Starting phenix.real_space_refine on Sun Jun 8 18:37:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qk6_18457/06_2025/8qk6_18457_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qk6_18457/06_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_18457/06_2025/8qk6_18457.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qk6_18457/06_2025/8qk6_18457.map" model { file = "/net/cci-nas-00/data/ceres_data/8qk6_18457/06_2025/8qk6_18457_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qk6_18457/06_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-5710/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: 7.12, per 1000 atoms: 0.71 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: 2.98 Conformation dependent library (CDL) restraints added in 1.3 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: 0.84 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: 3.03 Time building geometry restraints manager: 3.48 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: 3.460 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: 0.460 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 27.440 Find NCS groups from input model: 0.220 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:3.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.310 ------------------------------------------------------------------------------- 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 : 1.142 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 0 residues processed: 215 average time/residue: 0.2185 time to fit residues: 66.1627 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 : 1.107 ------------------------------------------------------------------------------- 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 = 26)----------------| | r_work = 0.2673 r_free = 0.2673 target = 0.049485 restraints weight = 26981.268| |-----------------------------------------------------------------------------| r_work (start): 0.2652 rms_B_bonded: 2.67 r_work: 0.2510 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8960 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 : 1.199 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 142 ARG cc_start: 0.8825 (ttt-90) cc_final: 0.8605 (ttt-90) REVERT: A 220 ARG cc_start: 0.8811 (tpp80) cc_final: 0.8556 (tpm170) REVERT: B 124 LYS cc_start: 0.8483 (ptpp) cc_final: 0.7892 (ptpp) REVERT: D 71 ILE cc_start: 0.9249 (mt) cc_final: 0.8996 (mp) REVERT: D 124 LYS cc_start: 0.8489 (ptpp) cc_final: 0.7900 (ptpp) REVERT: D 157 TYR cc_start: 0.9065 (m-80) cc_final: 0.8862 (m-80) REVERT: E 103 LYS cc_start: 0.9092 (tmmt) cc_final: 0.8892 (tmmt) REVERT: F 220 ARG cc_start: 0.8862 (tpp80) cc_final: 0.8642 (tpm170) outliers start: 26 outliers final: 6 residues processed: 220 average time/residue: 0.3208 time to fit residues: 91.6565 Evaluate side-chains 192 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 186 time to evaluate : 1.259 ------------------------------------------------------------------------------- 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: 2.9990 chunk 49 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 63 optimal weight: 3.9990 chunk 80 optimal weight: 6.9990 chunk 78 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 = 0.2998 r_free = 0.2998 target = 0.062539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.049735 restraints weight = 27437.869| |-----------------------------------------------------------------------------| r_work (start): 0.2665 rms_B_bonded: 2.67 r_work: 0.2519 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8958 moved from start: 0.1691 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= 0.159 Angle : 0.490 5.025 14166 Z= 0.257 Chirality : 0.039 0.122 1680 Planarity : 0.003 0.034 1656 Dihedral : 3.331 11.893 1728 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % 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: 3.85 (0.24), residues: 1206 helix: 3.75 (0.15), residues: 924 sheet: -2.34 (0.65), residues: 60 loop : -1.70 (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 0.008 0.001 PHE F 190 TYR 0.015 0.001 TYR F 211 ARG 0.004 0.000 ARG C 142 Details of bonding type rmsd hydrogen bonds : bond 0.03670 ( 780) hydrogen bonds : angle 3.02217 ( 2322) SS BOND : bond 0.00352 ( 18) SS BOND : angle 0.60776 ( 36) covalent geometry : bond 0.00374 (10344) covalent geometry : angle 0.48968 (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 