Starting phenix.real_space_refine on Sat Aug 23 04:57:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qk6_18457/08_2025/8qk6_18457_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qk6_18457/08_2025/8qk6_18457.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8qk6_18457/08_2025/8qk6_18457_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qk6_18457/08_2025/8qk6_18457_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8qk6_18457/08_2025/8qk6_18457.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qk6_18457/08_2025/8qk6_18457.map" } resolution = 3.18 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 90 5.16 5 C 6690 2.51 5 N 1650 2.21 5 O 1626 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 10056 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1648 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 7, 'TRANS': 197} Chain breaks: 1 Chain: "B" Number of atoms: 1648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1648 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 7, 'TRANS': 197} Chain breaks: 1 Chain: "C" Number of atoms: 1648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1648 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 7, 'TRANS': 197} Chain breaks: 1 Chain: "D" Number of atoms: 1648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1648 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 7, 'TRANS': 197} Chain breaks: 1 Chain: "E" Number of atoms: 1648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1648 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 7, 'TRANS': 197} Chain breaks: 1 Chain: "F" Number of atoms: 1648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1648 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 7, 'TRANS': 197} Chain breaks: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.99, per 1000 atoms: 0.20 Number of scatterers: 10056 At special positions: 0 Unit cell: (103.35, 103.35, 93.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 90 16.00 O 1626 8.00 N 1650 7.00 C 6690 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 53 " - pdb=" SG CYS A 179 " distance=2.03 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 173 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 168 " distance=2.03 Simple disulfide: pdb=" SG CYS B 53 " - pdb=" SG CYS B 179 " distance=2.03 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 173 " distance=2.03 Simple disulfide: pdb=" SG CYS B 64 " - pdb=" SG CYS B 168 " distance=2.03 Simple disulfide: pdb=" SG CYS C 53 " - pdb=" SG CYS C 179 " distance=2.03 Simple disulfide: pdb=" SG CYS C 60 " - pdb=" SG CYS C 173 " distance=2.03 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 168 " distance=2.03 Simple disulfide: pdb=" SG CYS D 53 " - pdb=" SG CYS D 179 " distance=2.03 Simple disulfide: pdb=" SG CYS D 60 " - pdb=" SG CYS D 173 " distance=2.03 Simple disulfide: pdb=" SG CYS D 64 " - pdb=" SG CYS D 168 " distance=2.03 Simple disulfide: pdb=" SG CYS E 53 " - pdb=" SG CYS E 179 " distance=2.03 Simple disulfide: pdb=" SG CYS E 60 " - pdb=" SG CYS E 173 " distance=2.03 Simple disulfide: pdb=" SG CYS E 64 " - pdb=" SG CYS E 168 " distance=2.03 Simple disulfide: pdb=" SG CYS F 53 " - pdb=" SG CYS F 179 " distance=2.03 Simple disulfide: pdb=" SG CYS F 60 " - pdb=" SG CYS F 173 " distance=2.03 Simple disulfide: pdb=" SG CYS F 64 " - pdb=" SG CYS F 168 " distance=2.03 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: 0.65 Conformation dependent library (CDL) restraints added in 348.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2364 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 6 sheets defined 79.0% alpha, 2.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 2 through 12 Processing helix chain 'A' and resid 18 through 23 Processing helix chain 'A' and resid 23 through 42 Processing helix chain 'A' and resid 46 through 51 Processing helix chain 'A' and resid 59 through 69 Processing helix chain 'A' and resid 72 through 105 Proline residue: A 87 - end of helix removed outlier: 3.702A pdb=" N MET A 105 " --> pdb=" O ILE A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 157 Processing helix chain 'A' and resid 183 through 221 Processing helix chain 'B' and resid 2 through 12 Processing helix chain 'B' and resid 18 through 23 Processing helix chain 'B' and resid 23 through 42 Processing helix chain 'B' and resid 46 through 51 Processing helix chain 'B' and resid 59 through 69 Processing helix chain 'B' and resid 72 through 105 Proline residue: B 87 - end of helix removed outlier: 3.703A pdb=" N MET B 105 " --> pdb=" O ILE B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 157 Processing helix chain 'B' and resid 183 through 221 Processing helix chain 'C' and resid 2 through 12 Processing helix chain 'C' and resid 18 through 23 Processing helix chain 'C' and resid 23 through 42 Processing helix