Starting phenix.real_space_refine on Tue May 13 07:18:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qk6_18457/05_2025/8qk6_18457_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qk6_18457/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8qk6_18457/05_2025/8qk6_18457.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qk6_18457/05_2025/8qk6_18457.map" model { file = "/net/cci-nas-00/data/ceres_data/8qk6_18457/05_2025/8qk6_18457_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qk6_18457/05_2025/8qk6_18457_neut.cif" } resolution = 3.18 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 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-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 6.16, per 1000 atoms: 0.61 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: 2.55 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.95 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: 2.79 Time building geometry restraints manager: 2.99 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 24.170 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.050 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:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.340 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.06 (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 TRP 0.009 0.001 TRP C 44 HIS 0.002 0.001 HIS A 100 PHE 0.007 0.001 PHE B 51 TYR 0.005 0.001 TYR D 7 ARG 0.004 0.001 ARG D 75 Details of bonding type rmsd hydrogen bonds : bond 0.10126 ( 780) hydrogen bonds : angle 4.09934 ( 2322) SS BOND : bond 0.00277 ( 18) SS BOND : angle 0.32957 ( 36) covalent geometry : bond 0.00472 (10344) covalent geometry : angle 0.56516 (14130) *********************** 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 : 1.101 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 0 residues processed: 215 average time/residue: 0.2144 time to fit residues: 64.9971 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 : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 4.9990 chunk 90 optimal weight: 0.6980 chunk 50 optimal weight: 9.9990 chunk 31 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 94 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 chunk 57 optimal weight: 5.9990 chunk 70 optimal weight: 10.0000 chunk 108 optimal weight: 6.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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 = 0.2997 r_free = 0.2997 target = 0.062578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2673 r_free = 0.2673 target = 0.049490 restraints weight = 26981.265| |-----------------------------------------------------------------------------| r_work (start): 0.2653 rms_B_bonded: 2.67 r_work: 0.2508 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8961 moved from start: 0.1164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10362 Z= 0.175 Angle : 0.517 5.079 14166 Z= 0.270 Chirality : 0.039 0.124 1680 Planarity : 0.004 0.048 1656 Dihedral : 3.430 12.392 1728 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.37 % Allowed : 8.74 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.90 (0.24), residues: 1206 helix: 3.76 (0.15), residues: 924 sheet: -2.55 (0.58), residues: 60 loop : -1.51 (0.42), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 44 HIS 0.003 0.001 HIS E 100 PHE 0.008 0.001 PHE C 31 TYR 0.010 0.001 TYR A 211 ARG 0.003 0.000 ARG A 22 Details of bonding type rmsd hydrogen bonds : bond 0.04010 ( 780) hydrogen bonds : angle 3.20787 ( 2322) SS BOND : bond 0.00365 ( 18) SS BOND : angle 0.70930 ( 36) covalent geometry : bond 0.00415 (10344) covalent geometry : angle 0.51663 (14130) *********************** 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 226 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 200 time to evaluate : 1.152 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 142 ARG cc_start: 0.8828 (ttt-90) cc_final: 0.8608 (ttt-90) REVERT: A 220 ARG cc_start: 0.8820 (tpp80) cc_final: 0.8559 (tpm170) REVERT: B 124 LYS cc_start: 0.8487 (ptpp) cc_final: 0.7897 (ptpp) REVERT: C 220 ARG cc_start: 0.8851 (tpp80) cc_final: 0.8647 (tpm170) REVERT: D 71 ILE cc_start: 0.9248 (mt) cc_final: 0.8994 (mp) REVERT: D 124 LYS cc_start: 0.8494 (ptpp) cc_final: 0.7907 (ptpp) REVERT: D 157 TYR cc_start: 0.9064 (m-80) cc_final: 0.8860 (m-80) REVERT: F 220 ARG cc_start: 0.8866 (tpp80) cc_final: 0.8643 (tpm170) outliers start: 26 outliers final: 6 residues processed: 220 average time/residue: 0.2883 time to fit residues: 82.0890 Evaluate side-chains 193 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 