Starting phenix.real_space_refine on Wed Mar 12 02:19:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6z1i_11030/03_2025/6z1i_11030.cif Found real_map, /net/cci-nas-00/data/ceres_data/6z1i_11030/03_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_11030/03_2025/6z1i_11030.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6z1i_11030/03_2025/6z1i_11030.map" model { file = "/net/cci-nas-00/data/ceres_data/6z1i_11030/03_2025/6z1i_11030.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6z1i_11030/03_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-5624/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: 2.98, per 1000 atoms: 0.42 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: 1.75 Conformation dependent library (CDL) restraints added in 612.8 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: 0.80 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: 2.39 Time building geometry restraints manager: 2.12 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: 1.220 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: 0.140 Extract box with map and model: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 18.370 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.840 ------------------------------------------------------------------------------- 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 : 0.493 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: 0.5098 time to fit residues: 98.5350 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 : 0.507 ------------------------------------------------------------------------------- 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 = 32)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.133813 restraints weight = 16949.983| |-----------------------------------------------------------------------------| r_work (start): 0.4047 rms_B_bonded: 2.11 r_work: 0.3966 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3857 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 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 : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 90 ARG cc_start: 0.8404 (ttp80) cc_final: 0.8180 (ttp-170) REVERT: F 48 PHE cc_start: 0.8209 (m-80) cc_final: 0.6459 (p90) REVERT: B 30 TYR cc_start: 0.8843 (m-10) cc_final: 0.8323 (m-10) REVERT: B 34 TRP cc_start: 0.7882 (t-100) cc_final: 0.6739 (t-100) REVERT: A 23 GLN cc_start: 0.8138 (tm-30) cc_final: 0.7570 (tm-30) REVERT: A 28 ARG cc_start: 0.6945 (pmt-80) cc_final: 0.6718 (pmt-80) REVERT: A 82 GLU cc_start: 0.7907 (mt-10) cc_final: 0.7506 (mt-10) outliers start: 12 outliers final: 10 residues processed: 113 average time/residue: 0.3366 time to fit residues: 46.4426 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: 0.9980 chunk 42 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 88 ASN F 96 HIS A 36 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.121782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.115671 restraints weight = 17879.673| |-----------------------------------------------------------------------------| r_work (start): 0.3815 rms_B_bonded: 1.97 r_work: 0.3738 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3637 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.7025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 3702 Z= 0.306 Angle : 0.695 5.654 5022 Z= 0.382 Chirality : 0.048 0.122 576 Planarity : 0.005 0.037 654 Dihedral : 6.544 18.028 522 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 3.59 % Allowed : 18.72 % Favored : 77.69 % 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: -3.78 (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 0.011 0.002 TRP D 34 HIS 0.003 0.002 HIS D 96 PHE 0.012 0.002 PHE B 99 TYR 0.019 0.003 TYR F 85 ARG 0.004 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 114 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 100 time to evaluate : 0.560 Fit side-chains REVERT: D 30 TYR cc_start: 0.8861 (m-10) cc_final: 0.8260 (m-10) REVERT: E 48 PHE cc_start: 0.8584 (OUTLIER) cc_final: 0.7300 (m-80) REVERT: E 97 GLN cc_start: 0.8784 (mt0) cc_final: 0.8579 (mt0) REVERT: F 30 TYR cc_start: 0.8524 (m-10) cc_final: 0.8195 (m-80) REVERT: F 48 PHE cc_start: 0.8305 (OUTLIER) cc_final: 0.6339 (p90) REVERT: C 25 ASP cc_start: 0.7700 (p0) cc_final: 0.7405 (p0) REVERT: A 23 GLN cc_start: 0.8408 (tm-30) cc_final: 0.8184 (tt0) REVERT: A 80 GLU cc_start: 0.7734 (mt-10) cc_final: 0.7523 (mt-10) outliers start: 14 outliers final: 8 residues processed: 106 average time/residue: 0.2837 time to fit residues: 37.8700 Evaluate side-chains 92 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 82 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 0.9980 chunk 4 optimal