chain 'C' and resid 46 through 51 Processing helix chain 'C' and resid 59 through 69 Processing helix chain 'C' and resid 72 through 105 Proline residue: C 87 - end of helix removed outlier: 3.702A pdb=" N MET C 105 " --> pdb=" O ILE C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 157 Processing helix chain 'C' and resid 183 through 221 Processing helix chain 'D' and resid 2 through 12 Processing helix chain 'D' and resid 18 through 23 Processing helix chain 'D' and resid 23 through 42 Processing helix chain 'D' and resid 46 through 51 Processing helix chain 'D' and resid 59 through 69 Processing helix chain 'D' and resid 72 through 105 Proline residue: D 87 - end of helix removed outlier: 3.702A pdb=" N MET D 105 " --> pdb=" O ILE D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 157 Processing helix chain 'D' and resid 183 through 221 Processing helix chain 'E' and resid 2 through 12 Processing helix chain 'E' and resid 18 through 23 Processing helix chain 'E' and resid 23 through 42 Processing helix chain 'E' and resid 46 through 51 Processing helix chain 'E' and resid 59 through 69 Processing helix chain 'E' and resid 72 through 105 Proline residue: E 87 - end of helix removed outlier: 3.702A pdb=" N MET E 105 " --> pdb=" O ILE E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 157 Processing helix chain 'E' and resid 183 through 221 Processing helix chain 'F' and resid 2 through 12 Processing helix chain 'F' and resid 18 through 23 Processing helix chain 'F' and resid 23 through 42 Processing helix chain 'F' and resid 46 through 51 Processing helix chain 'F' and resid 59 through 69 Processing helix chain 'F' and resid 72 through 105 Proline residue: F 87 - end of helix removed outlier: 3.702A pdb=" N MET F 105 " --> pdb=" O ILE F 101 " (cutoff:3.500A) Processing helix chain 'F' and resid 123 through 157 Processing helix chain 'F' and resid 183 through 221 Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 53 Processing sheet with id=AA2, first strand: chain 'B' and resid 52 through 53 Processing sheet with id=AA3, first strand: chain 'C' and resid 52 through 53 Processing sheet with id=AA4, first strand: chain 'D' and resid 52 through 53 Processing sheet with id=AA5, first strand: chain 'E' and resid 52 through 53 Processing sheet with id=AA6, first strand: chain 'F' and resid 52 through 53 780 hydrogen bonds defined for protein. 2322 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.64 Time building geometry restraints manager: 0.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2988 1.34 - 1.46: 2455 1.46 - 1.58: 4762 1.58 - 1.69: 7 1.69 - 1.81: 132 Bond restraints: 10344 Sorted by residual: bond pdb=" C6 CLR F 301 " pdb=" C7 CLR F 301 " ideal model delta sigma weight residual 1.492 1.539 -0.047 2.00e-02 2.50e+03 5.60e+00 bond pdb=" C6 CLR B 301 " pdb=" C7 CLR B 301 " ideal model delta sigma weight residual 1.492 1.539 -0.047 2.00e-02 2.50e+03 5.56e+00 bond pdb=" C6 CLR E 301 " pdb=" C7 CLR E 301 " ideal model delta sigma weight residual 1.492 1.539 -0.047 2.00e-02 2.50e+03 5.45e+00 bond pdb=" C6 CLR D 301 " pdb=" C7 CLR D 301 " ideal model delta sigma weight residual 1.492 1.538 -0.046 2.00e-02 2.50e+03 5.39e+00 bond pdb=" C6 CLR A 301 " pdb=" C7 CLR A 301 " ideal model delta sigma weight residual 1.492 1.538 -0.046 2.00e-02 2.50e+03 5.38e+00 ... (remaining 10339 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 13798 1.49 - 2.98: 230 2.98 - 4.46: 58 4.46 - 5.95: 32 5.95 - 7.44: 12 Bond angle restraints: 14130 Sorted by residual: angle pdb=" C22 CLR A 301 " pdb=" C23 CLR A 301 " pdb=" C24 CLR A 301 " ideal model delta sigma weight residual 111.95 104.51 7.44 3.00e+00 1.11e-01 6.15e+00 angle pdb=" C22 CLR F 301 " pdb=" C23 CLR F 301 " pdb=" C24 CLR F 301 " ideal model delta sigma weight residual 111.95 104.51 7.44 3.00e+00 1.11e-01 6.15e+00 angle pdb=" C22 CLR B 301 " pdb=" C23 CLR B 301 " pdb=" C24 CLR B 301 " ideal model delta sigma weight residual 111.95 104.54 7.41 3.00e+00 1.11e-01 6.10e+00 angle pdb=" C22 CLR E 301 " pdb=" C23 CLR E 301 " pdb=" C24 CLR E 301 " ideal model delta sigma weight residual 111.95 104.55 7.40 3.00e+00 1.11e-01 6.09e+00 angle pdb=" C22 CLR C 301 " pdb=" C23 CLR C 301 " pdb=" C24 CLR C 301 " ideal model delta sigma weight residual 111.95 104.55 7.40 3.00e+00 1.11e-01 6.09e+00 ... (remaining 14125 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 9.77: 5580 9.77 - 19.54: 496 19.54 - 29.31: 164 29.31 - 39.08: 66 39.08 - 48.85: 24 Dihedral angle restraints: 6330 sinusoidal: 2694 harmonic: 3636 Sorted by residual: dihedral pdb=" N LEU F 25 " pdb=" CA LEU F 25 " pdb=" CB LEU F 25 " pdb=" CG LEU F 25 " ideal model delta sinusoidal sigma weight residual -60.00 -108.85 48.85 3 1.50e+01 4.44e-03 8.70e+00 dihedral pdb=" N LEU B 25 " pdb=" CA LEU B 25 " pdb=" CB LEU B 25 " pdb=" CG LEU B 25 " ideal model delta sinusoidal sigma weight residual -60.00 -108.84 48.84 3 1.50e+01 4.44e-03 8.69e+00 dihedral pdb=" N LEU D 25 " pdb=" CA LEU D 25 " pdb=" CB LEU D 25 " pdb=" CG LEU D 25 " ideal model delta sinusoidal sigma weight residual -60.00 -108.84 48.84 3 1.50e+01 4.44e-03 8.69e+00 ... (remaining 6327 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 1572 0.080 - 0.159: 84 0.159 - 0.239: 0 0.239 - 0.319: 18 0.319 - 0.398: 6 Chirality restraints: 1680 Sorted by residual: chirality pdb=" C17 CLR D 301 " pdb=" C13 CLR D 301 " pdb=" C16 CLR D 301 " pdb=" C20 CLR D 301 " both_signs ideal model delta sigma weight residual False 2.55 2.95 -0.40 2.00e-01 2.50e+01 3.97e+00 chirality pdb=" C17 CLR A 301 " pdb=" C13 CLR A 301 " pdb=" C16 CLR A 301 " pdb=" C20 CLR A 301 " both_signs ideal model delta sigma weight residual False 2.55 2.95 -0.40 2.00e-01 2.50e+01 3.96e+00 chirality pdb=" C17 CLR E 301 " pdb=" C13 CLR E 301 " pdb=" C16 CLR E 301 " pdb=" C20 CLR E 301 " both_signs ideal model delta sigma weight residual False 2.55 2.95 -0.40 2.00e-01 2.50e+01 3.96e+00 ... (remaining 1677 not shown) Planarity restraints: 1656 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS F 173 " 0.013 5.00e-02 4.00e+02 1.89e-02 5.72e-01 pdb=" N PRO F 174 " -0.033 5.00e-02 4.00e+02 pdb=" CA PRO F 174 " 0.010 5.00e-02 4.00e+02 pdb=" CD PRO F 174 " 0.010 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A 173 " -0.012 5.00e-02 4.00e+02 1.88e-02 5.64e-01 pdb=" N PRO A 174 " 0.032 5.00e-02 4.00e+02 pdb=" CA PRO A 174 " -0.010 5.00e-02 4.00e+02 pdb=" CD PRO A 174 " -0.010 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS D 173 " 0.012 5.00e-02 4.00e+02 1.87e-02 5.60e-01 pdb=" N PRO D 174 " -0.032 5.00e-02 4.00e+02 pdb=" CA PRO D 174 " 0.010 5.00e-02 4.00e+02 pdb=" CD PRO D 174 " 0.010 5.00e-02 4.00e+02 ... (remaining 1653 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 180 2.70 - 3.25: 10786 3.25 - 3.80: 17135 3.80 - 4.35: 19113 4.35 - 4.90: 34085 Nonbonded interactions: 81299 Sorted by model distance: nonbonded pdb=" O ILE B 71 " pdb=" OH TYR B 157 " model vdw 2.154 3.040 nonbonded pdb=" O ILE C 71 " pdb=" OH TYR C 157 " model vdw 2.154 3.040 nonbonded pdb=" O ILE D 71 " pdb=" OH TYR D 157 " model vdw 2.155 3.040 nonbonded pdb=" O ILE F 71 " pdb=" OH TYR F 157 " model vdw 2.155 3.040 nonbonded pdb=" O ILE E 71 " pdb=" OH TYR E 157 " model vdw 2.155 3.040 ... (remaining 81294 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 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' 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: 5.360 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: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 9.100 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 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 : 0.005 0.047 10362 Z= 0.214 Angle : 0.565 7.439 14166 Z= 0.247 Chirality : 0.053 0.398 1680 Planarity : 0.002 0.019 1656 Dihedral : 9.589 48.849 3912 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.09 % Allowed : 4.92 % Favored : 93.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 4.06 (0.25), residues: 1206 helix: 3.92 (0.16), residues: 924 sheet: -3.09 (0.47), residues: 60 loop : -1.43 (0.41), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 75 TYR 0.005 0.001 TYR D 7 PHE 0.007 0.001 PHE B 51 TRP 0.009 0.001 TRP C 44 HIS 0.002 0.001 HIS A 100 Details of bonding type rmsd covalent geometry : bond 0.00472 (10344) covalent geometry : angle 0.56516 (14130) SS BOND : bond 0.00277 ( 18) SS BOND : angle 0.32957 ( 36) hydrogen bonds : bond 0.10126 ( 780) hydrogen bonds : angle 4.09934 ( 2322) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 203 time to evaluate : 0.267 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 0 residues processed: 215 average time/residue: 0.0811 time to fit residues: 24.9750 Evaluate side-chains 176 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 108 optimal weight: 6.9990 chunk 49 optimal weight: 7.9990 chunk 97 optimal weight: 0.9980 chunk 113 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 117 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 ASN D 205 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.062795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.049714 restraints weight = 27206.686| |-----------------------------------------------------------------------------| r_work (start): 0.2661 rms_B_bonded: 2.67 r_work: 0.2520 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8954 moved from start: 0.1181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10362 Z= 0.160 Angle : 0.511 5.060 14166 Z= 0.267 Chirality : 0.039 0.123 1680 Planarity : 0.004 0.049 1656 Dihedral : 3.397 12.461 1728 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.37 % Allowed : 8.56 % Favored : 89.07 % 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: 