Starting phenix.real_space_refine on Fri Aug 22 19:03:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6z1i_11030/08_2025/6z1i_11030.cif Found real_map, /net/cci-nas-00/data/ceres_data/6z1i_11030/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/6z1i_11030/08_2025/6z1i_11030.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6z1i_11030/08_2025/6z1i_11030.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6z1i_11030/08_2025/6z1i_11030.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6z1i_11030/08_2025/6z1i_11030.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7140 Number of models: 1 Model: "" Number of chains: 1 Chain: "D" 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: E, F, C, B, A Time building chain proxies: 0.98, per 1000 atoms: 0.14 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=6, symmetry=0 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 87 " distance=1.99 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 87 " distance=1.99 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 87 " distance=1.99 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 87 " distance=1.99 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 87 " distance=1.99 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 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: 0.41 Conformation dependent library (CDL) restraints added in 261.9 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 0.27 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: 1.62 Time building geometry restraints manager: 0.58 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: 2760 10.85 - 21.71: 342 21.71 - 32.56: 180 32.56 - 43.42: 108 43.42 - 54.27: 48 Dihedral angle restraints: 3438 sinusoidal: 1842 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 3435 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: 1838 2.33 - 2.90: 16259 2.90 - 3.47: 16676 3.47 - 4.03: 26517 4.03 - 4.60: 36183 Nonbonded interactions: 97473 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 97468 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: 0.02 Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'C' selection = chain 'B' selection = chain 'A' } 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: 1.740 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: 0.050 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.830 Find NCS groups from input model: 0.040 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:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.250 ------------------------------------------------------------------------------- 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 3708 Z= 0.905 Angle : 2.262 9.399 5034 Z= 1.593 Chirality : 0.116 0.365 576 Planarity : 0.012 0.045 654 Dihedral : 14.226 52.366 1290 Min Nonbonded Distance : 2.356 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.001 0.000 ARG E 28 TYR 0.028 0.006 TYR C 86 PHE 0.018 0.007 PHE A 99 TRP 0.031 0.007 TRP A 34 HIS 0.003 0.002 HIS E 96 Details of bonding type rmsd covalent geometry : bond 0.01288 ( 3702) covalent geometry : angle 2.25793 ( 5022) SS BOND : bond 0.04221 ( 6) SS BOND : angle 3.68551 ( 12) hydrogen bonds : bond 0.14092 ( 170) hydrogen bonds : angle 8.17674 ( 510) *********************** 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 : 0.204 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: 0.2661 time to fit residues: 51.1613 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 : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 0.9990 chunk 26 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 chunk 19 optimal weight: 0.2980 chunk 30 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.4155 r_free = 0.4155 target = 0.140303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.133851 restraints weight = 17101.070| |-----------------------------------------------------------------------------| r_work (start): 0.4065 rms_B_bonded: 2.09 r_work: 0.3987 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3878 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.5273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3708 Z= 0.160 Angle : 0.686 5.248 5034 Z= 0.378 Chirality : 0.048 0.143 576 Planarity : 0.005 0.041 654 Dihedral : 6.698 18.905 522 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 3.59 % Allowed : 15.90 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.94 (0.29), residues: 462 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.00 (0.22), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 19 