weight: 0.2980 chunk 38 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 26 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.3908 r_free = 0.3908 target = 0.121004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.115158 restraints weight = 18088.403| |-----------------------------------------------------------------------------| r_work (start): 0.3824 rms_B_bonded: 1.94 r_work: 0.3749 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3649 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.7661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3702 Z= 0.251 Angle : 0.636 4.887 5022 Z= 0.347 Chirality : 0.047 0.122 576 Planarity : 0.004 0.032 654 Dihedral : 6.307 17.601 522 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 3.59 % Allowed : 17.69 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.56 (0.29), residues: 462 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.71 (0.22), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 34 HIS 0.004 0.002 HIS A 96 PHE 0.007 0.001 PHE B 99 TYR 0.019 0.002 TYR F 85 ARG 0.003 0.000 ARG C 28 *********************** 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 101 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 0.645 Fit side-chains REVERT: D 30 TYR cc_start: 0.8869 (m-10) cc_final: 0.8435 (m-10) REVERT: E 31 SER cc_start: 0.9273 (t) cc_final: 0.8991 (p) REVERT: E 48 PHE cc_start: 0.8633 (OUTLIER) cc_final: 0.7426 (m-80) REVERT: E 97 GLN cc_start: 0.8786 (mt0) cc_final: 0.8584 (mt0) REVERT: F 48 PHE cc_start: 0.8259 (OUTLIER) cc_final: 0.6200 (p90) REVERT: C 48 PHE cc_start: 0.8215 (OUTLIER) cc_final: 0.7233 (m-80) REVERT: A 19 ARG cc_start: 0.6091 (mmp-170) cc_final: 0.4730 (mmp-170) REVERT: A 23 GLN cc_start: 0.8260 (tm-30) cc_final: 0.8034 (tt0) REVERT: A 80 GLU cc_start: 0.7785 (mt-10) cc_final: 0.7572 (mt-10) outliers start: 14 outliers final: 10 residues processed: 97 average time/residue: 0.2756 time to fit residues: 34.3394 Evaluate side-chains 96 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.532 ------------------------------------------------------------------------------- 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 89 SER Chi-restraints excluded: chain B residue 31 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: 0.4980 chunk 35 optimal weight: 0.2980 chunk 10 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3906 r_free = 0.3906 target = 0.120585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.114768 restraints weight = 17968.138| |-----------------------------------------------------------------------------| r_work (start): 0.3823 rms_B_bonded: 1.89 r_work: 0.3748 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3648 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.8052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3702 Z= 0.231 Angle : 0.611 4.746 5022 Z= 0.334 Chirality : 0.046 0.125 576 Planarity : 0.004 0.031 654 Dihedral : 6.199 18.351 522 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 3.85 % Allowed : 18.97 % Favored : 77.18 % 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: -3.42 (0.29), residues: 462 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.60 (0.22), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 34 HIS 0.003 0.001 HIS A 96 PHE 0.007 0.001 PHE B 99 TYR 0.018 0.002 TYR F 85 ARG 0.003 0.000 ARG C 28 *********************** 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: 15 poor density : 84 time to evaluate : 0.507 Fit side-chains revert: symmetry clash REVERT: D 30 TYR cc_start: 0.8871 (m-10) cc_final: 0.8407 (m-10) REVERT: D 34 TRP cc_start: 0.7919 (t-100) cc_final: 0.7675 (t-100) REVERT: D 80 GLU cc_start: 0.7926 (mt-10) cc_final: 0.7698 (mt-10) REVERT: E 31 SER cc_start: 0.9281 (t) cc_final: 0.9062 (p) REVERT: E 48 PHE cc_start: 0.8625 (OUTLIER) cc_final: 0.7459 (m-80) REVERT: E 97 GLN cc_start: 0.8809 (mt0) cc_final: 0.8573 (mt0) REVERT: F 48 PHE cc_start: 0.8247 (OUTLIER) cc_final: 0.6138 (p90) REVERT: C 25 ASP cc_start: 0.7681 (p0) cc_final: 0.7322 (p0) REVERT: C 30 TYR cc_start: 0.9047 (m-10) cc_final: 0.8788 (m-80) REVERT: C 48 PHE cc_start: 0.8225 (OUTLIER) cc_final: 0.7252 (m-80) REVERT: A 19 ARG cc_start: 0.6209 (mmp-170) cc_final: 0.4914 (mmp-170) outliers start: 15 outliers final: 9 residues processed: 93 average time/residue: 0.2401 time to fit residues: 29.0096 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 : 0.574 ------------------------------------------------------------------------------- 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 E residue 89 SER 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 89 SER Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain A residue 73 THR 