216 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 208 time to evaluate : 1.284 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 LYS cc_start: 0.8495 (ptpp) cc_final: 0.7908 (ptpp) REVERT: A 220 ARG cc_start: 0.8774 (tpp80) cc_final: 0.8571 (tpm170) REVERT: D 71 ILE cc_start: 0.9259 (mt) cc_final: 0.8948 (mp) REVERT: E 103 LYS cc_start: 0.9100 (tmmt) cc_final: 0.8869 (tmmt) REVERT: E 142 ARG cc_start: 0.8846 (ttt-90) cc_final: 0.8624 (ttt-90) outliers start: 8 outliers final: 8 residues processed: 212 average time/residue: 0.3662 time to fit residues: 98.0998 Evaluate side-chains 205 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 197 time to evaluate : 1.488 ------------------------------------------------------------------------------- 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: 1.9990 chunk 46 optimal weight: 0.9990 chunk 55 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 84 optimal weight: 10.0000 chunk 13 optimal weight: 0.9980 chunk 45 optimal weight: 6.9990 chunk 68 optimal weight: 0.9980 chunk 35 optimal weight: 4.9990 chunk 58 optimal weight: 6.9990 chunk 34 optimal weight: 6.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- 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 = 0.3018 r_free = 0.3018 target = 0.063290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.050598 restraints weight = 27050.873| |-----------------------------------------------------------------------------| r_work (start): 0.2685 rms_B_bonded: 2.62 r_work: 0.2544 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8962 moved from start: 0.2084 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= 0.147 Angle : 0.479 5.210 14166 Z= 0.251 Chirality : 0.039 0.129 1680 Planarity : 0.003 0.037 1656 Dihedral : 3.303 11.856 1728 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.28 % Allowed : 10.84 % 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: 3.81 (0.24), residues: 1206 helix: 3.76 (0.15), residues: 924 sheet: -2.46 (0.63), residues: 60 loop : -1.90 (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 0.007 0.001 PHE C 31 TYR 0.016 0.001 TYR E 211 ARG 0.008 0.001 ARG A 142 Details of bonding type rmsd hydrogen bonds : bond 0.03487 ( 780) hydrogen bonds : angle 3.01355 ( 2322) SS BOND : bond 0.00339 ( 18) SS BOND : angle 0.50749 ( 36) covalent geometry : bond 0.00343 (10344) covalent geometry : angle 0.47888 (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 211 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 197 time to evaluate : 1.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 ARG cc_start: 0.8765 (tpp80) cc_final: 0.8553 (tpm170) REVERT: B 124 LYS cc_start: 0.8511 (ptpp) cc_final: 0.7941 (ptpp) REVERT: C 124 LYS cc_start: 0.8435 (ptpp) cc_final: 0.8050 (ptpp) REVERT: D 15 ARG cc_start: 0.8848 (ptm-80) cc_final: 0.8143 (ptm-80) REVERT: D 124 LYS cc_start: 0.8472 (ptpp) cc_final: 0.7880 (ptpp) REVERT: D 200 ILE cc_start: 0.9656 (OUTLIER) cc_final: 0.9424 (mp) REVERT: E 103 LYS cc_start: 0.9105 (tmmt) cc_final: 0.8890 (tmmt) REVERT: E 124 LYS cc_start: 0.8438 (ptpp) cc_final: 0.8073 (ptpp) REVERT: E 142 ARG cc_start: 0.8861 (ttt-90) cc_final: 0.8599 (ttt-90) REVERT: F 124 LYS cc_start: 0.8411 (ptpp) cc_final: 0.8029 (ptpp) outliers start: 14 outliers final: 9 residues processed: 206 average time/residue: 0.3441 time to fit residues: 90.5079 Evaluate side-chains 204 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 194 time to evaluate : 1.196 ------------------------------------------------------------------------------- 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 200 ILE 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 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: 0.9990 chunk 1 optimal weight: 6.9990 chunk 65 optimal weight: 6.9990 chunk 87 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 chunk 56 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 48 optimal weight: 0.4980 chunk 28 optimal weight: 7.