TYR 0.019 0.002 TYR E 86 PHE 0.010 0.001 PHE E 99 TRP 0.015 0.001 TRP A 34 HIS 0.001 0.001 HIS E 96 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 3702) covalent geometry : angle 0.68652 ( 5022) SS BOND : bond 0.00531 ( 6) SS BOND : angle 0.62063 ( 12) hydrogen bonds : bond 0.02482 ( 170) hydrogen bonds : angle 5.88674 ( 510) *********************** 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 123 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 109 time to evaluate : 0.156 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 34 TRP cc_start: 0.7463 (t-100) cc_final: 0.7220 (t-100) REVERT: F 48 PHE cc_start: 0.8092 (m-80) cc_final: 0.6503 (p90) REVERT: B 30 TYR cc_start: 0.8847 (m-10) cc_final: 0.8354 (m-10) REVERT: B 34 TRP cc_start: 0.7872 (t-100) cc_final: 0.6832 (t-100) REVERT: A 82 GLU cc_start: 0.7794 (mt-10) cc_final: 0.7328 (mt-10) outliers start: 14 outliers final: 11 residues processed: 116 average time/residue: 0.1615 time to fit residues: 22.8374 Evaluate side-chains 99 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 34 TRP Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain C residue 89 SER 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 0 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 21 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 23 GLN A 36 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.120456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.114846 restraints weight = 18358.424| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 1.89 r_work: 0.3727 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3631 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.7021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 3708 Z= 0.246 Angle : 0.713 5.887 5034 Z= 0.391 Chirality : 0.047 0.119 576 Planarity : 0.005 0.036 654 Dihedral : 6.619 18.816 522 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.76 (0.29), residues: 462 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.86 (0.22), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 28 TYR 0.020 0.003 TYR F 85 PHE 0.013 0.002 PHE B 99 TRP 0.010 0.002 TRP D 34 HIS 0.003 0.002 HIS A 96 Details of bonding type rmsd covalent geometry : bond 0.00547 ( 3702) covalent geometry : angle 0.70934 ( 5022) SS BOND : bond 0.01297 ( 6) SS BOND : angle 1.57876 ( 12) hydrogen bonds : bond 0.02506 ( 170) hydrogen bonds : angle 5.35858 ( 510) *********************** 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 110 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 0.123 Fit side-chains revert: symmetry clash REVERT: D 30 TYR cc_start: 0.8808 (m-10) cc_final: 0.8328 (m-10) REVERT: E 48 PHE cc_start: 0.8568 (OUTLIER) cc_final: 0.7291 (m-80) REVERT: F 30 TYR cc_start: 0.8554 (m-10) cc_final: 0.8275 (m-80) REVERT: F 48 PHE cc_start: 0.8280 (OUTLIER) cc_final: 0.6372 (p90) REVERT: C 25 ASP cc_start: 0.7692 (p0) cc_final: 0.7214 (p0) outliers start: 16 outliers final: 10 residues processed: 102 average time/residue: 0.1295 time to fit residues: 16.7974 Evaluate side-chains 91 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 79 time to evaluate : 0.200 ------------------------------------------------------------------------------- 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 71 SER Chi-restraints excluded: chain C residue 89 SER Chi-restraints excluded: chain B residue 26 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 26 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 23 GLN C 23 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.118919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.113350 restraints weight = 18505.880| |-----------------------------------------------------------------------------| r_work (start): 0.3784 rms_B_bonded: 1.88 r_work: 0.3713 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3614 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.7694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 3708 Z= 0.202 Angle : 0.651 5.370 5034 Z= 0.354 Chirality : 0.047 0.120 576 Planarity : 0.004 0.031 654 Dihedral : 6.377 17.832 522 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 4.62 % Allowed : 17.44 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.57 (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 ARG 0.003 0.001 ARG A 90 TYR 0.018 0.002 TYR F 85 PHE 0.008 0.001 PHE B 99 TRP 0.009 0.002 TRP B 34 HIS 0.003 0.001 HIS A 96 Details of bonding type rmsd covalent geometry : bond 0.00451 ( 3702) covalent geometry : angle 0.64905 ( 5022) SS BOND : bond 0.00980 ( 6) SS BOND : angle 1.21680 ( 12) hydrogen bonds : bond 0.02028 ( 170) hydrogen bonds : angle 5.14595 ( 510) *********************** 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 102 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 84 time to evaluate : 0.216 Fit side-chains REVERT: D 30 TYR cc_start: 0.8901 (m-10) cc_final: 0.8546 (m-10) REVERT: E 31 SER cc_start: 0.9310 (t) cc_final: 0.9001 (p) REVERT: E 48 PHE cc_start: 0.8611 (OUTLIER) cc_final: 0.7403 (m-80) REVERT: F 48 PHE cc_start: 0.8261 (OUTLIER) cc_final: 0.6235 (p90) REVERT: C 25 ASP cc_start: 0.7706 (p0) cc_final: 0.7386 (p0) REVERT: C 48 PHE cc_start: 0.8212 (OUTLIER) cc_final: 0.7261 (m-80) REVERT: B 48 PHE cc_start: 0.8163 (OUTLIER) cc_final: 0.7903 (m-80) REVERT: B 106 THR cc_start: 0.8967 (OUTLIER) cc_final: 0.8757 (m) REVERT: A 19 ARG cc_start: 0.6094 (mmp-170) cc_final: 0.4605 (mmp-170) outliers start: 18 outliers final: 11 residues processed: 96 average time/residue: 0.1306 time to fit residues: 16.0876 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 : 0.210 ------------------------------------------------------------------------------- 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 11 SER Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 48 PHE 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 73 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 11 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 20 optimal weight: 0.0010 overall best weight: 0.7592 ------------------------------------------------------------------------------- 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 = 0.3872 r_free = 0.3872 target = 0.118553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.112893 restraints weight = 18406.488| |-----------------------------------------------------------------------------| r_work (start): 0.3783 rms_B_bonded: 1.90 r_work: 0.3710 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3610 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.8035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3708 Z= 0.180 Angle : 0.623 4.777 5034 Z= 0.340 Chirality : 0.046 0.121 576 Planarity : 0.004 0.031 654 Dihedral : 6.267 18.353 522 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 3.59 % Allowed : 19.23 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.43 (0.29), residues: 462 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.61 (0.22), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 28 TYR 0.019 0.002 TYR F 85 PHE 0.007 0.001 PHE B 99 TRP 0.008 0.002 TRP E 34 HIS 0.002 0.001 HIS A 96 Details of bonding type rmsd covalent geometry : bond 0.00405 ( 3702) covalent geometry : angle 0.62135 ( 5022) SS BOND : bond 0.00946 ( 6) SS BOND : angle 1.15551 ( 12) hydrogen bonds : bond 0.01988 ( 170) hydrogen bonds : angle 4.99439 ( 510) *********************** 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: 14 poor density : 85 time to evaluate : 0.200 Fit side-chains REVERT: D 30 TYR cc_start: 0.8881 (m-10) cc_final: 0.8411 (m-10) REVERT: E 31 SER cc_start: 0.9301 (t) cc_final: 0.9032 (p) REVERT: E 48 PHE cc_start: 0.8664 (OUTLIER) cc_final: 0.7426 (m-80) REVERT: F 48 PHE cc_start: 0.8284 (OUTLIER) cc_final: 0.6145 (p90) REVERT: C 25 ASP cc_start: 0.7687 (p0) cc_final: 0.7195 (p0) REVERT: C 48 PHE cc_start: 0.8223 (OUTLIER) cc_final: 0.7229 (m-80) REVERT: A 19 ARG cc_start: 0.6097 (mmp-170) cc_final: 0.4665 (mmp-170) outliers start: 14 outliers final: 9 residues processed: 93 average time/residue: 0.1184 time to fit residues: 14.2045 Evaluate side-chains 92 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 0.172 ------------------------------------------------------------------------------- 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 31 SER Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain A residue 73 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 5 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 6 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.3843 r_free = 0.3843 target = 0.116264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.110659 restraints weight = 18466.281| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 1.89 r_work: 0.3687 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3588 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.8302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3708 Z= 0.200 Angle : 0.640 5.201 5034 Z= 0.351 Chirality : 0.046 0.123 576 Planarity : 0.004 0.029 654 Dihedral : 6.273 18.375 522 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 