3.92 (0.24), residues: 1206 helix: 3.78 (0.15), residues: 924 sheet: -2.57 (0.57), residues: 60 loop : -1.51 (0.42), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 22 TYR 0.011 0.001 TYR A 211 PHE 0.008 0.001 PHE C 31 TRP 0.009 0.001 TRP A 44 HIS 0.002 0.001 HIS A 100 Details of bonding type rmsd covalent geometry : bond 0.00375 (10344) covalent geometry : angle 0.51091 (14130) SS BOND : bond 0.00344 ( 18) SS BOND : angle 0.69425 ( 36) hydrogen bonds : bond 0.03929 ( 780) hydrogen bonds : angle 3.17313 ( 2322) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 202 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 ILE cc_start: 0.9279 (mt) cc_final: 0.9019 (mp) REVERT: A 142 ARG cc_start: 0.8806 (ttt-90) cc_final: 0.8597 (ttt-90) REVERT: A 220 ARG cc_start: 0.8809 (tpp80) cc_final: 0.8562 (tpm170) REVERT: B 124 LYS cc_start: 0.8473 (ptpp) cc_final: 0.7902 (ptpp) REVERT: D 71 ILE cc_start: 0.9240 (mt) cc_final: 0.8990 (mp) REVERT: D 124 LYS cc_start: 0.8481 (ptpp) cc_final: 0.7890 (ptpp) REVERT: F 220 ARG cc_start: 0.8854 (tpp80) cc_final: 0.8648 (tpm170) outliers start: 26 outliers final: 4 residues processed: 222 average time/residue: 0.1219 time to fit residues: 35.3347 Evaluate side-chains 192 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 188 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain F residue 13 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 30 optimal weight: 0.9980 chunk 65 optimal weight: 8.9990 chunk 42 optimal weight: 0.6980 chunk 46 optimal weight: 0.9980 chunk 111 optimal weight: 7.9990 chunk 44 optimal weight: 7.9990 chunk 100 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 98 optimal weight: 0.9980 chunk 112 optimal weight: 0.8980 chunk 113 optimal weight: 1.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 205 ASN F 205 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.064165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.051577 restraints weight = 26923.452| |-----------------------------------------------------------------------------| r_work (start): 0.2709 rms_B_bonded: 2.61 r_work: 0.2566 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8927 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10362 Z= 0.115 Angle : 0.463 4.968 14166 Z= 0.244 Chirality : 0.038 0.126 1680 Planarity : 0.003 0.033 1656 Dihedral : 3.257 12.247 1728 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.00 % Allowed : 10.02 % Favored : 88.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 3.90 (0.24), residues: 1206 helix: 3.80 (0.15), residues: 924 sheet: -2.40 (0.64), residues: 60 loop : -1.78 (0.42), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 142 TYR 0.015 0.001 TYR F 211 PHE 0.009 0.001 PHE C 31 TRP 0.009 0.001 TRP A 44 HIS 0.001 0.000 HIS A 100 Details of bonding type rmsd covalent geometry : bond 0.00256 (10344) covalent geometry : angle 0.46231 (14130) SS BOND : bond 0.00287 ( 18) SS BOND : angle 0.55721 ( 36) hydrogen bonds : bond 0.03499 ( 780) hydrogen bonds : angle 2.98688 ( 2322) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 215 time to evaluate : 0.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 ARG cc_start: 0.8748 (ttt-90) cc_final: 0.8536 (ttt-90) REVERT: C 142 ARG cc_start: 0.8726 (ttt-90) cc_final: 0.8484 (ttt-90) REVERT: F 142 ARG cc_start: 0.8715 (ttt-90) cc_final: 0.8478 (ttt-90) outliers start: 11 outliers final: 10 residues processed: 219 average time/residue: 0.1188 time to fit residues: 33.6659 Evaluate side-chains 206 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 196 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain D residue 66 ASP Chi-restraints excluded: chain D residue 201 CYS Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 66 ASP Chi-restraints excluded: chain F residue 201 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 112 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 99 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 98 optimal weight: 0.9980 chunk 78 optimal weight: 0.7980 chunk 38 optimal weight: 7.9990 chunk 27 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 25 optimal weight: 6.