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.063973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.051459 restraints weight = 27094.272| |-----------------------------------------------------------------------------| r_work (start): 0.2713 rms_B_bonded: 2.56 r_work: 0.2570 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8951 moved from start: 0.2214 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= 0.116 Angle : 0.462 5.716 14166 Z= 0.244 Chirality : 0.038 0.122 1680 Planarity : 0.003 0.039 1656 Dihedral : 3.215 11.358 1728 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.09 % Allowed : 11.38 % 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: 3.87 (0.24), residues: 1206 helix: 3.81 (0.15), residues: 924 sheet: -2.54 (0.61), residues: 60 loop : -1.88 (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 A 73 PHE 0.008 0.001 PHE C 31 TYR 0.016 0.001 TYR D 211 ARG 0.010 0.001 ARG A 142 Details of bonding type rmsd hydrogen bonds : bond 0.03301 ( 780) hydrogen bonds : angle 2.93849 ( 2322) SS BOND : bond 0.00298 ( 18) SS BOND : angle 0.44174 ( 36) covalent geometry : bond 0.00264 (10344) covalent geometry : angle 0.46245 (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 226 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 203 time to evaluate : 1.436 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 LYS cc_start: 0.8399 (ptpp) cc_final: 0.8056 (ptpp) REVERT: A 220 ARG cc_start: 0.8766 (tpp80) cc_final: 0.8547 (tpm170) REVERT: D 15 ARG cc_start: 0.8864 (ptm-80) cc_final: 0.8129 (ptm-80) REVERT: D 178 ASP cc_start: 0.8783 (p0) cc_final: 0.8574 (p0) REVERT: D 200 ILE cc_start: 0.9654 (OUTLIER) cc_final: 0.9405 (mp) REVERT: E 103 LYS cc_start: 0.9091 (tmmt) cc_final: 0.8881 (tmmt) outliers start: 23 outliers final: 9 residues processed: 221 average time/residue: 0.3131 time to fit residues: 88.5356 Evaluate side-chains 205 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 195 time to evaluate : 1.080 ------------------------------------------------------------------------------- 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 66 ASP Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain D residue 200 ILE 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 63 optimal weight: 1.9990 chunk 90 optimal weight: 9.9990 chunk 53 optimal weight: 2.9990 chunk 25 optimal weight: 9.9990 chunk 29 optimal weight: 5.9990 chunk 34 optimal weight: 0.0970 chunk 16 optimal weight: 0.6980 chunk 71 optimal weight: 4.9990 chunk 37 optimal weight: 6.9990 chunk 116 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 overall best weight: 2.1584 ------------------------------------------------------------------------------- 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 = 0.3012 r_free = 0.3012 target = 0.063106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.050435 restraints weight = 27268.547| |-----------------------------------------------------------------------------| r_work (start): 0.2684 rms_B_bonded: 2.64 r_work: 0.2539 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8972 moved from start: 0.2337 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= 0.165 Angle : 0.505 6.432 14166 Z= 0.259 Chirality : 0.039 0.125 1680 Planarity : 0.004 0.039 1656 Dihedral : 3.225 12.141 1728 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.09 % Allowed : 11.75 % Favored : 86.16 % 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: 3.79 (0.15), residues: 924 sheet: -2.76 (0.57), residues: 60 loop : -1.83 (0.44), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 44 HIS 0.002 0.000 HIS F 73 PHE 0.008 0.001 PHE D 51 TYR 0.014 0.001 TYR E 211 ARG 0.010 0.001 ARG E 142 Details of bonding type rmsd hydrogen bonds : bond 0.03352 ( 780) hydrogen bonds : angle 2.94244 ( 2322) SS BOND : bond 0.00373 ( 18) SS BOND : angle 0.50473 ( 36) covalent geometry : bond 0.00388 (10344) covalent geometry : angle 0.50481 (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 232 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 209 time to evaluate : 1.350 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 220 ARG cc_start: 0.8779 (tpp80) cc_final: 0.8550 (tpm170) REVERT: B 124 LYS cc_start: 0.8458 (ptpp) cc_final: 0.8057 (ptpp) REVERT: B 142 ARG cc_start: 0.8909 (ttt-90) cc_final: 0.8695 (ttt-90) REVERT: C 124 LYS cc_start: 0.8429 (ptpp) cc_final: 0.8064 (ptpp) REVERT: D 15 ARG cc_start: 0.8901 (ptm-80) cc_final: 0.8159 (ptm-80) REVERT: D 124 LYS cc_start: 0.8465 (ptpp) cc_final: 0.8049 (ptpp) REVERT: D 178 ASP cc_start: 0.8754 (p0) cc_final: 0.8530 (p0) REVERT: D 200 ILE cc_start: 0.9656 (OUTLIER) cc_final: 0.9412 (mp) REVERT: E 103 LYS cc_start: 0.9131 (tmmt) cc_final: 0.8927 (tmmt) REVERT: E 124 LYS cc_start: 0.8386 (ptpp) cc_final: 0.8013 (ptpp) REVERT: F 124 LYS cc_start: 