Starting phenix.real_space_refine on Wed Feb 12 02:40:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6z1i_11030/02_2025/6z1i_11030.cif Found real_map, /net/cci-nas-00/data/ceres_data/6z1i_11030/02_2025/6z1i_11030.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6z1i_11030/02_2025/6z1i_11030.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6z1i_11030/02_2025/6z1i_11030.map" model { file = "/net/cci-nas-00/data/ceres_data/6z1i_11030/02_2025/6z1i_11030.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6z1i_11030/02_2025/6z1i_11030.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 12 5.16 5 C 2250 2.51 5 N 648 2.21 5 O 738 1.98 5 H 3492 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 7140 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 1190 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 2, 'TRANS': 78} Chain breaks: 1 Restraints were copied for chains: C, B, E, D, F Time building chain proxies: 3.06, per 1000 atoms: 0.43 Number of scatterers: 7140 At special positions: 0 Unit cell: (85.28, 73.84, 45.76, 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 12 16.00 O 738 8.00 N 648 7.00 C 2250 6.00 H 3492 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 87 " distance=1.99 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: 1.78 Conformation dependent library (CDL) restraints added in 595.8 milliseconds 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 888 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 12 sheets defined 0.0% alpha, 44.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 14 Processing sheet with id=AA2, first strand: chain 'A' and resid 17 through 23 Processing sheet with id=AA3, first strand: chain 'A' and resid 25 through 26 Processing sheet with id=AA4, first strand: chain 'A' and resid 28 through 31 Processing sheet with id=AA5, first strand: chain 'A' and resid 34 through 37 Processing sheet with id=AA6, first strand: chain 'A' and resid 43 through 47 Processing sheet with id=AA9, first strand: chain 'A' and resid 72 through 75 Processing sheet with id=AB1, first strand: chain 'A' and resid 79 through 82 Processing sheet with id=AB2, first strand: chain 'A' and resid 85 through 86 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 85 through 86 current: chain 'B' and resid 85 through 86 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 85 through 86 current: chain 'C' and resid 85 through 86 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 85 through 86 current: chain 'D' and resid 85 through 86 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 85 through 86 current: chain 'E' and resid 85 through 86 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 85 through 86 current: chain 'F' and resid 85 through 86 No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 88 through 91 Processing sheet with id=AB4, first strand: chain 'A' and resid 95 through 97 removed outlier: 3.531A pdb=" N HIS B 96 " --> pdb=" O ASN A 95 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N HIS C 96 " --> pdb=" O ASN B 95 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N HIS D 96 " --> pdb=" O ASN C 95 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N HIS E 96 " --> pdb=" O ASN D 95 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N HIS F 96 " --> pdb=" O ASN E 95 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 103 through 106 170 hydrogen bonds defined for protein. 510 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: 2.60 Time building geometry restraints manager: 2.15 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: 3492 1.03 - 1.23: 138 1.23 - 1.42: 1464 1.42 - 1.62: 2088 1.62 - 1.81: 12 Bond restraints: 7194 Sorted by residual: bond pdb=" N LYS B 38 " pdb=" CA LYS B 38 " ideal model delta sigma weight residual 1.461 1.499 -0.038 1.07e-02 8.73e+03 1.24e+01 bond pdb=" N LYS E 38 " pdb=" CA LYS E 38 " ideal model delta sigma weight residual 1.461 1.498 -0.037 1.07e-02 8.73e+03 1.22e+01 bond pdb=" N LYS D 38 " pdb=" CA LYS D 38 " ideal model delta sigma weight residual 1.461 1.498 -0.037 1.07e-02 8.73e+03 1.20e+01 bond pdb=" N LYS A 38 " pdb=" CA LYS A 38 " ideal model delta sigma weight residual 1.461 1.498 -0.037 1.07e-02 8.73e+03 1.20e+01 bond pdb=" N LYS F 38 " pdb=" CA LYS F 38 " ideal model delta