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 205 ASN E 205 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.064561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.051850 restraints weight = 26989.386| |-----------------------------------------------------------------------------| r_work (start): 0.2718 rms_B_bonded: 2.58 r_work: 0.2577 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8947 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10362 Z= 0.119 Angle : 0.467 5.449 14166 Z= 0.246 Chirality : 0.038 0.124 1680 Planarity : 0.003 0.032 1656 Dihedral : 3.192 11.197 1728 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.00 % Allowed : 10.75 % Favored : 88.25 % 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: 3.86 (0.24), residues: 1206 helix: 3.80 (0.15), residues: 924 sheet: -2.49 (0.63), residues: 60 loop : -1.89 (0.43), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 142 TYR 0.014 0.001 TYR C 211 PHE 0.007 0.001 PHE A 31 TRP 0.011 0.001 TRP D 44 HIS 0.001 0.000 HIS A 16 Details of bonding type rmsd covalent geometry : bond 0.00264 (10344) covalent geometry : angle 0.46669 (14130) SS BOND : bond 0.00301 ( 18) SS BOND : angle 0.46417 ( 36) hydrogen bonds : bond 0.03320 ( 780) hydrogen bonds : angle 2.97193 ( 2322) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 195 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 LYS cc_start: 0.8436 (ptpp) cc_final: 0.8061 (ptpp) REVERT: B 124 LYS cc_start: 0.8440 (ptpp) cc_final: 0.7888 (ptpp) REVERT: B 200 ILE cc_start: 0.9662 (OUTLIER) cc_final: 0.9436 (mp) REVERT: C 124 LYS cc_start: 0.8389 (ptpp) cc_final: 0.8016 (ptpp) REVERT: D 124 LYS cc_start: 0.8432 (ptpp) cc_final: 0.7877 (ptpp) REVERT: E 124 LYS cc_start: 0.8428 (ptpp) cc_final: 0.8068 (ptpp) REVERT: F 124 LYS cc_start: 0.8371 (ptpp) cc_final: 0.8001 (ptpp) outliers start: 11 outliers final: 4 residues processed: 200 average time/residue: 0.1221 time to fit residues: 31.6272 Evaluate side-chains 192 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 187 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain D residue 201 CYS Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain F residue 13 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 25 optimal weight: 10.0000 chunk 72 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 35 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 1 optimal weight: 8.9990 chunk 36 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.064189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.051302 restraints weight = 27035.902| |-----------------------------------------------------------------------------| r_work (start): 0.2700 rms_B_bonded: 2.65 r_work: 0.2558 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8950 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 10362 Z= 0.139 Angle : 0.480 5.823 14166 Z= 0.252 Chirality : 0.038 0.119 1680 Planarity : 0.003 0.037 1656 Dihedral : 3.156 11.616 1728 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.64 % Allowed : 11.38 % Favored : 86.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 3.89 (0.24), residues: 1206 helix: 3.83 (0.15), residues: 924 sheet: -2.64 (0.60), residues: 60 loop : -1.87 (0.43), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 142 TYR 0.016 0.001 TYR E 211 PHE 0.007 0.001 PHE F 190 TRP 0.013 0.001 TRP B 44 HIS 0.001 0.000 HIS A 16 Details of bonding type rmsd covalent geometry : bond 0.00332 (10344) covalent geometry : angle 0.48028 (14130) SS BOND : bond 0.00341 ( 18) SS BOND : angle 0.50505 ( 36) hydrogen bonds : bond 0.03322 ( 780) hydrogen bonds : angle 2.97319 ( 2322) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 202 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 142 ARG cc_start: 0.8864 (ttt-90) cc_final: 0.8620 (ttt-90) REVERT: B 200 ILE cc_start: 0.9654 (OUTLIER) cc_final: 0.9401 (mp) REVERT: C 200 ILE cc_start: 0.9646 (mp) cc_final: 0.9445 (mp) REVERT: D 142 ARG cc_start: 0.8898 (ttt-90) cc_final: 0.8656 (ttt-90) REVERT: F 200 ILE cc_start: 0.9631 (mp) cc_final: 0.9418 (mp) outliers start: 18 outliers final: 10 residues processed: 214 average time/residue: 0.1448 time to fit residues: 38.8369 Evaluate side-chains 207 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 196 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 201 CYS Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain D residue 201 CYS Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 201 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 72 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 chunk 119 optimal weight: 4.9990 chunk 14 optimal weight: 6.9990 chunk 83 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.064119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.051569 restraints weight = 27131.913| |-----------------------------------------------------------------------------| r_work (start): 0.2709 rms_B_bonded: 2.62 r_work: 0.2568 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8948 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10362 Z= 0.126 Angle : 0.488 6.374 14166 Z= 0.249 Chirality : 0.038 0.118 1680 Planarity : 0.003 0.044 1656 Dihedral : 3.149 11.856 1728 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.46 % Allowed : 11.20 % Favored : 86.34 % 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: 3.85 (0.24), residues: 1206 helix: 3.81 (0.15), residues: 924 sheet: -2.79 (0.57), residues: 60 loop : -1.88 (0.43), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 142 TYR 0.018 0.001 TYR D 211 PHE 0.006 0.001 PHE B 31 TRP 0.013 0.001 TRP B 44 HIS 0.002 0.000 HIS B 73 Details of bonding type rmsd covalent geometry : bond 0.00293 (10344) covalent geometry : angle 0.48806 (14130) SS BOND : bond 0.00328 ( 18) SS BOND : angle 0.45321 ( 36) hydrogen bonds : bond 0.03234 ( 780) hydrogen bonds : angle 2.93594 ( 2322) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 205 time to evaluate : 0.