3.85 % Allowed : 19.74 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.36 (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 ARG 0.002 0.000 ARG A 90 TYR 0.021 0.003 TYR F 85 PHE 0.008 0.001 PHE B 99 TRP 0.010 0.002 TRP D 34 HIS 0.002 0.001 HIS F 96 Details of bonding type rmsd covalent geometry : bond 0.00448 ( 3702) covalent geometry : angle 0.63777 ( 5022) SS BOND : bond 0.01012 ( 6) SS BOND : angle 1.32639 ( 12) hydrogen bonds : bond 0.02082 ( 170) hydrogen bonds : angle 4.91501 ( 510) *********************** 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 92 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 77 time to evaluate : 0.238 Fit side-chains REVERT: D 30 TYR cc_start: 0.8934 (m-10) cc_final: 0.8518 (m-10) REVERT: E 31 SER cc_start: 0.9281 (t) cc_final: 0.8983 (p) REVERT: E 48 PHE cc_start: 0.8668 (OUTLIER) cc_final: 0.7546 (m-80) REVERT: F 48 PHE cc_start: 0.8324 (OUTLIER) cc_final: 0.6050 (p90) REVERT: C 25 ASP cc_start: 0.7742 (p0) cc_final: 0.7222 (p0) REVERT: C 30 TYR cc_start: 0.9020 (m-10) cc_final: 0.8792 (m-10) REVERT: C 48 PHE cc_start: 0.8214 (OUTLIER) cc_final: 0.7256 (m-80) REVERT: B 68 ASN cc_start: 0.6383 (OUTLIER) cc_final: 0.5859 (m-40) REVERT: A 19 ARG cc_start: 0.5865 (mmp-170) cc_final: 0.4253 (mmp-170) REVERT: A 48 PHE cc_start: 0.8078 (OUTLIER) cc_final: 0.6606 (m-80) outliers start: 15 outliers final: 9 residues processed: 86 average time/residue: 0.0971 time to fit residues: 11.1116 Evaluate side-chains 87 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 73 time to evaluate : 0.179 ------------------------------------------------------------------------------- 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 31 SER Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain A residue 48 PHE Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 89 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 46 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 chunk 14 optimal weight: 0.7980 chunk 0 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3849 r_free = 0.3849 target = 0.116351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.110765 restraints weight = 18401.172| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 1.88 r_work: 0.3695 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3596 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.8423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3708 Z= 0.192 Angle : 0.632 5.211 5034 Z= 0.345 Chirality : 0.046 0.126 576 Planarity : 0.004 0.029 654 Dihedral : 6.218 18.279 522 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 3.85 % Allowed : 20.26 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.34 (0.29), residues: 462 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.54 (0.22), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 28 TYR 0.020 0.002 TYR F 85 PHE 0.007 0.001 PHE B 99 TRP 0.008 0.002 TRP E 34 HIS 0.002 0.001 HIS B 96 Details of bonding type rmsd covalent geometry : bond 0.00433 ( 3702) covalent geometry : angle 0.63004 ( 5022) SS BOND : bond 0.00952 ( 6) SS BOND : angle 1.23651 ( 12) hydrogen bonds : bond 0.02079 ( 170) hydrogen bonds : angle 4.87519 ( 510) *********************** 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: 15 poor density : 77 time to evaluate : 0.158 Fit side-chains REVERT: D 30 TYR cc_start: 0.8943 (m-10) cc_final: 0.8570 (m-10) REVERT: E 48 PHE cc_start: 0.8662 (OUTLIER) cc_final: 0.7590 (m-80) REVERT: F 48 PHE cc_start: 0.8314 (OUTLIER) cc_final: 0.6021 (p90) REVERT: C 25 ASP cc_start: 0.7759 (p0) cc_final: 0.7256 (p0) REVERT: C 48 PHE cc_start: 0.8193 (OUTLIER) cc_final: 0.7218 (m-80) REVERT: A 19 ARG cc_start: 0.5713 (mmp-170) cc_final: 0.4095 (mmp80) REVERT: A 48 PHE cc_start: 0.8099 (OUTLIER) cc_final: 0.6573 (m-80) outliers start: 15 outliers final: 10 residues processed: 86 average time/residue: 0.1209 time to fit residues: 13.4968 Evaluate side-chains 88 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 74 time to evaluate : 0.237 ------------------------------------------------------------------------------- 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 F residue 89 SER 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 31 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 18 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 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 = 0.3875 r_free = 0.3875 target = 0.117869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.112244 restraints weight = 