sigma weight residual 1.461 1.498 -0.037 1.07e-02 8.73e+03 1.17e+01 ... (remaining 7189 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 10349 1.88 - 3.76: 1916 3.76 - 5.64: 425 5.64 - 7.52: 150 7.52 - 9.40: 24 Bond angle restraints: 12864 Sorted by residual: angle pdb=" C PRO D 39 " pdb=" CA PRO D 39 " pdb=" CB PRO D 39 " ideal model delta sigma weight residual 111.11 103.02 8.09 1.17e+00 7.31e-01 4.78e+01 angle pdb=" C PRO A 39 " pdb=" CA PRO A 39 " pdb=" CB PRO A 39 " ideal model delta sigma weight residual 111.11 103.02 8.09 1.17e+00 7.31e-01 4.78e+01 angle pdb=" C PRO E 39 " pdb=" CA PRO E 39 " pdb=" CB PRO E 39 " ideal model delta sigma weight residual 111.11 103.02 8.09 1.17e+00 7.31e-01 4.78e+01 angle pdb=" C PRO F 39 " pdb=" CA PRO F 39 " pdb=" CB PRO F 39 " ideal model delta sigma weight residual 111.11 103.04 8.07 1.17e+00 7.31e-01 4.75e+01 angle pdb=" C PRO B 39 " pdb=" CA PRO B 39 " pdb=" CB PRO B 39 " ideal model delta sigma weight residual 111.11 103.05 8.06 1.17e+00 7.31e-01 4.75e+01 ... (remaining 12859 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.85: 2755 10.85 - 21.71: 342 21.71 - 32.56: 175 32.56 - 43.42: 103 43.42 - 54.27: 48 Dihedral angle restraints: 3423 sinusoidal: 1827 harmonic: 1596 Sorted by residual: dihedral pdb=" C CYS E 87 " pdb=" N CYS E 87 " pdb=" CA CYS E 87 " pdb=" CB CYS E 87 " ideal model delta harmonic sigma weight residual -122.60 -132.19 9.59 0 2.50e+00 1.60e-01 1.47e+01 dihedral pdb=" C CYS D 87 " pdb=" N CYS D 87 " pdb=" CA CYS D 87 " pdb=" CB CYS D 87 " ideal model delta harmonic sigma weight residual -122.60 -132.16 9.56 0 2.50e+00 1.60e-01 1.46e+01 dihedral pdb=" C CYS F 87 " pdb=" N CYS F 87 " pdb=" CA CYS F 87 " pdb=" CB CYS F 87 " ideal model delta harmonic sigma weight residual -122.60 -132.16 9.56 0 2.50e+00 1.60e-01 1.46e+01 ... (remaining 3420 not shown) Histogram of chiral volume deviations from ideal: 0.002 - 0.075: 248 0.075 - 0.147: 208 0.147 - 0.220: 94 0.220 - 0.292: 20 0.292 - 0.365: 6 Chirality restraints: 576 Sorted by residual: chirality pdb=" CA CYS E 87 " pdb=" N CYS E 87 " pdb=" C CYS E 87 " pdb=" CB CYS E 87 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.32e+00 chirality pdb=" CA CYS D 87 " pdb=" N CYS D 87 " pdb=" C CYS D 87 " pdb=" CB CYS D 87 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.30e+00 chirality pdb=" CA CYS A 87 " pdb=" N CYS A 87 " pdb=" C CYS A 87 " pdb=" CB CYS A 87 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.29e+00 ... (remaining 573 not shown) Planarity restraints: 1116 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN F 41 " 0.196 2.00e-02 2.50e+03 2.26e-01 7.65e+02 pdb=" CD GLN F 41 " -0.011 2.00e-02 2.50e+03 pdb=" OE1 GLN F 41 " -0.188 2.00e-02 2.50e+03 pdb=" NE2 GLN F 41 " -0.001 2.00e-02 2.50e+03 pdb="HE21 GLN F 41 " -0.339 2.00e-02 2.50e+03 pdb="HE22 GLN F 41 " 0.343 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 41 " 0.195 2.00e-02 2.50e+03 2.26e-01 7.65e+02 pdb=" CD GLN A 41 " -0.010 2.00e-02 2.50e+03 pdb=" OE1 GLN A 41 " -0.188 2.00e-02 2.50e+03 pdb=" NE2 GLN A 41 " -0.001 2.00e-02 2.50e+03 pdb="HE21 GLN A 41 " -0.339 2.00e-02 2.50e+03 pdb="HE22 GLN A 41 " 0.343 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN D 41 " 0.195 2.00e-02 2.50e+03 2.26e-01 7.64e+02 pdb=" CD GLN D 41 " -0.011 2.00e-02 2.50e+03 pdb=" OE1 GLN D 41 " -0.188 2.00e-02 2.50e+03 pdb=" NE2 GLN D 41 " -0.001 2.00e-02 2.50e+03 pdb="HE21 GLN D 41 " -0.339 2.00e-02 2.50e+03 pdb="HE22 GLN D 41 " 0.342 2.00e-02 2.50e+03 ... (remaining 1113 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.33: 1843 2.33 - 2.90: 16264 2.90 - 3.47: 16681 3.47 - 4.03: 26517 4.03 - 4.60: 36183 Nonbonded interactions: 97488 Sorted by model distance: nonbonded pdb=" HG1 THR D 75 " pdb=" O SER C 92 " model vdw 1.764 2.450 nonbonded pdb=" O SER D 92 " pdb=" HG1 THR E 75 " model vdw 1.764 2.450 nonbonded pdb=" HG1 THR B 75 " pdb=" O SER A 92 " model vdw 1.765 2.450 nonbonded pdb=" HG1 THR C 75 " pdb=" O SER B 92 " model vdw 1.765 2.450 nonbonded pdb=" O SER E 92 " pdb=" HG1 THR F 75 " model vdw 1.765 2.450 ... (remaining 97483 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'F' } 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: 1.530 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: 0.150 