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: 0.9980 chunk 10 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 36 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3872 r_free = 0.3872 target = 0.117853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.111945 restraints weight = 18126.081| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 1.91 r_work: 0.3722 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3622 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.8325 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= 0.277 Angle : 0.636 5.024 5022 Z= 0.348 Chirality : 0.047 0.121 576 Planarity : 0.004 0.030 654 Dihedral : 6.229 16.869 522 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.44 % Favored : 91.56 % Rotamer: Outliers : 4.10 % Allowed : 19.74 % Favored : 76.15 % 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: -3.39 (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 0.007 0.001 TRP E 34 HIS 0.003 0.001 HIS A 96 PHE 0.008 0.001 PHE B 99 TYR 0.018 0.003 TYR B 35 ARG 0.003 0.000 ARG B 28 *********************** 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 98 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 82 time to evaluate : 0.546 Fit side-chains REVERT: D 30 TYR cc_start: 0.8962 (m-10) cc_final: 0.8618 (m-10) REVERT: E 31 SER cc_start: 0.9288 (t) cc_final: 0.9058 (p) REVERT: E 48 PHE cc_start: 0.8650 (OUTLIER) cc_final: 0.7451 (m-80) REVERT: F 48 PHE cc_start: 0.8303 (OUTLIER) cc_final: 0.6063 (p90) REVERT: C 25 ASP cc_start: 0.7808 (p0) cc_final: 0.7387 (p0) REVERT: C 34 TRP cc_start: 0.8885 (OUTLIER) cc_final: 0.8204 (t60) REVERT: C 48 PHE cc_start: 0.8213 (OUTLIER) cc_final: 0.7260 (m-80) REVERT: A 19 ARG cc_start: 0.6040 (mmp-170) cc_final: 0.4689 (mmp-170) REVERT: A 48 PHE cc_start: 0.8057 (OUTLIER) cc_final: 0.6610 (m-80) outliers start: 16 outliers final: 9 residues processed: 92 average time/residue: 0.2589 time to fit residues: 30.8604 Evaluate side-chains 91 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 0.570 ------------------------------------------------------------------------------- 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 E residue 89 SER Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 48 PHE Chi-restraints excluded: chain C residue 34 TRP 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 48 PHE Chi-restraints excluded: chain A residue 73 THR 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: 0.5980 chunk 15 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 = 0.3872 r_free = 0.3872 target = 0.117969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.112143 restraints weight = 17886.050| |-----------------------------------------------------------------------------| r_work (start): 0.3783 rms_B_bonded: 1.88 r_work: 0.3706 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3608 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.8483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 3702 Z= 0.297 Angle : 0.636 5.242 5022 Z= 0.349 Chirality : 0.046 0.123 576 Planarity : 0.004 0.029 654 Dihedral : 6.280 17.985 522 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 4.10 % Allowed : 19.74 % Favored : 76.15 % 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 0.002 TRP E 34 HIS 0.002 0.001 HIS B 96 PHE 0.008 0.001 PHE B 99 TYR 0.020 0.003 TYR C 30 ARG 0.003 0.000 ARG A 90 *********************** 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 93 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 77 time to evaluate : 0.589 Fit side-chains revert: symmetry clash REVERT: D 30 TYR cc_start: 0.8934 (m-10) cc_final: 0.8520 (m-10) REVERT: E 31 SER cc_start: 0.9301 (t) cc_final: 0.9040 (p) REVERT: E 48 PHE cc_start: 0.8663 (OUTLIER) cc_final: 0.7607 (m-80) REVERT: F 23 GLN cc_start: 0.8977 (OUTLIER) cc_final: 0.8721 (tt0) REVERT: F 48 PHE cc_start: 0.8322 (OUTLIER) cc_final: 0.6012 (p90) REVERT: C 25 ASP cc_start: 0.7832 (p0) cc_final: 0.7395 (p0) REVERT: C 30 TYR cc_start: 0.9029 (m-10) cc_final: 0.8761 (m-80) REVERT: C 34 TRP cc_start: 0.8893 (OUTLIER) cc_final: 0.8074 (t60) REVERT: C 48 PHE cc_start: 0.8203 (OUTLIER) cc_final: 0.7289 (m-80) REVERT: A 19 ARG cc_start: 0.5708 (mmp-170) cc_final: 0.4245 (mmp-170) REVERT: A 34 TRP cc_start: 0.6002 (t60) cc_final: 0.5632 (t60) REVERT: A 48 PHE cc_start: 0.8109 (OUTLIER) cc_final: 0.6591 (m-80) outliers start: 16 outliers final: 10 residues processed: 86 average time/residue: 0.2819 time to fit residues: 31.2927 Evaluate side-chains 90 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 74 time to evaluate : 0.580 ------------------------------------------------------------------------------- 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 