favored : 76.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.55 (0.36), residues: 594 helix: 2.86 (0.23), residues: 504 sheet: None (None), residues: 0 loop : -0.90 (0.78), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS F 112 PHE 0.032 0.002 PHE A 127 TYR 0.005 0.001 TYR B 77 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 102 time to evaluate : 0.725 Fit side-chains revert: symmetry clash REVERT: A 58 MET cc_start: 0.8008 (mpt) cc_final: 0.7397 (mpt) REVERT: A 104 TYR cc_start: 0.8011 (OUTLIER) cc_final: 0.6409 (t80) REVERT: B 58 MET cc_start: 0.7666 (mtp) cc_final: 0.7389 (mtm) REVERT: C 70 GLN cc_start: 0.8388 (tt0) cc_final: 0.8188 (tp-100) REVERT: D 44 LYS cc_start: 0.6999 (mmtt) cc_final: 0.5886 (tmtt) REVERT: D 58 MET cc_start: 0.8304 (mpt) cc_final: 0.8080 (mpt) REVERT: D 88 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.7745 (mt) REVERT: D 101 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7660 (tt) outliers start: 12 outliers final: 3 residues processed: 108 average time/residue: 0.6753 time to fit residues: 77.8310 Evaluate side-chains 99 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 93 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 104 TYR Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 102 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 32 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 13 optimal weight: 6.9990 chunk 50 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 60 ASN E 63 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4546 r_free = 0.4546 target = 0.186820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.156017 restraints weight = 6525.774| |-----------------------------------------------------------------------------| r_work (start): 0.4211 rms_B_bonded: 2.49 r_work: 0.4097 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.4097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4902 Z= 0.204 Angle : 0.538 8.141 6708 Z= 0.265 Chirality : 0.036 0.109 870 Planarity : 0.002 0.015 780 Dihedral : 9.150 49.730 1008 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Rotamer: Outliers : 2.16 % Allowed : 21.76 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.44 (0.36), residues: 594 helix: 2.76 (0.23), residues: 504 sheet: None (None), residues: 0 loop : -0.78 (0.80), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS F 112 PHE 0.028 0.002 PHE A 127 TYR 0.005 0.001 TYR E 104 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 97 time to evaluate : 0.507 Fit side-chains revert: symmetry clash REVERT: A 58 MET cc_start: 0.8018 (OUTLIER) cc_final: 0.7520 (mpt) REVERT: A 104 TYR cc_start: 0.7982 (OUTLIER) cc_final: 0.6419 (t80) REVERT: B 58 MET cc_start: 0.7687 (mtp) cc_final: 0.7383 (mtm) REVERT: D 44 LYS cc_start: 0.6973 (mmtt) cc_final: 0.5805 (tmtt) REVERT: D 58 MET cc_start: 0.8286 (mpt) cc_final: 0.8029 (mpt) REVERT: D 88 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.7740 (mt) REVERT: D 101 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.7528 (tt) outliers start: 11 outliers final: 4 residues processed: 101 average time/residue: 0.6979 time to fit residues: 74.9911 Evaluate side-chains 98 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 90 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 104 TYR Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 102 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 27 optimal weight: 0.0020 chunk 38 optimal weight: 3.9990 chunk 20 optimal weight: 0.0030 chunk 0 optimal weight: 6.9990 chunk 57 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 46 optimal weight: 0.0670 chunk 28 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 37 optimal weight: 0.0670 overall best weight: 0.1874 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 107 ASN ** B 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4579 r_free = 0.4579 target = 0.190980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.161165 restraints weight = 6594.091| |-----------------------------------------------------------------------------| r_work (start): 0.4274 rms_B_bonded: 2.50 r_work: 0.4166 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.4166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 4902 Z= 0.150 Angle : 0.536 10.382 6708 Z= 0.260 Chirality : 0.034 0.109 870 Planarity : 0.002 0.016 780 Dihedral : 8.948 48.318 1008 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 2.16 % Allowed : 22.75 % Favored : 75.