187 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 66 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 7.9990 chunk 73 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 63 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 chunk 78 optimal weight: 0.9980 chunk 68 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- 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 = 0.3004 r_free = 0.3004 target = 0.062775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.050060 restraints weight = 27415.730| |-----------------------------------------------------------------------------| r_work (start): 0.2674 rms_B_bonded: 2.68 r_work: 0.2527 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8962 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 10362 Z= 0.150 Angle : 0.484 5.017 14166 Z= 0.254 Chirality : 0.038 0.122 1680 Planarity : 0.003 0.034 1656 Dihedral : 3.309 11.727 1728 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.73 % Allowed : 10.47 % Favored : 88.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.87 (0.24), residues: 1206 helix: 3.76 (0.15), residues: 924 sheet: -2.35 (0.65), residues: 60 loop : -1.69 (0.42), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 44 HIS 0.001 0.000 HIS A 16 PHE 0.009 0.001 PHE F 31 TYR 0.015 0.001 TYR F 211 ARG 0.004 0.000 ARG C 142 Details of bonding type rmsd hydrogen bonds : bond 0.03636 ( 780) hydrogen bonds : angle 3.01443 ( 2322) SS BOND : bond 0.00337 ( 18) SS BOND : angle 0.58947 ( 36) covalent geometry : bond 0.00351 (10344) covalent geometry : angle 0.48327 (14130) *********************** 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 219 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 211 time to evaluate : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 LYS cc_start: 0.8478 (ptpp) cc_final: 0.7887 (ptpp) REVERT: A 142 ARG cc_start: 0.8814 (ttt-90) cc_final: 0.8596 (ttt-90) REVERT: A 220 ARG cc_start: 0.8775 (tpp80) cc_final: 0.8574 (tpm170) REVERT: D 71 ILE cc_start: 0.9256 (mt) cc_final: 0.8932 (mp) REVERT: D 157 TYR cc_start: 0.9018 (m-80) cc_final: 0.8817 (m-80) REVERT: E 142 ARG cc_start: 0.8837 (ttt-90) cc_final: 0.8635 (ttt-90) REVERT: F 157 TYR cc_start: 0.8994 (m-80) cc_final: 0.8789 (m-80) outliers start: 8 outliers final: 8 residues processed: 215 average time/residue: 0.3407 time to fit residues: 92.5652 Evaluate side-chains 206 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 198 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL 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 D residue 66 ASP Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 66 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 53 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 84 optimal weight: 10.0000 chunk 13 optimal weight: 2.9990 chunk 45 optimal weight: 6.9990 chunk 68 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 58 optimal weight: 6.9990 chunk 34 optimal weight: 0.4980 overall best weight: 2.0988 ------------------------------------------------------------------------------- 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 = 0.3009 r_free = 0.3009 target = 0.062987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.050460 restraints weight = 27181.002| |-----------------------------------------------------------------------------| r_work (start): 0.2681 rms_B_bonded: 2.65 r_work: 0.2534 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8967 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10362 Z= 0.163 Angle : 0.488 5.394 14166 Z= 0.255 Chirality : 0.039 0.124 1680 Planarity : 0.003 0.028 1656 Dihedral : 3.300 12.169 1728 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.18 % Allowed : 10.93 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.75 (0.24), residues: 1206 helix: 3.71 (0.15), residues: 924 sheet: -2.48 (0.62), residues: 60 loop : -1.87 (0.42), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 44 HIS 0.001 0.000 HIS A 16 PHE 0.008 0.001 PHE A 51 TYR 0.014 0.001 TYR C 211 ARG 0.006 0.001 ARG D 142 Details of bonding type rmsd hydrogen bonds : bond 0.03544 ( 780) hydrogen bonds : angle 3.04286 ( 2322) SS BOND : bond 0.00366 ( 18) SS BOND : angle 0.53152 ( 36) covalent geometry : bond 0.00384 (10344) covalent geometry : angle 0.48822 (14130) *********************** 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 216 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 203 time to evaluate : 1.