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 LYS cc_start: 0.8383 (ptpp) cc_final: 0.8031 (ptpp) REVERT: B 124 LYS cc_start: 0.8461 (ptpp) cc_final: 0.8058 (ptpp) REVERT: B 142 ARG cc_start: 0.8856 (ttt-90) cc_final: 0.8627 (ttt-90) REVERT: B 200 ILE cc_start: 0.9663 (OUTLIER) cc_final: 0.9420 (mp) REVERT: C 124 LYS cc_start: 0.8390 (ptpp) cc_final: 0.8016 (ptpp) REVERT: D 124 LYS cc_start: 0.8440 (ptpp) cc_final: 0.8038 (ptpp) REVERT: D 142 ARG cc_start: 0.8891 (ttt-90) cc_final: 0.8661 (ttt-90) REVERT: E 124 LYS cc_start: 0.8385 (ptpp) cc_final: 0.8028 (ptpp) REVERT: F 124 LYS cc_start: 0.8386 (ptpp) cc_final: 0.8014 (ptpp) REVERT: F 200 ILE cc_start: 0.9608 (OUTLIER) cc_final: 0.9408 (mp) outliers start: 27 outliers final: 16 residues processed: 227 average time/residue: 0.1311 time to fit residues: 37.7051 Evaluate side-chains 214 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 196 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 201 CYS Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 201 CYS Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 165 LEU Chi-restraints excluded: chain F residue 200 ILE Chi-restraints excluded: chain F residue 201 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 79 optimal weight: 5.9990 chunk 25 optimal weight: 9.9990 chunk 104 optimal weight: 10.0000 chunk 119 optimal weight: 5.9990 chunk 43 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 34 optimal weight: 7.9990 chunk 63 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.062708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2682 r_free = 0.2682 target = 0.049911 restraints weight = 27128.031| |-----------------------------------------------------------------------------| r_work (start): 0.2668 rms_B_bonded: 2.59 r_work: 0.2526 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8991 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 10362 Z= 0.194 Angle : 0.531 6.686 14166 Z= 0.272 Chirality : 0.040 0.119 1680 Planarity : 0.003 0.040 1656 Dihedral : 3.273 13.134 1728 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.19 % Allowed : 11.75 % Favored : 86.07 % 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 (0.25), residues: 1206 helix: 3.73 (0.15), residues: 924 sheet: -2.81 (0.55), residues: 60 loop : -1.84 (0.44), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 142 TYR 0.016 0.001 TYR F 211 PHE 0.009 0.001 PHE B 190 TRP 0.015 0.001 TRP B 44 HIS 0.002 0.001 HIS B 73 Details of bonding type rmsd covalent geometry : bond 0.00457 (10344) covalent geometry : angle 0.53101 (14130) SS BOND : bond 0.00428 ( 18) SS BOND : angle 0.59264 ( 36) hydrogen bonds : bond 0.03516 ( 780) hydrogen bonds : angle 3.05611 ( 2322) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 198 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 LYS cc_start: 0.8423 (ptpp) cc_final: 0.8040 (ptpp) REVERT: B 124 LYS cc_start: 0.8461 (ptpp) cc_final: 0.8017 (ptpp) REVERT: B 142 ARG cc_start: 0.8918 (ttt-90) cc_final: 0.8686 (ttt-90) REVERT: B 200 ILE cc_start: 0.9675 (OUTLIER) cc_final: 0.9428 (mp) REVERT: C 124 LYS cc_start: 0.8409 (ptpp) cc_final: 0.8025 (ptpp) REVERT: D 124 LYS cc_start: 0.8458 (ptpp) cc_final: 0.8008 (ptpp) REVERT: D 142 ARG cc_start: 0.8947 (ttt-90) cc_final: 0.8728 (ttt-90) REVERT: E 124 LYS cc_start: 0.8381 (ptpp) cc_final: 0.8005 (ptpp) REVERT: E 200 ILE cc_start: 0.9674 (OUTLIER) cc_final: 0.9458 (mp) REVERT: F 124 LYS cc_start: 0.8418 (ptpp) cc_final: 0.8038 (ptpp) REVERT: F 200 ILE cc_start: 0.9631 (OUTLIER) cc_final: 0.9428 (mp) outliers start: 24 outliers final: 18 residues processed: 218 average time/residue: 0.1342 time to fit residues: 37.0283 Evaluate side-chains 216 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 195 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 201 CYS Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 201 CYS Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 200 ILE Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 165 LEU Chi-restraints excluded: chain F residue 200 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 103 optimal weight: 0.9980 chunk 51 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 56 optimal weight: 0.7980 chunk 117 optimal weight: 0.7980 chunk 55 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 chunk 116 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 205 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.064519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.051729 