18619.433| |-----------------------------------------------------------------------------| r_work (start): 0.3781 rms_B_bonded: 1.87 r_work: 0.3707 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3610 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.8537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3708 Z= 0.193 Angle : 0.633 5.316 5034 Z= 0.345 Chirality : 0.046 0.120 576 Planarity : 0.004 0.028 654 Dihedral : 6.216 17.927 522 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 4.36 % Allowed : 20.26 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.002 0.000 ARG A 90 TYR 0.026 0.003 TYR C 30 PHE 0.007 0.001 PHE B 99 TRP 0.009 0.002 TRP A 34 HIS 0.002 0.001 HIS B 96 Details of bonding type rmsd covalent geometry : bond 0.00435 ( 3702) covalent geometry : angle 0.63020 ( 5022) SS BOND : bond 0.00980 ( 6) SS BOND : angle 1.29233 ( 12) hydrogen bonds : bond 0.02159 ( 170) hydrogen bonds : angle 4.84454 ( 510) *********************** 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: 17 poor density : 76 time to evaluate : 0.205 Fit side-chains REVERT: D 30 TYR cc_start: 0.8948 (m-10) cc_final: 0.8544 (m-10) REVERT: E 48 PHE cc_start: 0.8694 (OUTLIER) cc_final: 0.7726 (m-80) REVERT: F 30 TYR cc_start: 0.8487 (m-80) cc_final: 0.8227 (m-80) REVERT: F 48 PHE cc_start: 0.8347 (OUTLIER) cc_final: 0.6024 (p90) REVERT: C 25 ASP cc_start: 0.7832 (p0) cc_final: 0.7339 (p0) REVERT: C 30 TYR cc_start: 0.8992 (m-10) cc_final: 0.8723 (m-80) REVERT: C 34 TRP cc_start: 0.8846 (OUTLIER) cc_final: 0.8097 (t60) REVERT: C 48 PHE cc_start: 0.8197 (OUTLIER) cc_final: 0.7287 (m-80) REVERT: A 19 ARG cc_start: 0.5751 (mmp-170) cc_final: 0.4133 (mmp80) REVERT: A 48 PHE cc_start: 0.8125 (OUTLIER) cc_final: 0.6489 (m-80) outliers start: 17 outliers final: 11 residues processed: 87 average time/residue: 0.1269 time to fit residues: 14.1992 Evaluate side-chains 91 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 75 time to evaluate : 0.211 ------------------------------------------------------------------------------- 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 F residue 89 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 31 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 26 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 43 optimal weight: 0.0980 overall best weight: 0.6582 ------------------------------------------------------------------------------- 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 = 0.3892 r_free = 0.3892 target = 0.118997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.113463 restraints weight = 18366.327| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 1.85 r_work: 0.3724 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3626 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.8611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3708 Z= 0.161 Angle : 0.602 4.943 5034 Z= 0.329 Chirality : 0.046 0.121 576 Planarity : 0.003 0.028 654 Dihedral : 6.112 17.980 522 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.87 % Favored : 91.13 % Rotamer: Outliers : 4.10 % Allowed : 20.00 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.27 (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 ARG 0.004 0.000 ARG B 28 TYR 0.022 0.002 TYR C 30 PHE 0.006 0.001 PHE B 99 TRP 0.008 0.002 TRP D 34 HIS 0.002 0.001 HIS B 96 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 3702) covalent geometry : angle 0.60096 ( 5022) SS BOND : bond 0.00819 ( 6) SS BOND : angle 1.06573 ( 12) hydrogen bonds : bond 0.01997 ( 170) hydrogen bonds : angle 4.78727 ( 510) *********************** 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 96 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 0.253 Fit side-chains revert: symmetry clash REVERT: E 48 PHE cc_start: 0.8667 (OUTLIER) cc_final: 0.7762 (m-80) REVERT: F 30 TYR cc_start: 0.8460 (m-80) cc_final: 0.8241 (m-80) REVERT: F 48 PHE cc_start: 0.8331 (OUTLIER) cc_final: 0.5983 (p90) REVERT: C 25 ASP cc_start: 0.7808 (p0) cc_final: 0.7315 (p0) REVERT: C 30 TYR cc_start: 0.8970 (m-10) cc_final: 0.8576 (m-80) REVERT: C 34 TRP cc_start: 0.8850 (OUTLIER) cc_final: 0.7991 (t60) REVERT: C 48 PHE cc_start: 0.8189 (OUTLIER) cc_final: 0.7562 (m-80) REVERT: A 19 ARG cc_start: 0.5707 (mmp-170) cc_final: 0.4110 (mmp80) REVERT: A 34 TRP cc_start: 0.6105 (t60) cc_final: 0.5827 (t60) REVERT: A 48 PHE cc_start: 0.8089 (OUTLIER) cc_final: 0.6405 (m-80) outliers start: 16 outliers final: 11 residues processed: 89 average time/residue: 0.1226 time to fit residues: 14.0909 Evaluate