0.8396 (ptpp) cc_final: 0.8031 (ptpp) outliers start: 23 outliers final: 16 residues processed: 223 average time/residue: 0.3730 time to fit residues: 103.6190 Evaluate side-chains 216 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 199 time to evaluate : 1.268 ------------------------------------------------------------------------------- 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 66 ASP 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 200 ILE 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: 1.9990 chunk 46 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 112 optimal weight: 0.8980 chunk 33 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.064031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.051526 restraints weight = 27362.960| |-----------------------------------------------------------------------------| r_work (start): 0.2712 rms_B_bonded: 2.64 r_work: 0.2570 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8947 moved from start: 0.2543 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= 0.118 Angle : 0.496 7.156 14166 Z= 0.254 Chirality : 0.038 0.115 1680 Planarity : 0.004 0.037 1656 Dihedral : 3.174 11.653 1728 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.46 % Allowed : 12.48 % 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: 3.76 (0.24), residues: 1206 helix: 3.74 (0.15), residues: 924 sheet: -2.80 (0.56), residues: 60 loop : -1.87 (0.44), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 44 HIS 0.003 0.000 HIS B 16 PHE 0.008 0.001 PHE F 31 TYR 0.015 0.001 TYR A 211 ARG 0.009 0.001 ARG E 142 Details of bonding type rmsd hydrogen bonds : bond 0.03227 ( 780) hydrogen bonds : angle 2.95112 ( 2322) SS BOND : bond 0.00308 ( 18) SS BOND : angle 0.42592 ( 36) covalent geometry : bond 0.00272 (10344) covalent geometry : angle 0.49603 (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 227 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 211 time to evaluate : 1.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 ARG cc_start: 0.8753 (tpp80) cc_final: 0.8526 (tpm170) REVERT: B 124 LYS cc_start: 0.8469 (ptpp) cc_final: 0.8043 (ptpp) REVERT: C 124 LYS cc_start: 0.8389 (ptpp) cc_final: 0.8026 (ptpp) REVERT: D 15 ARG cc_start: 0.8907 (ptm-80) cc_final: 0.8159 (ptm-80) REVERT: D 124 LYS cc_start: 0.8463 (ptpp) cc_final: 0.8036 (ptpp) REVERT: D 178 ASP cc_start: 0.8650 (p0) cc_final: 0.8374 (p0) REVERT: D 200 ILE cc_start: 0.9648 (OUTLIER) cc_final: 0.9400 (mp) REVERT: E 103 LYS cc_start: 0.9133 (tmmt) cc_final: 0.8923 (tmmt) REVERT: E 124 LYS cc_start: 0.8389 (ptpp) cc_final: 0.8017 (ptpp) REVERT: F 124 LYS cc_start: 0.8380 (ptpp) cc_final: 0.8013 (ptpp) outliers start: 16 outliers final: 10 residues processed: 222 average time/residue: 0.3360 time to fit residues: 93.9637 Evaluate side-chains 213 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 202 time to evaluate : 1.223 ------------------------------------------------------------------------------- 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 66 ASP Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain D residue 200 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 76 optimal weight: 0.8980 chunk 37 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 86 optimal weight: 0.0870 chunk 50 optimal weight: 9.9990 chunk 16 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 overall best weight: 0.9762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 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 = 0.3037 r_free = 0.3037 target = 0.064215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.051869 restraints weight = 27414.120| |-----------------------------------------------------------------------------| r_work (start): 0.2719 rms_B_bonded: 2.63 r_work: 0.2578 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8942 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10362 Z= 0.113 Angle : 0.508 8.429 14166 Z= 0.257 Chirality : 0.038 0.118 1680 Planarity : 0.004 0.043 1656 Dihedral : 3.154 11.983 1728 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.37 % Allowed : 13.11 % 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: 3.79 (0.24), residues: 1206 helix: 3.75 (0.15), residues: 924 sheet: -2.82 (0.55), residues: 60 loop : -1.80 (0.44), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 44 HIS 0.001 0.000 HIS D 73 PHE 0.007 0.001 PHE B 31 TYR 0.019 0.001 