restraints weight = 26976.045| |-----------------------------------------------------------------------------| r_work (start): 0.2711 rms_B_bonded: 2.60 r_work: 0.2575 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8934 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10362 Z= 0.112 Angle : 0.505 7.613 14166 Z= 0.257 Chirality : 0.038 0.126 1680 Planarity : 0.003 0.031 1656 Dihedral : 3.185 11.723 1728 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.46 % Allowed : 12.84 % Favored : 85.70 % 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: 3.71 (0.24), residues: 1206 helix: 3.69 (0.15), residues: 924 sheet: -2.85 (0.55), residues: 60 loop : -1.82 (0.44), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 142 TYR 0.015 0.001 TYR C 211 PHE 0.008 0.001 PHE B 31 TRP 0.014 0.001 TRP B 44 HIS 0.001 0.000 HIS B 73 Details of bonding type rmsd covalent geometry : bond 0.00249 (10344) covalent geometry : angle 0.50546 (14130) SS BOND : bond 0.00316 ( 18) SS BOND : angle 0.45493 ( 36) hydrogen bonds : bond 0.03266 ( 780) hydrogen bonds : angle 2.99093 ( 2322) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 205 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 LYS cc_start: 0.8402 (ptpp) cc_final: 0.8026 (ptpp) REVERT: A 200 ILE cc_start: 0.9669 (OUTLIER) cc_final: 0.9464 (mp) REVERT: B 15 ARG cc_start: 0.8950 (ptt-90) cc_final: 0.8574 (ptt90) REVERT: B 124 LYS cc_start: 0.8449 (ptpp) cc_final: 0.8014 (ptpp) REVERT: B 200 ILE cc_start: 0.9654 (OUTLIER) cc_final: 0.9406 (mp) REVERT: C 124 LYS cc_start: 0.8396 (ptpp) cc_final: 0.8035 (ptpp) REVERT: D 15 ARG cc_start: 0.8966 (ptt-90) cc_final: 0.8591 (ptt90) REVERT: D 124 LYS cc_start: 0.8438 (ptpp) cc_final: 0.8002 (ptpp) REVERT: D 142 ARG cc_start: 0.8895 (ttt-90) cc_final: 0.8666 (ttt-90) REVERT: E 124 LYS cc_start: 0.8386 (ptpp) cc_final: 0.8000 (ptpp) REVERT: E 200 ILE cc_start: 0.9649 (OUTLIER) cc_final: 0.9423 (mp) REVERT: F 124 LYS cc_start: 0.8398 (ptpp) cc_final: 0.8031 (ptpp) REVERT: F 200 ILE cc_start: 0.9594 (OUTLIER) cc_final: 0.9386 (mp) outliers start: 16 outliers final: 10 residues processed: 216 average time/residue: 0.1423 time to fit residues: 38.1717 Evaluate side-chains 211 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 197 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 201 CYS Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain D residue 201 CYS Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 200 ILE Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 200 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 67 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 75 optimal weight: 0.0970 chunk 83 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 104 optimal weight: 5.9990 chunk 61 optimal weight: 6.9990 chunk 34 optimal weight: 4.9990 chunk 15 optimal weight: 7.9990 chunk 47 optimal weight: 1.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 205 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.064389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.051578 restraints weight = 27070.535| |-----------------------------------------------------------------------------| r_work (start): 0.2707 rms_B_bonded: 2.66 r_work: 0.2569 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8951 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10362 Z= 0.122 Angle : 0.521 8.857 14166 Z= 0.264 Chirality : 0.038 0.128 1680 Planarity : 0.004 0.038 1656 Dihedral : 3.176 11.698 1728 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.37 % Allowed : 13.84 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 3.73 (0.24), residues: 1206 helix: 3.70 (0.15), residues: 924 sheet: -2.84 (0.54), residues: 60 loop : -1.80 (0.44), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 142 TYR 0.018 0.001 TYR E 211 PHE 0.007 0.001 PHE A 31 TRP 0.013 0.001 TRP D 44 HIS 0.001 0.000 HIS B 73 Details of bonding type rmsd covalent geometry : bond 0.00282 (10344) covalent geometry : angle 0.52135 (14130) SS BOND : bond 0.00342 ( 18) SS BOND : angle 0.45009 ( 36) hydrogen bonds : bond 0.03227 ( 780) hydrogen bonds : angle 2.96451 ( 2322) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 200 time to evaluate : 0.264 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 LYS cc_start: 0.8394 (ptpp) cc_final: 0.8004 (ptpp) REVERT: B 15 ARG cc_start: 0.8979 (ptt-90) cc_final: 0.8590 (ptt90) REVERT: B 200 ILE cc_start: 0.9666 (OUTLIER) cc_final: 0.9423 (mp) REVERT: D 15 ARG cc_start: 0.8973 (ptt-90) cc_final: 0.8589 (ptt90) REVERT: D 142 ARG cc_start: 0.8897 (ttt-90) cc_final: 0.8660 (ttt-90) REVERT: E 124 LYS cc_start: 0.8389 (ptpp) cc_final: 0.7992 (ptpp) REVERT: E 200 ILE cc_start: 0.9658 (OUTLIER) cc_final: 0.9429 (mp) REVERT: F 200 ILE cc_start: 0.9613 (OUTLIER) cc_final: 0.9404 (mp) outliers start: 15 outliers final: 11 residues processed: 210 average