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 18.780 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 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 : 0.013 0.046 3702 Z= 0.849 Angle : 2.258 9.399 5022 Z= 1.593 Chirality : 0.116 0.365 576 Planarity : 0.012 0.045 654 Dihedral : 14.226 52.366 1290 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.66 % Favored : 91.34 % Rotamer: Outliers : 0.00 % Allowed : 10.77 % Favored : 89.23 % 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: -4.29 (0.28), residues: 462 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.26 (0.22), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.007 TRP A 34 HIS 0.003 0.002 HIS E 96 PHE 0.018 0.007 PHE A 99 TYR 0.028 0.006 TYR C 86 ARG 0.001 0.000 ARG E 28 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.561 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: D 30 TYR cc_start: 0.8351 (m-10) cc_final: 0.7753 (m-80) REVERT: D 91 ASP cc_start: 0.8943 (t0) cc_final: 0.8568 (t70) REVERT: E 35 TYR cc_start: 0.7139 (m-80) cc_final: 0.6712 (m-80) REVERT: E 88 ASN cc_start: 0.8870 (m-40) cc_final: 0.8257 (m110) REVERT: F 48 PHE cc_start: 0.8095 (m-80) cc_final: 0.6652 (p90) REVERT: F 84 ASP cc_start: 0.8010 (t0) cc_final: 0.7226 (m-30) REVERT: F 88 ASN cc_start: 0.7734 (m-40) cc_final: 0.7354 (m-40) REVERT: F 90 ARG cc_start: 0.7610 (ttp80) cc_final: 0.6871 (ttp-170) REVERT: F 103 THR cc_start: 0.7830 (m) cc_final: 0.7580 (t) REVERT: C 17 THR cc_start: 0.8887 (m) cc_final: 0.8554 (t) REVERT: C 34 TRP cc_start: 0.7715 (t-100) cc_final: 0.6109 (t-100) REVERT: B 34 TRP cc_start: 0.7048 (t-100) cc_final: 0.5752 (t-100) outliers start: 0 outliers final: 0 residues processed: 170 average time/residue: 0.5284 time to fit residues: 101.8710 Evaluate side-chains 108 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 40 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 19 optimal weight: 0.3980 chunk 37 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 chunk 28 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 95 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.140359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.133838 restraints weight = 16949.983| |-----------------------------------------------------------------------------| r_work (start): 0.4048 rms_B_bonded: 2.10 r_work: 0.3968 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3859 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.5236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3702 Z= 0.247 Angle : 0.705 5.673 5022 Z= 0.389 Chirality : 0.049 0.141 576 Planarity : 0.006 0.041 654 Dihedral : 6.825 19.915 522 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 3.08 % Allowed : 16.41 % Favored : 80.51 % 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: -3.94 (0.29), residues: 462 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.99 (0.22), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 34 HIS 0.001 0.001 HIS E 96 PHE 0.011 0.001 PHE E 99 TYR 0.023 0.003 TYR E 86 ARG 0.005 0.001 ARG F 19 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 106 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 90 ARG cc_start: 0.8400 (ttp80) cc_final: 0.8173 (ttp-170) REVERT: F 48 PHE cc_start: 0.8206 (m-80) cc_final: 0.6459 (p90) REVERT: B 30 TYR cc_start: 0.8839 (m-10) cc_final: 0.8317 (m-10) REVERT: B 34 TRP cc_start: 0.7879 (t-100) cc_final: 0.6734 (t-100) REVERT: A 23 GLN cc_start: 0.8142 (tm-30) cc_final: 0.7573 (tm-30) REVERT: A 28 ARG cc_start: 0.6938 (pmt-80) cc_final: 0.6710 (pmt-80) REVERT: A 82 GLU cc_start: 0.7904 (mt-10) cc_final: 0.7497 (mt-10) outliers start: 12 outliers final: 10 residues processed: 113 average time/residue: 0.3383 time to fit residues: 46.6508 Evaluate side-chains 98 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 88 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 34 TRP Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 106 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 18 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 96 HIS A 36 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.121625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.115597 restraints weight = 17874.443| |-----------------------------------------------------------------------------| r_work (start): 0.3806 rms_B_bonded: 1.95 r_work: 0.3731 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3630 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.7179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 3702 Z= 0.307 Angle : 0.705 5.842 5022 Z= 0.388 Chirality : 0.048 0.123 576 Planarity : 0.005 0.039 654 Dihedral : 6.565 18.278 522 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 4.10 % Allowed : 17.69 % Favored : 78.21 % 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: -3.77 (0.29), residues: 462 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.87 (0.22), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 34 HIS 0.004 0.002 HIS D 96 PHE 0.014 0.002 PHE B 99 TYR 0.019 0.003 TYR F 85 ARG 0.005 0.001 ARG C 28 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 0.563 Fit side-chains REVERT: D 30 TYR cc_start: 0.8880 (m-10) cc_final: 0.8178 (m-10) REVERT: E 48 PHE cc_start: 0.8584 (OUTLIER) cc_final: 0.7291 (m-80) REVERT: F 30 TYR cc_start: 0.8484 (m-10) cc_final: 0.8173 (m-80) REVERT: F 48 PHE cc_start: 0.8312 (OUTLIER) cc_final: 0.6333 (p90) REVERT: C 48 PHE cc_start: 0.8209 (OUTLIER) cc_final: 0.7209 (m-80) REVERT: A 23 GLN cc_start: 0.8391 (tm-30) cc_final: 0.8175 (tt0) REVERT: A 35 TYR cc_start: 0.8545 (m-80) cc_final: 0.8302 (m-10) outliers start: 16 outliers final: 10 residues processed: 109 average time/residue: 0.2864 time to fit residues: 38.7277 Evaluate side-chains 98 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 48 PHE Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain E residue 34 TRP Chi-restraints excluded: chain E residue 48 PHE Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 48 PHE Chi-restraints excluded: chain C residue 48 PHE Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 89 SER Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain A residue 17 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 33 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 4 optimal weight: 0.0970 chunk 38 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 18 optimal weight: 0.0770 chunk 6 optimal weight: 0.5980 overall best weight: 0.3936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 88 ASN ** 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 = 0.3964 r_free = 0.3964 target = 0.125265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.119461 restraints weight = 17779.341| |-----------------------------------------------------------------------------| r_work (start): 0.3871 rms_B_bonded: 1.94 r_work: 0.3793 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3690 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.7620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3702 Z= 0.169 Angle : 0.593 4.587 5022 Z= 0.325 Chirality : 0.047 0.124 576 Planarity : 0.004 0.033 654 Dihedral : 6.192 17.547 522 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 2.56 % Allowed : 19.49 % Favored : 77.95 % 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: -3.51 (0.29), residues: 462 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.66 (0.22), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 34 HIS 0.003 0.001 HIS B 96 PHE 0.004 0.001 PHE E 99 TYR 0.016 0.002 TYR F 85 ARG 0.002 0.000 ARG F 19 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 0.595 Fit side-chains revert: symmetry clash REVERT: D 23 GLN cc_start: 0.8706 (tt0) cc_final: 0.8470 (tt0) REVERT: D 30 TYR cc_start: 0.8822 (m-10) cc_final: 0.8299 (m-10) REVERT: D 80 GLU cc_start: 0.8070 (mt-10) cc_final: 0.7727 (mt-10) REVERT: E 31 SER cc_start: 0.9237 (t) cc_final: 0.8991 (p) REVERT: E 48 PHE cc_start: 0.8555 (OUTLIER) cc_final: 0.7374 (m-80) REVERT: F 48 PHE cc_start: 0.8198 (m-80) cc_final: 0.6226 (p90) REVERT: A 23 GLN cc_start: 0.8164 (tm-30) cc_final: 0.7943 (tt0) outliers start: 10 outliers final: 6 residues processed: 103 average time/residue: 0.3053 time to fit residues: 38.9306 Evaluate side-chains 96 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 89 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 34 TRP Chi-restraints excluded: chain E residue 48 PHE Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain C residue 89 SER Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain A residue 17 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 