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 ARG cc_start: 0.8834 (ttt-90) cc_final: 0.8512 (ttt-90) REVERT: A 220 ARG cc_start: 0.8776 (tpp80) cc_final: 0.8561 (tpm170) REVERT: C 124 LYS cc_start: 0.8444 (ptpp) cc_final: 0.8057 (ptpp) REVERT: D 15 ARG cc_start: 0.8873 (ptm-80) cc_final: 0.8133 (ptm-80) REVERT: D 71 ILE cc_start: 0.9253 (mt) cc_final: 0.8910 (mp) REVERT: D 124 LYS cc_start: 0.8475 (ptpp) cc_final: 0.7880 (ptpp) REVERT: E 124 LYS cc_start: 0.8449 (ptpp) cc_final: 0.8073 (ptpp) REVERT: E 142 ARG cc_start: 0.8876 (ttt-90) cc_final: 0.8619 (ttt-90) REVERT: F 124 LYS cc_start: 0.8377 (ptpp) cc_final: 0.8005 (ptpp) REVERT: F 157 TYR cc_start: 0.9009 (m-80) cc_final: 0.8790 (m-80) outliers start: 13 outliers final: 9 residues processed: 210 average time/residue: 0.3432 time to fit residues: 90.4425 Evaluate side-chains 208 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 199 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 31 optimal weight: 0.9980 chunk 1 optimal weight: 6.9990 chunk 65 optimal weight: 0.0970 chunk 87 optimal weight: 4.9990 chunk 81 optimal weight: 8.9990 chunk 80 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 48 optimal weight: 0.4980 chunk 28 optimal weight: 6.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- 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 = 0.3041 r_free = 0.3041 target = 0.064331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.051887 restraints weight = 26989.745| |-----------------------------------------------------------------------------| r_work (start): 0.2721 rms_B_bonded: 2.58 r_work: 0.2579 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8944 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10362 Z= 0.106 Angle : 0.454 5.631 14166 Z= 0.240 Chirality : 0.038 0.133 1680 Planarity : 0.003 0.029 1656 Dihedral : 3.207 11.432 1728 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.91 % Allowed : 11.84 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.80 (0.24), residues: 1206 helix: 3.77 (0.15), residues: 924 sheet: -2.51 (0.62), residues: 60 loop : -1.97 (0.43), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 44 HIS 0.002 0.000 HIS B 16 PHE 0.008 0.001 PHE C 31 TYR 0.016 0.001 TYR D 211 ARG 0.007 0.001 ARG D 142 Details of bonding type rmsd hydrogen bonds : bond 0.03276 ( 780) hydrogen bonds : angle 2.93213 ( 2322) SS BOND : bond 0.00282 ( 18) SS BOND : angle 0.42946 ( 36) covalent geometry : bond 0.00233 (10344) covalent geometry : angle 0.45431 (14130) *********************** 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 233 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 212 time to evaluate : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 LYS cc_start: 0.8415 (ptpp) cc_final: 0.8053 (ptpp) REVERT: A 142 ARG cc_start: 0.8811 (ttt-90) cc_final: 0.8506 (ttt-90) REVERT: B 124 LYS cc_start: 0.8436 (ptpp) cc_final: 0.8024 (ptpp) REVERT: D 15 ARG cc_start: 0.8872 (ptm-80) cc_final: 0.8135 (ptm-80) outliers start: 21 outliers final: 9 residues processed: 229 average time/residue: 0.3233 time to fit residues: 93.2007 Evaluate side-chains 208 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 199 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain B residue 201 CYS Chi-restraints excluded: chain C residue 13 VAL 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 E residue 83 LEU 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 63 optimal weight: 3.9990 chunk 90 optimal weight: 0.3980 chunk 53 optimal weight: 2.9990 chunk 25 optimal weight: 9.9990 chunk 29 optimal weight: 5.9990 chunk 34 optimal weight: 9.9990 chunk 16 optimal weight: 0.0570 chunk 71 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 overall best weight: 1.8904 ------------------------------------------------------------------------------- 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 = 0.3016 r_free = 0.3016 target = 0.063300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.050644 restraints weight = 27135.928| |-----------------------------------------------------------------------------| r_work (start): 0.2688 rms_B_bonded: 2.64 r_work: 0.2546 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8965 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 10362 Z= 0.151 Angle : 0.499 6.242 14166 Z= 0.257 Chirality : 0.039 0.122 1680 Planarity : 0.003 0.044 1656 Dihedral : 3.209 11.851 1728 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.09 % Allowed : 11.84 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.83 (0.25), residues: 1206 helix: 3.80 (0.15), residues: 924 sheet: -2.72 (0.58), residues: 60 loop : -1.94 (0.44), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 44 HIS 0.002 0.000 HIS B 73 PHE 0.007 0.001 PHE F 51 TYR 0.016 0.001 TYR B 211 ARG 0.010 0.001 ARG E 142 Details of bonding type rmsd hydrogen bonds : bond 0.03324 ( 780) hydrogen bonds : angle 2.90545 ( 2322) SS BOND : bond 0.00352 ( 18) SS BOND : angle 0.47758 ( 36) covalent geometry : bond 0.00354 (10344) covalent geometry : angle 0.49908 (14130) *********************** 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 229 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 206 time to evaluate : 1.