time/residue: 0.1292 time to fit residues: 34.2307 Evaluate side-chains 212 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 198 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 201 CYS Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain D residue 201 CYS Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 200 ILE Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 200 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 92 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 117 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 75 optimal weight: 6.9990 chunk 50 optimal weight: 0.3980 chunk 59 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.064752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.052311 restraints weight = 26791.088| |-----------------------------------------------------------------------------| r_work (start): 0.2727 rms_B_bonded: 2.56 r_work: 0.2590 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8940 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 10362 Z= 0.112 Angle : 0.529 9.102 14166 Z= 0.266 Chirality : 0.038 0.126 1680 Planarity : 0.003 0.040 1656 Dihedral : 3.174 11.941 1728 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.28 % Allowed : 14.03 % Favored : 84.70 % 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: 3.69 (0.25), residues: 1206 helix: 3.66 (0.15), residues: 924 sheet: -2.86 (0.54), residues: 60 loop : -1.76 (0.45), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 142 TYR 0.019 0.001 TYR D 211 PHE 0.007 0.001 PHE F 31 TRP 0.014 0.001 TRP D 44 HIS 0.002 0.000 HIS C 73 Details of bonding type rmsd covalent geometry : bond 0.00260 (10344) covalent geometry : angle 0.52887 (14130) SS BOND : bond 0.00308 ( 18) SS BOND : angle 0.41835 ( 36) hydrogen bonds : bond 0.03168 ( 780) hydrogen bonds : angle 3.00290 ( 2322) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 209 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 LYS cc_start: 0.8375 (ptpp) cc_final: 0.7989 (ptpp) REVERT: B 15 ARG cc_start: 0.8940 (ptt-90) cc_final: 0.8698 (ptt90) REVERT: B 124 LYS cc_start: 0.8410 (ptpp) cc_final: 0.8024 (ptpp) REVERT: B 200 ILE cc_start: 0.9677 (OUTLIER) cc_final: 0.9433 (mp) REVERT: D 15 ARG cc_start: 0.8946 (ptt-90) cc_final: 0.8705 (ptt90) REVERT: D 124 LYS cc_start: 0.8410 (ptpp) cc_final: 0.8030 (ptpp) REVERT: D 142 ARG cc_start: 0.8878 (ttt-90) cc_final: 0.8616 (ttt-90) REVERT: E 124 LYS cc_start: 0.8369 (ptpp) cc_final: 0.7972 (ptpp) REVERT: E 171 TYR cc_start: 0.8781 (t80) cc_final: 0.8535 (t80) REVERT: E 200 ILE cc_start: 0.9659 (OUTLIER) cc_final: 0.9438 (mp) REVERT: F 150 MET cc_start: 0.9546 (tpp) cc_final: 0.9320 (mmt) REVERT: F 200 ILE cc_start: 0.9616 (OUTLIER) cc_final: 0.9406 (mp) outliers start: 14 outliers final: 9 residues processed: 218 average time/residue: 0.1331 time to fit residues: 36.4635 Evaluate side-chains 214 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 202 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 201 CYS Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain D residue 201 CYS Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 200 ILE Chi-restraints excluded: chain F residue 200 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 88 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 56 optimal weight: 0.0060 chunk 9 optimal weight: 1.9990 chunk 118 optimal weight: 4.9990 chunk 83 optimal weight: 0.7980 overall best weight: 0.9400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 ASN C 205 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.064790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.052201 restraints weight = 27330.860| |-----------------------------------------------------------------------------| r_work (start): 0.2725 rms_B_bonded: 2.62 r_work: 0.2588 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8949 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10362 Z= 0.114 Angle : 0.531 9.062 14166 Z= 0.267 Chirality : 0.038 0.128 1680 Planarity : 0.004 0.041 1656 Dihedral : 3.184 12.502 1728 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.28 % Allowed : 14.21 % Favored : 84.52 % 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: 3.72 (0.25), residues: 1206 helix: 3.68 (0.15), residues: 924 sheet: -2.85 (0.54), residues: 60 loop : -1.74 (0.45), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 142 TYR 0.017 0.001 TYR B 211 PHE 0.006 0.001 PHE F 31 TRP 0.014 0.001 TRP D 44 HIS 0.002 0.000 HIS B 73 Details of bonding type rmsd covalent geometry : bond 0.00265 (10344) covalent geometry : angle 0.53087 (14130) SS BOND : bond 0.00319 ( 18) SS BOND : angle 0.42526 ( 36) hydrogen bonds : bond 0.03158 ( 780) hydrogen bonds : angle 2.98323 ( 2322) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1712.38 seconds wall clock time: 30 minutes 12.54 seconds (1812.54 seconds total)