39 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 35 optimal weight: 0.0870 chunk 10 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 97 GLN ** F 88 ASN ** 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 = 0.3918 r_free = 0.3918 target = 0.121395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.115467 restraints weight = 17965.996| |-----------------------------------------------------------------------------| r_work (start): 0.3834 rms_B_bonded: 1.93 r_work: 0.3758 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3655 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.7923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3702 Z= 0.240 Angle : 0.608 4.775 5022 Z= 0.332 Chirality : 0.046 0.121 576 Planarity : 0.004 0.031 654 Dihedral : 6.168 17.157 522 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 3.08 % Allowed : 20.00 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.38 (0.29), residues: 462 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.57 (0.22), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 34 HIS 0.003 0.001 HIS B 96 PHE 0.008 0.001 PHE B 99 TYR 0.018 0.002 TYR F 85 ARG 0.002 0.000 ARG A 90 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 87 time to evaluate : 0.535 Fit side-chains REVERT: D 30 TYR cc_start: 0.8903 (m-10) cc_final: 0.8441 (m-10) REVERT: D 80 GLU cc_start: 0.7997 (mt-10) cc_final: 0.7758 (mt-10) REVERT: E 31 SER cc_start: 0.9260 (t) cc_final: 0.9018 (p) REVERT: E 48 PHE cc_start: 0.8612 (OUTLIER) cc_final: 0.7445 (m-80) REVERT: F 48 PHE cc_start: 0.8296 (OUTLIER) cc_final: 0.6172 (p90) REVERT: C 25 ASP cc_start: 0.7664 (p0) cc_final: 0.7322 (p0) REVERT: C 48 PHE cc_start: 0.8208 (OUTLIER) cc_final: 0.7217 (m-80) REVERT: A 19 ARG cc_start: 0.6075 (mmp-170) cc_final: 0.4776 (mmp-170) outliers start: 12 outliers final: 8 residues processed: 94 average time/residue: 0.2937 time to fit residues: 34.6941 Evaluate side-chains 92 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 81 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 48 PHE Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain E residue 34 TRP Chi-restraints excluded: chain E residue 48 PHE Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 48 PHE Chi-restraints excluded: chain C residue 48 PHE Chi-restraints excluded: chain C residue 89 SER Chi-restraints excluded: chain B residue 11 SER Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 89 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 8 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 36 optimal weight: 0.9980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 88 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.116663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.110886 restraints weight = 18260.716| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 1.85 r_work: 0.3694 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3595 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.8259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 3702 Z= 0.330 Angle : 0.663 5.391 5022 Z= 0.364 Chirality : 0.047 0.119 576 Planarity : 0.004 0.030 654 Dihedral : 6.365 17.449 522 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.23 % Favored : 91.77 % Rotamer: Outliers : 4.10 % Allowed : 19.49 % Favored : 76.41 % 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: -3.37 (0.29), residues: 462 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.56 (0.22), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 34 HIS 0.003 0.002 HIS A 96 PHE 0.010 0.001 PHE B 99 TYR 0.020 0.003 TYR F 85 ARG 0.003 0.001 ARG A 90 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 81 time to evaluate : 0.569 Fit side-chains revert: symmetry clash REVERT: D 30 TYR cc_start: 0.8958 (m-10) cc_final: 0.8499 (m-10) REVERT: D 80 GLU cc_start: 0.7977 (mt-10) cc_final: 0.7754 (mt-10) REVERT: E 48 PHE cc_start: 0.8668 (OUTLIER) cc_final: 0.7488 (m-80) REVERT: F 48 PHE cc_start: 0.8335 (OUTLIER) cc_final: 0.6087 (p90) REVERT: C 25 ASP cc_start: 0.7778 (p0) cc_final: 0.7363 (p0) REVERT: C 30 TYR cc_start: 0.9031 (m-10) cc_final: 0.8775 (m-80) REVERT: C 48 PHE cc_start: 0.8268 (OUTLIER) cc_final: 0.7296 (m-80) REVERT: A 19 ARG cc_start: 0.6060 (mmp-170) cc_final: 0.4700 (mmp-170) REVERT: A 48 PHE