TYR C 211 ARG 0.010 0.001 ARG E 142 Details of bonding type rmsd hydrogen bonds : bond 0.03147 ( 780) hydrogen bonds : angle 2.90218 ( 2322) SS BOND : bond 0.00303 ( 18) SS BOND : angle 0.40599 ( 36) covalent geometry : bond 0.00261 (10344) covalent geometry : angle 0.50818 (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 224 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 209 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 ARG cc_start: 0.8782 (tpp80) cc_final: 0.8572 (tpm170) REVERT: C 124 LYS cc_start: 0.8370 (ptpp) cc_final: 0.8004 (ptpp) REVERT: D 15 ARG cc_start: 0.8914 (ptm-80) cc_final: 0.8160 (ptm-80) REVERT: D 178 ASP cc_start: 0.8582 (p0) cc_final: 0.8343 (p0) REVERT: D 200 ILE cc_start: 0.9652 (OUTLIER) cc_final: 0.9407 (mp) REVERT: E 103 LYS cc_start: 0.9133 (tmmt) cc_final: 0.8928 (tmmt) REVERT: E 124 LYS cc_start: 0.8390 (ptpp) cc_final: 0.8001 (ptpp) REVERT: F 124 LYS cc_start: 0.8362 (ptpp) cc_final: 0.7991 (ptpp) REVERT: F 150 MET cc_start: 0.9569 (tpp) cc_final: 0.9358 (mmt) outliers start: 15 outliers final: 12 residues processed: 218 average time/residue: 0.3442 time to fit residues: 93.7168 Evaluate side-chains 215 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 202 time to evaluate : 1.165 ------------------------------------------------------------------------------- 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 47 GLU Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain D residue 200 ILE 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 71 ILE 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: 2.9990 chunk 19 optimal weight: 6.9990 chunk 26 optimal weight: 0.8980 chunk 54 optimal weight: 9.9990 chunk 112 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 76 optimal weight: 0.8980 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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 = 0.3025 r_free = 0.3025 target = 0.063758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.051210 restraints weight = 27391.439| |-----------------------------------------------------------------------------| r_work (start): 0.2702 rms_B_bonded: 2.58 r_work: 0.2564 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8965 moved from start: 0.2665 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= 0.135 Angle : 0.528 8.553 14166 Z= 0.267 Chirality : 0.038 0.121 1680 Planarity : 0.004 0.046 1656 Dihedral : 3.186 12.108 1728 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.64 % Allowed : 12.93 % 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: 3.80 (0.25), residues: 1206 helix: 3.74 (0.15), residues: 924 sheet: -2.81 (0.55), residues: 60 loop : -1.72 (0.45), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 44 HIS 0.002 0.000 HIS F 73 PHE 0.007 0.001 PHE F 190 TYR 0.017 0.001 TYR A 211 ARG 0.009 0.001 ARG E 142 Details of bonding type rmsd hydrogen bonds : bond 0.03210 ( 780) hydrogen bonds : angle 2.91333 ( 2322) SS BOND : bond 0.00349 ( 18) SS BOND : angle 0.46062 ( 36) covalent geometry : bond 0.00317 (10344) covalent geometry : angle 0.52825 (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 220 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 202 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 ARG cc_start: 0.8788 (tpp80) cc_final: 0.8553 (tpm170) REVERT: B 124 LYS cc_start: 0.8415 (ptpp) cc_final: 0.7970 (ptpp) REVERT: D 15 ARG cc_start: 0.8936 (ptm-80) cc_final: 0.8184 (ptm-80) REVERT: D 75 ARG cc_start: 0.8685 (mtm-85) cc_final: 0.8442 (mtm-85) REVERT: D 124 LYS cc_start: 0.8417 (ptpp) cc_final: 0.7989 (ptpp) REVERT: D 178 ASP cc_start: 0.8585 (p0) cc_final: 0.8323 (p0) REVERT: D 200 ILE cc_start: 0.9667 (OUTLIER) cc_final: 0.9418 (mp) REVERT: E 171 TYR cc_start: 0.8780 (t80) cc_final: 0.8522 (t80) REVERT: E 208 GLU cc_start: 0.9244 (mm-30) cc_final: 0.8783 (mm-30) REVERT: F 150 MET cc_start: 0.9554 (tpp) cc_final: 0.9352 (mmt) outliers start: 18 outliers final: 15 residues processed: 215 average time/residue: 0.3483 time to fit residues: 94.2685 Evaluate side-chains 218 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 202 time to evaluate : 1.147 ------------------------------------------------------------------------------- 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 66 ASP 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 200 ILE 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 71 ILE 