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 ARG cc_start: 0.8887 (ttt-90) cc_final: 0.8680 (ttt-90) REVERT: C 124 LYS cc_start: 0.8424 (ptpp) cc_final: 0.8047 (ptpp) REVERT: D 15 ARG cc_start: 0.8894 (ptm-80) cc_final: 0.8154 (ptm-80) REVERT: D 124 LYS cc_start: 0.8464 (ptpp) cc_final: 0.8051 (ptpp) REVERT: E 124 LYS cc_start: 0.8383 (ptpp) cc_final: 0.8017 (ptpp) REVERT: F 124 LYS cc_start: 0.8372 (ptpp) cc_final: 0.7996 (ptpp) outliers start: 23 outliers final: 15 residues processed: 223 average time/residue: 0.3606 time to fit residues: 101.5846 Evaluate side-chains 211 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 196 time to evaluate : 1.144 ------------------------------------------------------------------------------- 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 165 LEU Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 42 SER 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 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 201 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 98 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 83 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 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 = 0.3040 r_free = 0.3040 target = 0.064322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.051769 restraints weight = 27318.523| |-----------------------------------------------------------------------------| r_work (start): 0.2717 rms_B_bonded: 2.67 r_work: 0.2576 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8941 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10362 Z= 0.115 Angle : 0.507 6.855 14166 Z= 0.260 Chirality : 0.038 0.123 1680 Planarity : 0.004 0.042 1656 Dihedral : 3.183 11.233 1728 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.28 % Allowed : 12.20 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.69 (0.24), residues: 1206 helix: 3.70 (0.15), residues: 924 sheet: -2.81 (0.56), residues: 60 loop : -1.95 (0.43), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 44 HIS 0.001 0.000 HIS F 73 PHE 0.008 0.001 PHE B 31 TYR 0.016 0.001 TYR E 211 ARG 0.009 0.001 ARG E 142 Details of bonding type rmsd hydrogen bonds : bond 0.03229 ( 780) hydrogen bonds : angle 2.99262 ( 2322) SS BOND : bond 0.00295 ( 18) SS BOND : angle 0.44682 ( 36) covalent geometry : bond 0.00262 (10344) covalent geometry : angle 0.50728 (14130) *********************** 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 220 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 206 time to evaluate : 1.129 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 142 ARG cc_start: 0.8815 (ttt-90) cc_final: 0.8539 (ttt-90) REVERT: C 124 LYS cc_start: 0.8384 (ptpp) cc_final: 0.8009 (ptpp) REVERT: D 15 ARG cc_start: 0.8892 (ptm-80) cc_final: 0.8146 (ptm-80) REVERT: D 124 LYS cc_start: 0.8460 (ptpp) cc_final: 0.8031 (ptpp) REVERT: E 124 LYS cc_start: 0.8371 (ptpp) cc_final: 0.8000 (ptpp) REVERT: F 124 LYS cc_start: 0.8373 (ptpp) cc_final: 0.7995 (ptpp) outliers start: 14 outliers final: 9 residues processed: 215 average time/residue: 0.3366 time to fit residues: 91.1451 Evaluate side-chains 210 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 201 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain B residue 201 CYS Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain D residue 201 CYS Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 201 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 76 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 86 optimal weight: 0.4980 chunk 50 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 chunk 44 optimal weight: 0.0270 chunk 97 optimal weight: 0.7980 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 ASN B 205 ASN D 205 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.064973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.052482 restraints weight = 27291.942| |-----------------------------------------------------------------------------| r_work (start): 0.2736 rms_B_bonded: 2.62 r_work: 0.2597 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8937 