E residue 89 SER Chi-restraints excluded: chain F residue 23 GLN Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 48 PHE Chi-restraints excluded: chain C residue 34 TRP 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: 0.8980 chunk 25 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3897 r_free = 0.3897 target = 0.119317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.113473 restraints weight = 18133.241| |-----------------------------------------------------------------------------| r_work (start): 0.3814 rms_B_bonded: 1.88 r_work: 0.3740 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3639 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.8591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3702 Z= 0.227 Angle : 0.602 4.932 5022 Z= 0.330 Chirality : 0.046 0.122 576 Planarity : 0.004 0.028 654 Dihedral : 6.166 16.939 522 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 7.27 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: -3.31 (0.29), residues: 462 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.51 (0.22), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 34 HIS 0.002 0.001 HIS B 96 PHE 0.006 0.001 PHE B 99 TYR 0.017 0.002 TYR F 85 ARG 0.003 0.000 ARG B 28 *********************** 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 93 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 0.561 Fit side-chains revert: symmetry clash REVERT: D 30 TYR cc_start: 0.8977 (m-10) cc_final: 0.8620 (m-10) REVERT: D 34 TRP cc_start: 0.7902 (t-100) cc_final: 0.7691 (t-100) REVERT: E 31 SER cc_start: 0.9289 (t) cc_final: 0.9058 (p) REVERT: E 48 PHE cc_start: 0.8661 (OUTLIER) cc_final: 0.7692 (m-80) REVERT: F 48 PHE cc_start: 0.8311 (OUTLIER) cc_final: 0.5999 (p90) REVERT: C 25 ASP cc_start: 0.7854 (p0) cc_final: 0.7424 (p0) REVERT: C 30 TYR cc_start: 0.8980 (m-10) cc_final: 0.8723 (m-80) REVERT: C 34 TRP cc_start: 0.8859 (OUTLIER) cc_final: 0.8012 (t60) REVERT: C 48 PHE cc_start: 0.8178 (OUTLIER) cc_final: 0.7276 (m-80) REVERT: A 19 ARG cc_start: 0.5734 (mmp-170) cc_final: 0.4270 (mmp-170) REVERT: A 34 TRP cc_start: 0.6060 (t60) cc_final: 0.5811 (t60) REVERT: A 48 PHE cc_start: 0.8098 (OUTLIER) cc_final: 0.6501 (m-80) outliers start: 14 outliers final: 7 residues processed: 89 average time/residue: 0.2601 time to fit residues: 30.0077 Evaluate side-chains 90 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 0.538 ------------------------------------------------------------------------------- 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 34 TRP Chi-restraints excluded: chain C residue 48 PHE Chi-restraints excluded: chain C residue 89 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 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: 0.9990 chunk 29 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 chunk 30 optimal weight: 0.5980 chunk 20 optimal weight: 0.0020 chunk 37 optimal weight: 0.7980 chunk 3 optimal weight: 0.5980 overall best weight: 0.4788 ------------------------------------------------------------------------------- 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 = 0.3951 r_free = 0.3951 target = 0.122611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.116827 restraints weight = 18029.619| |-----------------------------------------------------------------------------| r_work (start): 0.3865 rms_B_bonded: 1.90 r_work: 0.3792 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3692 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.8669 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= 0.189 Angle : 0.575 4.647 5022 Z= 0.315 Chirality : 0.046 0.127 576 Planarity : 0.003 0.024 654 Dihedral : 6.000 16.860 522 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.23 % Favored : 91.77 % Rotamer: Outliers : 3.08 % Allowed : 21.54 % Favored : 75.38 % 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: -3.25 (0.30), residues: 462 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.47 (0.23), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 34 HIS 0.002 0.001 HIS B 96 PHE 0.005 0.001 PHE B 99 TYR 0.016 0.002 TYR F 85 ARG 0.002 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 98 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 0.522 Fit side-chains revert: symmetry clash REVERT: D 34 TRP cc_start: 0.7866 (t-100) cc_final: 0.7625 (t-100) REVERT: E 31 SER cc_start: 0.9286 (t) cc_final: 0.9052 (p) REVERT: F 48 PHE cc_start: 0.8283 (m-80) cc_final: 0.5977 (p90) REVERT: C 25 ASP cc_start: 0.7775 (p0) cc_final: 0.7350 (p0) REVERT: C 30 TYR cc_start: 0.9022 (m-10) cc_final: 0.8662 (m-80) REVERT: C 34 TRP cc_start: 0.8833 (OUTLIER) cc_final: 0.7970 (t60) REVERT: C 48 PHE cc_start: 0.8169 (OUTLIER) cc_final: 