cc_start: 0.8093 (OUTLIER) cc_final: 0.6605 (m-80) outliers start: 16 outliers final: 9 residues processed: 90 average time/residue: 0.2845 time to fit residues: 32.4271 Evaluate side-chains 90 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 48 PHE Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain E residue 34 TRP Chi-restraints excluded: chain E residue 48 PHE Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 48 PHE Chi-restraints excluded: chain C residue 48 PHE Chi-restraints excluded: chain C residue 89 SER Chi-restraints excluded: chain B residue 11 SER Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain A residue 48 PHE Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 95 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 38 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.117508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.111633 restraints weight = 17895.227| |-----------------------------------------------------------------------------| r_work (start): 0.3787 rms_B_bonded: 1.88 r_work: 0.3712 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3612 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.8412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3702 Z= 0.288 Angle : 0.629 4.962 5022 Z= 0.344 Chirality : 0.046 0.121 576 Planarity : 0.004 0.029 654 Dihedral : 6.320 17.355 522 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.23 % Favored : 91.77 % Rotamer: Outliers : 3.59 % Allowed : 20.77 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.32 (0.29), residues: 462 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.52 (0.22), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP E 34 HIS 0.002 0.001 HIS F 96 PHE 0.007 0.001 PHE B 99 TYR 0.018 0.002 TYR F 85 ARG 0.002 0.000 ARG B 28 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 78 time to evaluate : 0.560 Fit side-chains REVERT: D 30 TYR cc_start: 0.8937 (m-10) cc_final: 0.8559 (m-10) REVERT: D 80 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7757 (mt-10) REVERT: E 31 SER cc_start: 0.9285 (t) cc_final: 0.9009 (p) REVERT: E 48 PHE cc_start: 0.8652 (OUTLIER) cc_final: 0.7591 (m-80) REVERT: F 48 PHE cc_start: 0.8306 (OUTLIER) cc_final: 0.6061 (p90) REVERT: C 25 ASP cc_start: 0.7865 (p0) cc_final: 0.7441 (p0) REVERT: C 48 PHE cc_start: 0.8194 (OUTLIER) cc_final: 0.7277 (m-80) REVERT: A 19 ARG cc_start: 0.5754 (mmp-170) cc_final: 0.4322 (mmp-170) REVERT: A 34 TRP cc_start: 0.6045 (t60) cc_final: 0.5668 (t60) REVERT: A 48 PHE cc_start: 0.8126 (OUTLIER) cc_final: 0.6593 (m-80) outliers start: 14 outliers final: 9 residues processed: 86 average time/residue: 0.2540 time to fit residues: 28.1631 Evaluate side-chains 90 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 48 PHE Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain E residue 34 TRP Chi-restraints excluded: chain E residue 48 PHE Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 48 PHE Chi-restraints excluded: chain C residue 48 PHE Chi-restraints excluded: chain C residue 89 SER Chi-restraints excluded: chain B residue 11 SER Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain A residue 48 PHE Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 95 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 32 optimal weight: 1.9990 chunk 40 optimal weight: 0.3980 chunk 10 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 = 0.3906 r_free = 0.3906 target = 0.120043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.114120 restraints weight = 18058.867| |-----------------------------------------------------------------------------| r_work (start): 0.3821 rms_B_bonded: 1.89 r_work: 0.3750 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3650 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.8507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3702 Z= 0.242 Angle : 0.608 4.787 5022 Z= 0.333 Chirality : 0.046 0.122 576 Planarity : 0.004 0.028 654 Dihedral : 6.224 17.279 522 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.66 % Favored : 91.34 % Rotamer: Outliers : 3.59 % Allowed : 20.51 % Favored : 75.90 % 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: -3.28 (0.29), residues: 462 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.49 (0.22), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 