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10362 Z= 0.109 Angle : 0.510 7.910 14166 Z= 0.260 Chirality : 0.038 0.126 1680 Planarity : 0.004 0.049 1656 Dihedral : 3.175 11.768 1728 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.18 % Allowed : 12.93 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.72 (0.25), residues: 1206 helix: 3.71 (0.15), residues: 924 sheet: -2.82 (0.55), residues: 60 loop : -1.89 (0.44), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 44 HIS 0.001 0.000 HIS D 73 PHE 0.007 0.001 PHE A 31 TYR 0.019 0.001 TYR C 211 ARG 0.011 0.001 ARG E 142 Details of bonding type rmsd hydrogen bonds : bond 0.03100 ( 780) hydrogen bonds : angle 2.92304 ( 2322) SS BOND : bond 0.00282 ( 18) SS BOND : angle 0.41116 ( 36) covalent geometry : bond 0.00247 (10344) covalent geometry : angle 0.51032 (14130) *********************** 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 223 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 210 time to evaluate : 1.078 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 142 ARG cc_start: 0.8833 (ttt-90) cc_final: 0.8535 (ttt-90) REVERT: B 124 LYS cc_start: 0.8396 (ptpp) cc_final: 0.8180 (ptpp) REVERT: B 200 ILE cc_start: 0.9655 (mp) cc_final: 0.9414 (mp) REVERT: C 124 LYS cc_start: 0.8354 (ptpp) cc_final: 0.7987 (ptpp) REVERT: D 15 ARG cc_start: 0.8891 (ptm-80) cc_final: 0.8151 (ptm-80) REVERT: D 124 LYS cc_start: 0.8448 (ptpp) cc_final: 0.8011 (ptpp) REVERT: D 200 ILE cc_start: 0.9646 (mp) cc_final: 0.9404 (mp) REVERT: E 124 LYS cc_start: 0.8362 (ptpp) cc_final: 0.7975 (ptpp) REVERT: F 124 LYS cc_start: 0.8353 (ptpp) cc_final: 0.7982 (ptpp) REVERT: F 150 MET cc_start: 0.9542 (tpp) cc_final: 0.9337 (mmt) outliers start: 13 outliers final: 11 residues processed: 219 average time/residue: 0.3249 time to fit residues: 89.4205 Evaluate side-chains 214 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 203 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain B residue 201 CYS Chi-restraints excluded: chain C residue 13 VAL 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 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 201 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 10 optimal weight: 8.9990 chunk 75 optimal weight: 4.9990 chunk 19 optimal weight: 6.9990 chunk 26 optimal weight: 0.9990 chunk 54 optimal weight: 9.9990 chunk 112 optimal weight: 5.9990 chunk 43 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 2 optimal weight: 0.0170 chunk 40 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 overall best weight: 1.7624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.063613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.051117 restraints weight = 27316.327| |-----------------------------------------------------------------------------| r_work (start): 0.2702 rms_B_bonded: 2.57 r_work: 0.2563 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8967 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10362 Z= 0.147 Angle : 0.532 8.509 14166 Z= 0.269 Chirality : 0.039 0.123 1680 Planarity : 0.004 0.047 1656 Dihedral : 3.198 12.289 1728 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.28 % Allowed : 13.21 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.74 (0.25), residues: 1206 helix: 3.71 (0.15), residues: 924 sheet: -2.80 (0.55), residues: 60 loop : -1.82 (0.45), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 44 HIS 0.002 0.000 HIS C 73 PHE 0.008 0.001 PHE F 190 TYR 0.017 0.001 TYR A 211 ARG 0.009 0.001 ARG B 142 Details of bonding type rmsd hydrogen bonds : bond 0.03272 ( 780) hydrogen bonds : angle 2.96845 ( 2322) SS BOND : bond 0.00372 ( 18) SS BOND : angle 0.51649 ( 36) covalent geometry : bond 0.00345 (10344) covalent geometry : angle 0.53182 (14130) *********************** 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 218 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 204 time to evaluate : 1.113 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 142 ARG cc_start: 0.8869 (ttt-90) cc_final: 0.8483 (ttt-90) REVERT: A 146 GLU cc_start: 0.8847 (mm-30) cc_final: 0.8589 (mm-30) REVERT: B 15 ARG cc_start: 0.8957 (ptt-90) cc_final: 0.8746 (ptt90) REVERT: B 124 LYS cc_start: 0.8408 (ptpp) cc_final: 0.8116 (ptpp) REVERT: B 200 ILE cc_start: 0.9663 (mp) cc_final: 0.9431 (mp) REVERT: D 15 ARG cc_start: 0.8911 (ptm-80) cc_final: 0.8167 (ptm-80) REVERT: D 200 ILE cc_start: 0.9649 (mp) cc_final: 0.9413 (mp) REVERT: F 150 MET cc_start: 0.9561 (tpp) cc_final: 0.9360 (mmt) outliers start: 14 outliers final: 13 residues processed: 214 average