side-chains 94 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 78 time to evaluate : 0.193 ------------------------------------------------------------------------------- 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 F residue 89 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 49 ARG Chi-restraints excluded: chain B residue 89 SER 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 40 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 0 optimal weight: 0.9990 chunk 39 optimal weight: 0.5980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3873 r_free = 0.3873 target = 0.117550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.111979 restraints weight = 18387.832| |-----------------------------------------------------------------------------| r_work (start): 0.3778 rms_B_bonded: 1.85 r_work: 0.3706 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3608 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.8692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3708 Z= 0.197 Angle : 0.633 5.369 5034 Z= 0.345 Chirality : 0.046 0.131 576 Planarity : 0.003 0.026 654 Dihedral : 6.166 17.328 522 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.44 % Favored : 91.56 % Rotamer: Outliers : 4.10 % Allowed : 20.26 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.30 (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 ARG 0.004 0.000 ARG B 28 TYR 0.021 0.002 TYR C 30 PHE 0.007 0.001 PHE B 99 TRP 0.012 0.002 TRP D 34 HIS 0.002 0.001 HIS B 96 Details of bonding type rmsd covalent geometry : bond 0.00446 ( 3702) covalent geometry : angle 0.63103 ( 5022) SS BOND : bond 0.00988 ( 6) SS BOND : angle 1.29436 ( 12) hydrogen bonds : bond 0.02095 ( 170) hydrogen bonds : angle 4.83299 ( 510) ********************** 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 92 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 76 time to evaluate : 0.188 Fit side-chains revert: symmetry clash REVERT: E 48 PHE cc_start: 0.8677 (OUTLIER) cc_final: 0.7834 (m-80) REVERT: F 30 TYR cc_start: 0.8472 (m-80) cc_final: 0.8205 (m-80) REVERT: F 48 PHE cc_start: 0.8347 (OUTLIER) cc_final: 0.6019 (p90) REVERT: C 25 ASP cc_start: 0.7842 (p0) cc_final: 0.7367 (p0) REVERT: C 30 TYR cc_start: 0.9021 (m-10) cc_final: 0.8568 (m-80) REVERT: C 34 TRP cc_start: 0.8859 (OUTLIER) cc_final: 0.7833 (t60) REVERT: C 48 PHE cc_start: 0.8229 (OUTLIER) cc_final: 0.7763 (m-80) REVERT: A 19 ARG cc_start: 0.5729 (mmp-170) cc_final: 0.4130 (mmp80) REVERT: A 34 TRP cc_start: 0.6137 (t60) cc_final: 0.5784 (t60) REVERT: A 48 PHE cc_start: 0.8200 (OUTLIER) cc_final: 0.7508 (m-80) outliers start: 16 outliers final: 11 residues processed: 85 average time/residue: 0.1097 time to fit residues: 12.0853 Evaluate side-chains 92 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 76 time to evaluate : 0.215 ------------------------------------------------------------------------------- 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 F residue 89 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 49 ARG Chi-restraints excluded: chain B residue 89 SER 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: 0.9990 chunk 1 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 22 optimal weight: 0.3980 chunk 41 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3896 r_free = 0.3896 target = 0.118924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.113358 restraints weight = 18108.624| |-----------------------------------------------------------------------------| r_work (start): 0.3810 rms_B_bonded: 1.83 r_work: 0.3741 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3647 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.8737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3708 Z= 0.142 Angle : 0.595 4.782 5034 Z= 0.324 Chirality : 0.046 0.122 576 Planarity : 0.003 0.024 654 Dihedral : 6.042 18.110 522 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.87 % Favored : 91.13 % Rotamer: Outliers : 3.33 % Allowed : 21.28 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.003 0.000 ARG B 28 TYR 0.018 0.002 TYR C 30 PHE 0.005 0.001 PHE B 99 TRP 0.009 0.002 TRP D 34 HIS 0.003 0.001 HIS B 96 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 3702) covalent geometry : angle 0.59342 ( 5022) SS BOND : bond 0.00743 ( 6) SS BOND : angle 0.98791 ( 12) hydrogen bonds : bond 0.01952 ( 170) hydrogen bonds : angle 4.74822 ( 510) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2250.11 seconds wall clock time: 38 minutes 54.31 seconds (2334.31 seconds total)