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: 0.9990 chunk 6 optimal weight: 0.8980 chunk 100 optimal weight: 0.9990 chunk 76 optimal weight: 0.8980 chunk 99 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 105 optimal weight: 0.4980 chunk 91 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 107 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN 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 = 0.064441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.052062 restraints weight = 27573.099| |-----------------------------------------------------------------------------| r_work (start): 0.2726 rms_B_bonded: 2.58 r_work: 0.2587 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8950 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10362 Z= 0.113 Angle : 0.532 9.078 14166 Z= 0.268 Chirality : 0.038 0.121 1680 Planarity : 0.004 0.041 1656 Dihedral : 3.175 11.719 1728 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.18 % Allowed : 13.30 % 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: 3.75 (0.25), residues: 1206 helix: 3.70 (0.15), residues: 924 sheet: -2.83 (0.54), residues: 60 loop : -1.70 (0.45), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 44 HIS 0.003 0.000 HIS E 100 PHE 0.007 0.001 PHE F 31 TYR 0.018 0.001 TYR D 211 ARG 0.009 0.001 ARG D 142 Details of bonding type rmsd hydrogen bonds : bond 0.03139 ( 780) hydrogen bonds : angle 2.95328 ( 2322) SS BOND : bond 0.00304 ( 18) SS BOND : angle 0.39950 ( 36) covalent geometry : bond 0.00261 (10344) covalent geometry : angle 0.53195 (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: 13 poor density : 208 time to evaluate : 1.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 ARG cc_start: 0.8763 (tpp80) cc_final: 0.8542 (tpm170) REVERT: B 124 LYS cc_start: 0.8404 (ptpp) cc_final: 0.7967 (ptpp) REVERT: B 200 ILE cc_start: 0.9668 (mp) cc_final: 0.9442 (mp) REVERT: D 15 ARG cc_start: 0.8905 (ptm-80) cc_final: 0.8179 (ptm-80) REVERT: D 124 LYS cc_start: 0.8399 (ptpp) cc_final: 0.7987 (ptpp) REVERT: D 178 ASP cc_start: 0.8524 (p0) cc_final: 0.8258 (p0) REVERT: D 200 ILE cc_start: 0.9668 (OUTLIER) cc_final: 0.9419 (mp) REVERT: E 171 TYR cc_start: 0.8765 (t80) cc_final: 0.8525 (t80) REVERT: E 208 GLU cc_start: 0.9206 (mm-30) cc_final: 0.8762 (mm-30) REVERT: F 150 MET cc_start: 0.9528 (tpp) cc_final: 0.9323 (mmt) outliers start: 13 outliers final: 11 residues processed: 216 average time/residue: 0.3524 time to fit residues: 95.1947 Evaluate side-chains 217 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 205 time to evaluate : 1.128 ------------------------------------------------------------------------------- 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 66 ASP Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 200 ILE 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 71 ILE 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: 0.9980 chunk 114 optimal weight: 0.4980 chunk 102 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 117 optimal weight: 0.7980 chunk 85 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN A 205 ASN ** F 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.064729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.052378 restraints weight = 27783.385| |-----------------------------------------------------------------------------| r_work (start): 0.2732 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: 0.8945 moved from start: 0.2835 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= 0.113 Angle : 0.538 9.219 14166 Z= 0.270 Chirality : 0.038 0.124 1680 Planarity : 0.004 0.042 1656 Dihedral : 3.184 12.809 1728 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.18 % Allowed : 13.48 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.91 (0.25), residues: 1206 helix: 3.83 (0.15), residues: 912 sheet: -2.84 (0.54), residues: 60 loop : -1.40 (0.45), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 44 HIS 0.002 0.000 HIS A 123 PHE 0.007 0.001 PHE C 31 TYR 0.016 0.001 TYR A 211 ARG 0.009 0.001 ARG D 142 Details of bonding type rmsd hydrogen bonds : bond 0.03124 ( 780) hydrogen bonds : angle 2.91736 ( 2322) SS BOND : bond 0.00300 ( 18) SS BOND : angle 0.40610 ( 36) covalent geometry : bond 0.00261 (10344) covalent geometry : angle 0.53787 (14130) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4419.97 seconds wall clock time: 78 minutes 32.96 seconds (4712.96 seconds total)