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.84 (0.36), residues: 594 helix: 3.05 (0.23), residues: 504 sheet: None (None), residues: 0 loop : -0.76 (0.81), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS F 40 PHE 0.031 0.001 PHE F 127 TYR 0.012 0.001 TYR B 77 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 106 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 MET cc_start: 0.7961 (OUTLIER) cc_final: 0.7544 (mpt) REVERT: B 58 MET cc_start: 0.7658 (mtp) cc_final: 0.7360 (mtm) REVERT: D 44 LYS cc_start: 0.6981 (mmtt) cc_final: 0.5826 (tmtt) REVERT: D 54 ILE cc_start: 0.7440 (mm) cc_final: 0.6850 (mm) REVERT: D 88 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.7748 (mt) REVERT: D 101 LEU cc_start: 0.8024 (OUTLIER) cc_final: 0.7648 (tt) REVERT: E 88 LEU cc_start: 0.8190 (tm) cc_final: 0.7780 (mt) outliers start: 11 outliers final: 4 residues processed: 111 average time/residue: 0.7446 time to fit residues: 88.0197 Evaluate side-chains 97 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 90 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 107 ASN Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 102 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 41 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 46 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4553 r_free = 0.4553 target = 0.188000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.157775 restraints weight = 6485.561| |-----------------------------------------------------------------------------| r_work (start): 0.4232 rms_B_bonded: 2.48 r_work: 0.4122 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.4122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4902 Z= 0.194 Angle : 0.559 8.729 6708 Z= 0.274 Chirality : 0.036 0.108 870 Planarity : 0.003 0.041 780 Dihedral : 8.992 48.703 1008 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Rotamer: Outliers : 1.57 % Allowed : 25.29 % Favored : 73.14 % 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: 3.64 (0.36), residues: 594 helix: 2.88 (0.23), residues: 504 sheet: None (None), residues: 0 loop : -0.62 (0.83), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS F 112 PHE 0.031 0.002 PHE A 127 TYR 0.010 0.001 TYR B 77 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 91 time to evaluate : 0.560 Fit side-chains revert: symmetry clash REVERT: A 58 MET cc_start: 0.7935 (OUTLIER) cc_final: 0.7538 (mpt) REVERT: B 58 MET cc_start: 0.7714 (mtp) cc_final: 0.7403 (mtm) REVERT: D 44 LYS cc_start: 0.7000 (mmtt) cc_final: 0.5787 (tmtt) REVERT: D 88 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.7740 (mt) REVERT: D 101 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7646 (tt) outliers start: 8 outliers final: 5 residues processed: 94 average time/residue: 0.8314 time to fit residues: 83.8247 Evaluate side-chains 97 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 89 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain F residue 52 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 55 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 52 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.185909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.155233 restraints weight = 6550.790| |-----------------------------------------------------------------------------| r_work (start): 0.4207 rms_B_bonded: 2.50 r_work: 0.4094 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.4094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4902 Z= 0.214 Angle : 0.598 9.338 6708 Z= 0.290 Chirality : 0.037 0.124 870 Planarity : 0.003 0.031 780 Dihedral : 9.115 49.202 1008 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 1.57 % Allowed : 26.47 % Favored : 71.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.43 (0.35), residues: 594 helix: 2.75 (0.22), residues: 498 sheet: None (None), residues: 0 loop : -0.48 (0.77), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 112 PHE 0.028 0.002 PHE F 127 TYR 0.013 0.001 TYR B 77 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 92 time to evaluate : 0.496 Fit side-chains REVERT: A 58 MET cc_start: 0.7966 (OUTLIER) cc_final: 0.7611 (mpt) REVERT: A 104 TYR cc_start: 0.7952 (OUTLIER) cc_final: 0.6412 (t80) REVERT: B 58 MET cc_start: 0.7746 (mtp) cc_final: 0.7434 (mtm) REVERT: C 70 GLN cc_start: 0.8512 (tp-100) cc_final: 0.8221 (tp-100) REVERT: D 44 LYS cc_start: 0.7033 (mmtt) cc_final: 0.5752 (tmtt) REVERT: D 88 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.7746 (mt) REVERT: D 101 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7671 (tt) outliers start: 8 outliers final: 4 residues processed: 96 average time/residue: 0.7442 time to fit residues: 76.2088 Evaluate side-chains 96 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 88 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 104 TYR Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 102 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 16 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 43 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 20 optimal weight: 0.2980 chunk 21 optimal weight: 0.4980 chunk 45 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 120 ASN ** C 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4541 r_free = 0.4541 target = 0.186848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.156663 restraints weight = 6461.564| |-----------------------------------------------------------------------------| r_work (start): 0.4226 rms_B_bonded: 2.46 r_work: 0.4115 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.4115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4902 Z= 0.184 Angle : 0.569 8.655 6708 Z= 0.282 Chirality : 0.036 0.205 870 Planarity : 0.003 0.029 780 Dihedral : 9.043 48.470 1008 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Rotamer: Outliers : 2.35 % Allowed : 26.47 % Favored : 71.