0.7529 (m-80) REVERT: C 91 ASP cc_start: 0.8623 (t0) cc_final: 0.8243 (t70) REVERT: B 104 LYS cc_start: 0.8436 (mmmt) cc_final: 0.8197 (tptt) REVERT: A 19 ARG cc_start: 0.5716 (mmp-170) cc_final: 0.4256 (mmp-170) REVERT: A 34 TRP cc_start: 0.6058 (t60) cc_final: 0.5770 (t60) REVERT: A 48 PHE cc_start: 0.8037 (OUTLIER) cc_final: 0.7113 (m-80) REVERT: A 84 ASP cc_start: 0.7103 (m-30) cc_final: 0.5857 (p0) outliers start: 12 outliers final: 8 residues processed: 94 average time/residue: 0.2731 time to fit residues: 33.3413 Evaluate side-chains 91 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 0.533 ------------------------------------------------------------------------------- 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 C residue 34 TRP 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 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: 1.9990 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: 0.6980 chunk 20 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 68 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.118225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.112345 restraints weight = 18310.255| |-----------------------------------------------------------------------------| r_work (start): 0.3817 rms_B_bonded: 1.89 r_work: 0.3746 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3648 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.8770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3702 Z= 0.276 Angle : 0.622 5.377 5022 Z= 0.339 Chirality : 0.046 0.130 576 Planarity : 0.003 0.024 654 Dihedral : 6.151 22.665 522 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.23 % Favored : 91.77 % Rotamer: Outliers : 3.08 % Allowed : 22.31 % Favored : 74.62 % 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: -3.31 (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 B 34 HIS 0.002 0.001 HIS A 96 PHE 0.006 0.001 PHE B 99 TYR 0.016 0.002 TYR F 85 ARG 0.003 0.000 ARG A 90 ********************** 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 93 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 81 time to evaluate : 0.543 Fit side-chains revert: symmetry clash REVERT: D 34 TRP cc_start: 0.7882 (t-100) cc_final: 0.7652 (t-100) REVERT: E 31 SER cc_start: 0.9208 (t) cc_final: 0.8999 (p) REVERT: F 48 PHE cc_start: 0.8299 (m-80) cc_final: 0.5996 (p90) REVERT: F 90 ARG cc_start: 0.8295 (ttp80) cc_final: 0.7826 (ttp-170) REVERT: C 25 ASP cc_start: 0.7852 (p0) cc_final: 0.7445 (p0) REVERT: C 30 TYR cc_start: 0.9002 (m-10) cc_final: 0.8703 (m-80) REVERT: C 34 TRP cc_start: 0.8896 (OUTLIER) cc_final: 0.7842 (t60) REVERT: C 48 PHE cc_start: 0.8194 (OUTLIER) cc_final: 0.7630 (m-80) REVERT: B 68 ASN cc_start: 0.6493 (OUTLIER) cc_final: 0.5925 (m-40) REVERT: A 19 ARG cc_start: 0.5843 (mmp-170) cc_final: 0.4348 (mmp80) REVERT: A 34 TRP cc_start: 0.6056 (t60) cc_final: 0.5768 (t60) REVERT: A 48 PHE cc_start: 0.8114 (OUTLIER) cc_final: 0.7370 (m-80) outliers start: 12 outliers final: 8 residues processed: 90 average time/residue: 0.3028 time to fit residues: 34.3349 Evaluate side-chains 93 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 81 time to evaluate : 0.573 ------------------------------------------------------------------------------- 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 C residue 34 TRP 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 68 ASN Chi-restraints excluded: chain A residue 48 PHE Chi-restraints excluded: chain A residue 89 SER 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: 0.9980 chunk 2 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 36 optimal weight: 0.3980 chunk 29 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 68 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.118755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.112862 restraints weight = 18065.643| |-----------------------------------------------------------------------------| r_work (start): 0.3820 rms_B_bonded: 1.86 r_work: 0.3751 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3654 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.8755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.133 3702 Z= 0.380 Angle : 1.222 59.200 5022 Z= 0.751 Chirality : 0.051 0.515 576 Planarity : 0.004 0.024 654 Dihedral : 6.145 22.689 522 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.44 % Favored : 91.56 % Rotamer: Outliers : 3.59 % Allowed : 22.05 % Favored : 74.36 % 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 B 34 HIS 0.002 0.001 HIS A 96 PHE 0.006 0.001 PHE C 99 TYR 0.016 0.002 TYR F 85 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: 4348.25 seconds wall clock time: 74 minutes 34.51 seconds (4474.51 seconds total)