time/residue: 0.3284 time to fit residues: 88.1154 Evaluate side-chains 214 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 201 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 201 CYS Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 201 CYS 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 201 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 73 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 100 optimal weight: 8.9990 chunk 76 optimal weight: 0.5980 chunk 99 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 105 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.064463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.052024 restraints weight = 27495.422| |-----------------------------------------------------------------------------| r_work (start): 0.2725 rms_B_bonded: 2.59 r_work: 0.2588 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8941 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10362 Z= 0.111 Angle : 0.522 8.952 14166 Z= 0.263 Chirality : 0.038 0.127 1680 Planarity : 0.004 0.040 1656 Dihedral : 3.176 11.663 1728 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.37 % Allowed : 13.02 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.74 (0.25), residues: 1206 helix: 3.71 (0.15), residues: 924 sheet: -2.82 (0.55), residues: 60 loop : -1.80 (0.45), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 44 HIS 0.001 0.000 HIS C 73 PHE 0.007 0.001 PHE C 31 TYR 0.016 0.001 TYR B 211 ARG 0.010 0.001 ARG E 142 Details of bonding type rmsd hydrogen bonds : bond 0.03157 ( 780) hydrogen bonds : angle 2.94643 ( 2322) SS BOND : bond 0.00309 ( 18) SS BOND : angle 0.41023 ( 36) covalent geometry : bond 0.00253 (10344) covalent geometry : angle 0.52205 (14130) ********************** 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 221 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 206 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 142 ARG cc_start: 0.8820 (ttt-90) cc_final: 0.8521 (ttt-90) REVERT: B 124 LYS cc_start: 0.8378 (ptpp) cc_final: 0.8092 (ptpp) REVERT: B 200 ILE cc_start: 0.9657 (mp) cc_final: 0.9432 (mp) REVERT: D 15 ARG cc_start: 0.8893 (ptm-80) cc_final: 0.8172 (ptm-80) REVERT: D 124 LYS cc_start: 0.8389 (ptpp) cc_final: 0.8031 (ptpp) REVERT: D 200 ILE cc_start: 0.9648 (mp) cc_final: 0.9421 (mp) REVERT: E 171 TYR cc_start: 0.8775 (t80) cc_final: 0.8533 (t80) REVERT: F 150 MET cc_start: 0.9568 (tpp) cc_final: 0.9360 (mmt) outliers start: 15 outliers final: 13 residues processed: 217 average time/residue: 0.3492 time to fit residues: 95.5071 Evaluate side-chains 216 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 203 time to evaluate : 1.201 ------------------------------------------------------------------------------- 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 165 LEU Chi-restraints excluded: chain B residue 201 CYS Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 201 CYS Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 201 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 46 optimal weight: 2.9990 chunk 114 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 chunk 45 optimal weight: 0.3980 chunk 117 optimal weight: 3.9990 chunk 85 optimal weight: 8.9990 chunk 31 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.064395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.051812 restraints weight = 27507.264| |-----------------------------------------------------------------------------| r_work (start): 0.2706 rms_B_bonded: 2.60 r_work: 0.2572 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8959 moved from start: 0.2786 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= 0.140 Angle : 0.541 9.290 14166 Z= 0.272 Chirality : 0.039 0.128 1680 Planarity : 0.004 0.043 1656 Dihedral : 3.227 12.195 1728 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.55 % Allowed : 13.02 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.78 (0.25), residues: 1206 helix: 3.78 (0.15), residues: 918 sheet: -2.82 (0.54), residues: 60 loop : -1.85 (0.44), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 44 HIS 0.002 0.000 HIS B 73 PHE 0.008 0.001 PHE F 190 TYR 0.017 0.001 TYR D 211 ARG 0.009 0.001 ARG B 142 Details of bonding type rmsd hydrogen bonds : bond 0.03278 ( 780) hydrogen bonds : angle 2.95139 ( 2322) SS BOND : bond 0.00348 ( 18) SS BOND : angle 0.47338 ( 36) covalent geometry : bond 0.00330 (10344) covalent geometry : angle 0.54119 (14130) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4182.14 seconds wall clock time: 73 minutes 48.01 seconds (4428.01 seconds total)