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.52 (0.36), residues: 594 helix: 2.80 (0.22), residues: 504 sheet: None (None), residues: 0 loop : -0.60 (0.81), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 40 PHE 0.030 0.002 PHE A 127 TYR 0.010 0.001 TYR B 77 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 94 time to evaluate : 0.824 Fit side-chains revert: symmetry clash REVERT: A 58 MET cc_start: 0.7883 (OUTLIER) cc_final: 0.7587 (mpt) REVERT: A 104 TYR cc_start: 0.7943 (OUTLIER) cc_final: 0.6481 (t80) REVERT: B 58 MET cc_start: 0.7751 (mtp) cc_final: 0.7485 (mtp) REVERT: C 70 GLN cc_start: 0.8466 (tp-100) cc_final: 0.8198 (tp-100) REVERT: D 44 LYS cc_start: 0.7035 (mmtt) cc_final: 0.5750 (tmtt) REVERT: D 88 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.7740 (mt) REVERT: D 101 LEU cc_start: 0.8111 (OUTLIER) cc_final: 0.7680 (tt) REVERT: E 62 SER cc_start: 0.8099 (t) cc_final: 0.7681 (m) outliers start: 12 outliers final: 6 residues processed: 98 average time/residue: 0.7417 time to fit residues: 78.3801 Evaluate side-chains 99 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 89 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 104 TYR Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain F residue 52 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 21 optimal weight: 0.0970 chunk 8 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4536 r_free = 0.4536 target = 0.185935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.155226 restraints weight = 6537.397| |-----------------------------------------------------------------------------| r_work (start): 0.4221 rms_B_bonded: 2.50 r_work: 0.4108 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.4108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 4902 Z= 0.202 Angle : 0.592 10.290 6708 Z= 0.294 Chirality : 0.037 0.197 870 Planarity : 0.003 0.029 780 Dihedral : 9.044 48.188 1008 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Rotamer: Outliers : 1.96 % Allowed : 26.67 % Favored : 71.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.46 (0.35), residues: 594 helix: 2.78 (0.22), residues: 498 sheet: None (None), residues: 0 loop : -0.49 (0.75), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS F 40 PHE 0.029 0.002 PHE F 127 TYR 0.011 0.001 TYR B 77 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 92 time to evaluate : 1.187 Fit side-chains revert: symmetry clash REVERT: A 58 MET cc_start: 0.7902 (OUTLIER) cc_final: 0.7544 (mpt) REVERT: A 104 TYR cc_start: 0.7947 (OUTLIER) cc_final: 0.6488 (t80) REVERT: B 58 MET cc_start: 0.7739 (mtp) cc_final: 0.7466 (mtp) REVERT: C 70 GLN cc_start: 0.8459 (tp-100) cc_final: 0.8204 (tp-100) REVERT: D 44 LYS cc_start: 0.7094 (mmtt) cc_final: 0.5775 (tmtt) REVERT: D 88 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.7739 (mt) REVERT: D 101 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7660 (tt) REVERT: E 62 SER cc_start: 0.8093 (t) cc_final: 0.7670 (m) outliers start: 10 outliers final: 6 residues processed: 96 average time/residue: 1.1257 time to fit residues: 116.6286 Evaluate side-chains 98 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 88 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 104 TYR Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain F residue 52 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 28 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 21 optimal weight: 0.3980 chunk 48 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 6 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 55 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 107 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4546 r_free = 0.4546 target = 0.186970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.156762 restraints weight = 6552.763| |-----------------------------------------------------------------------------| r_work (start): 0.4229 rms_B_bonded: 2.50 r_work: 0.4118 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.4118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4902 Z= 0.181 Angle : 0.570 8.606 6708 Z= 0.284 Chirality : 0.036 0.194 870 Planarity : 0.003 0.028 780 Dihedral : 8.983 47.563 1008 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Rotamer: Outliers : 2.55 % Allowed : 26.47 % Favored : 70.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.61 (0.35), residues: 594 helix: 2.87 (0.22), residues: 498 sheet: None (None), residues: 0 loop : -0.44 (0.76), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS F 40 PHE 0.029 0.001 PHE A 127 TYR 0.009 0.001 TYR B 77 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4059.69 seconds wall clock time: 73 minutes 44.25 seconds (4424.25 seconds total)