34 HIS 0.002 0.001 HIS B 96 PHE 0.006 0.001 PHE B 99 TYR 0.024 0.002 TYR C 30 ARG 0.002 0.000 ARG A 90 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 0.581 Fit side-chains REVERT: D 80 GLU cc_start: 0.7989 (mt-10) cc_final: 0.7726 (mt-10) REVERT: E 31 SER cc_start: 0.9292 (t) cc_final: 0.9051 (p) REVERT: E 48 PHE cc_start: 0.8673 (OUTLIER) cc_final: 0.7694 (m-80) REVERT: F 48 PHE cc_start: 0.8316 (OUTLIER) cc_final: 0.6040 (p90) REVERT: C 25 ASP cc_start: 0.7837 (p0) cc_final: 0.7415 (p0) REVERT: C 30 TYR cc_start: 0.8986 (m-10) cc_final: 0.8628 (m-80) REVERT: C 48 PHE cc_start: 0.8174 (OUTLIER) cc_final: 0.7223 (m-80) REVERT: A 19 ARG cc_start: 0.5795 (mmp-170) cc_final: 0.4332 (mmp80) REVERT: A 34 TRP cc_start: 0.6005 (t60) cc_final: 0.5713 (t60) REVERT: A 48 PHE cc_start: 0.8109 (OUTLIER) cc_final: 0.6475 (m-80) outliers start: 14 outliers final: 10 residues processed: 91 average time/residue: 0.2516 time to fit residues: 29.7471 Evaluate side-chains 93 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 48 PHE Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain E residue 34 TRP Chi-restraints excluded: chain E residue 48 PHE Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 48 PHE Chi-restraints excluded: chain C residue 48 PHE Chi-restraints excluded: chain C residue 89 SER Chi-restraints excluded: chain B residue 11 SER Chi-restraints excluded: chain B residue 48 PHE Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain A residue 48 PHE Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 95 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 28 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 34 optimal weight: 0.3980 chunk 11 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 3 optimal weight: 0.2980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3923 r_free = 0.3923 target = 0.120867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.115018 restraints weight = 18053.619| |-----------------------------------------------------------------------------| r_work (start): 0.3829 rms_B_bonded: 1.87 r_work: 0.3753 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3651 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.8624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3702 Z= 0.215 Angle : 0.590 4.695 5022 Z= 0.323 Chirality : 0.046 0.126 576 Planarity : 0.003 0.027 654 Dihedral : 6.131 17.174 522 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.66 % Favored : 91.34 % Rotamer: Outliers : 3.59 % Allowed : 20.51 % Favored : 75.90 % 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: -3.26 (0.30), residues: 462 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.48 (0.23), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 34 HIS 0.002 0.001 HIS B 96 PHE 0.006 0.001 PHE B 99 TYR 0.020 0.002 TYR C 30 ARG 0.003 0.000 ARG B 28 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 0.549 Fit side-chains revert: symmetry clash REVERT: D 30 TYR cc_start: 0.9049 (m-10) cc_final: 0.8557 (m-10) REVERT: D 80 GLU cc_start: 0.8096 (mt-10) cc_final: 0.7785 (mt-10) REVERT: E 31 SER cc_start: 0.9288 (t) cc_final: 0.9021 (p) REVERT: E 48 PHE cc_start: 0.8659 (OUTLIER) cc_final: 0.7734 (m-80) REVERT: F 48 PHE cc_start: 0.8305 (OUTLIER) cc_final: 0.6032 (p90) REVERT: F 84 ASP cc_start: 0.8720 (m-30) cc_final: 0.8475 (m-30) REVERT: C 25 ASP cc_start: 0.7813 (p0) cc_final: 0.7392 (p0) REVERT: C 30 TYR cc_start: 0.9026 (m-10) cc_final: 0.8765 (m-80) REVERT: C 48 PHE cc_start: 0.8177 (OUTLIER) cc_final: 0.7350 (m-80) REVERT: A 19 ARG cc_start: 0.5791 (mmp-170) cc_final: 0.4336 (mmp80) REVERT: A 34 TRP cc_start: 0.5986 (t60) cc_final: 0.5708 (t60) REVERT: A 48 PHE cc_start: 0.8076 (OUTLIER) cc_final: 0.6386 (m-80) outliers start: 14 outliers final: 10 residues processed: 93 average time/residue: 0.2467 time to fit residues: 29.7460 Evaluate side-chains 95 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 81 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 48 PHE Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain E residue 34 TRP Chi-restraints excluded: chain E residue 48 PHE Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 48 PHE Chi-restraints excluded: chain C residue 48 PHE Chi-restraints excluded: chain C residue 89 SER Chi-restraints excluded: chain B residue 11 SER Chi-restraints excluded: chain B residue 48 PHE Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain A residue 48 PHE Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 95 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 42 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 27 optimal weight: 0.0970 chunk 20 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 16 optimal weight: 0.1980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 96 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.122628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.116762 restraints weight = 18001.194| |-----------------------------------------------------------------------------| r_work (start): 0.3853 rms_B_bonded: 1.88 r_work: 0.3780 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3680 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.8681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3702 Z= 0.202 Angle : 0.583 4.751 5022 Z= 0.319 Chirality : 0.046 0.134 576 Planarity : 0.003 0.024 654 Dihedral : 6.049 17.068 522 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.87 % Favored : 91.13 % Rotamer: Outliers : 3.33 % Allowed : 21.54 % Favored : 75.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.22 (0.30), residues: 462 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.44 (0.23), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 34 HIS 0.002 0.001 HIS B 96 PHE 0.004 0.001 PHE B 99 TYR 0.020 0.002 TYR C 30 ARG 0.002 0.000 ARG B 28 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 924 Ramachandran restraints generated. 462 Oldfield, 0 Emsley, 462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 86 time to evaluate : 0.535 Fit side-chains revert: symmetry clash REVERT: D 30 TYR cc_start: 0.9050 (m-10) cc_final: 0.8524 (m-10) REVERT: D 80 GLU cc_start: 0.8148 (mt-10) cc_final: 0.7833 (mt-10) REVERT: F 48 PHE cc_start: 0.8275 (OUTLIER) cc_final: 0.6013 (p90) REVERT: F 90 ARG cc_start: 0.8155 (ttp80) cc_final: 0.7700 (ttp-170) REVERT: C 25 ASP cc_start: 0.7768 (p0) cc_final: 0.7363 (p0) REVERT: C 30 TYR cc_start: 0.9008 (m-10) cc_final: 0.8711 (m-80) REVERT: C 48 PHE cc_start: 0.8187 (OUTLIER) cc_final: 0.7670 (m-80) REVERT: B 104 LYS cc_start: 0.8452 (mmmt) cc_final: 0.8199 (tptt) REVERT: A 19 ARG cc_start: 0.5846 (mmp-170) cc_final: 0.4382 (mmp80) REVERT: A 48 PHE cc_start: 0.8104 (OUTLIER) cc_final: 0.7397 (m-80) REVERT: A 84 ASP cc_start: 0.7229 (m-30) cc_final: 0.5739 (p0) outliers start: 13 outliers final: 9 residues processed: 94 average time/residue: 0.3328 time to fit residues: 38.2623 Evaluate side-chains 94 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 48 PHE Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain E residue 34 TRP Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 48 PHE Chi-restraints excluded: chain C residue 48 PHE Chi-restraints excluded: chain C residue 89 SER Chi-restraints excluded: chain B residue 11 SER Chi-restraints excluded: chain B residue 48 PHE Chi-restraints excluded: chain A residue 48 PHE Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 95 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 25 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.117756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.111812 restraints weight = 18120.988| |-----------------------------------------------------------------------------| r_work (start): 0.3804 rms_B_bonded: 1.87 r_work: 0.3734 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3638 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.8722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3702 Z= 0.276 Angle : 0.622 5.290 5022 Z= 0.339 Chirality : 0.046 0.123 576 Planarity : 0.003 0.025 654 Dihedral : 6.173 16.893 522 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 3.59 % Allowed : 21.28 % Favored : 75.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.26 (0.30), residues: 462 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.48 (0.23), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 34 HIS 0.002 0.001 HIS A 96 PHE 0.006 0.001 PHE C 99 TYR 0.021 0.003 TYR C 30 ARG 0.003 0.000 ARG B 28 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4363.92 seconds wall clock time: 77 minutes 41.11 seconds (4661.11 seconds total)