Starting phenix.real_space_refine on Fri Nov 15 23:15:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qk6_18457/11_2024/8qk6_18457_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qk6_18457/11_2024/8qk6_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qk6_18457/11_2024/8qk6_18457.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qk6_18457/11_2024/8qk6_18457.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qk6_18457/11_2024/8qk6_18457_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qk6_18457/11_2024/8qk6_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-5513/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: 6.92, per 1000 atoms: 0.69 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: 2.94 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: 0.94 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: 3.28 Time building geometry restraints manager: 3.31 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.760 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: 0.020 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 25.870 Find NCS groups from input model: 0.380 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: 34.760 ------------------------------------------------------------------------------- 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 10344 Z= 0.305 Angle : 0.565 7.439 14130 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 *********************** 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 : 1.114 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 0 residues processed: 215 average time/residue: 0.2195 time to fit residues: 66.7776 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 : 1.142 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 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 10344 Z= 0.273 Angle : 0.517 5.079 14130 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 *********************** 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 : 1.221 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 6 residues processed: 220 average time/residue: 0.2933 time to fit residues: 83.8362 Evaluate side-chains 188 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 182 time to evaluate : 1.250 ------------------------------------------------------------------------------- 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 60 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 90 optimal weight: 0.8980 chunk 74 optimal weight: 5.9990 chunk 30 optimal weight: 0.7980 chunk 109 optimal weight: 3.9990 chunk 117 optimal weight: 4.9990 chunk 97 optimal weight: 4.9990 chunk 108 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 87 optimal weight: 0.8980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10344 Z= 0.213 Angle : 0.487 4.996 14130 Z= 0.257 Chirality : 0.038 0.124 1680 Planarity : 0.003 0.039 1656 Dihedral : 3.320 11.844 1728 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.91 % Allowed : 10.47 % Favored : 88.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.86 (0.24), residues: 1206 helix: 3.76 (0.15), residues: 924 sheet: -2.36 (0.64), residues: 60 loop : -1.71 (0.42), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 44 HIS 0.002 0.000 HIS A 100 PHE 0.008 0.001 PHE F 190 TYR 0.014 0.001 TYR F 211 ARG 0.008 0.001 ARG A 142 *********************** 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 225 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 215 time to evaluate : 1.236 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 8 residues processed: 219 average time/residue: 0.3613 time to fit residues: 99.0290 Evaluate side-chains 210 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 202 time to evaluate : 1.279 ------------------------------------------------------------------------------- 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 107 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 12 optimal weight: 0.4980 chunk 52 optimal weight: 0.3980 chunk 73 optimal weight: 4.9990 chunk 109 optimal weight: 0.9990 chunk 115 optimal weight: 5.9990 chunk 57 optimal weight: 0.9980 chunk 103 optimal weight: 0.9980 chunk 31 optimal weight: 7.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 205 ASN C 205 ASN E 205 ASN F 205 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10344 Z= 0.161 Angle : 0.463 5.265 14130 Z= 0.245 Chirality : 0.038 0.128 1680 Planarity : 0.003 0.035 1656 Dihedral : 3.256 11.461 1728 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.37 % Allowed : 11.02 % Favored : 87.61 % 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: 3.85 (0.24), residues: 1206 helix: 3.79 (0.15), residues: 924 sheet: -2.40 (0.64), residues: 60 loop : -1.91 (0.42), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 44 HIS 0.002 0.000 HIS B 123 PHE 0.008 0.001 PHE A 31 TYR 0.014 0.001 TYR C 211 ARG 0.010 0.001 ARG A 142 *********************** 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 223 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 208 time to evaluate : 1.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 54 ASN cc_start: 0.7246 (p0) cc_final: 0.7018 (p0) outliers start: 15 outliers final: 6 residues processed: 214 average time/residue: 0.3414 time to fit residues: 92.3269 Evaluate side-chains 201 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 195 time to evaluate : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain D residue 201 CYS Chi-restraints excluded: chain F residue 13 VAL 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 96 optimal weight: 1.9990 chunk 65 optimal weight: 8.9990 chunk 1 optimal weight: 8.9990 chunk 86 optimal weight: 2.9990 chunk 47 optimal weight: 6.9990 chunk 98 optimal weight: 0.9990 chunk 80 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 59 optimal weight: 4.9990 chunk 104 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 10344 Z= 0.320 Angle : 0.527 5.850 14130 Z= 0.273 Chirality : 0.040 0.129 1680 Planarity : 0.004 0.043 1656 Dihedral : 3.373 12.436 1728 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.55 % Allowed : 11.48 % Favored : 85.97 % 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: 3.74 (0.15), residues: 924 sheet: -2.61 (0.60), residues: 60 loop : -1.96 (0.43), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 44 HIS 0.003 0.001 HIS E 123 PHE 0.009 0.001 PHE C 51 TYR 0.016 0.002 TYR E 211 ARG 0.010 0.001 ARG E 142 *********************** 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 222 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 194 time to evaluate : 1.132 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 54 ASN cc_start: 0.7304 (p0) cc_final: 0.7080 (p0) outliers start: 28 outliers final: 11 residues processed: 210 average time/residue: 0.3500 time to fit residues: 92.3679 Evaluate side-chains 205 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 194 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 201 CYS Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain D residue 201 CYS Chi-restraints excluded: chain E residue 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 39 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 68 optimal weight: 0.6980 chunk 28 optimal weight: 6.9990 chunk 116 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 60 optimal weight: 4.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10344 Z= 0.177 Angle : 0.482 6.214 14130 Z= 0.249 Chirality : 0.038 0.116 1680 Planarity : 0.003 0.033 1656 Dihedral : 3.259 11.400 1728 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.00 % Allowed : 12.57 % 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: 3.76 (0.25), residues: 1206 helix: 3.75 (0.15), residues: 924 sheet: -2.72 (0.59), residues: 60 loop : -1.98 (0.43), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 44 HIS 0.001 0.000 HIS B 73 PHE 0.008 0.001 PHE F 31 TYR 0.016 0.001 TYR C 211 ARG 0.007 0.001 ARG E 75 *********************** 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 233 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 211 time to evaluate : 1.171 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 LYS cc_start: 0.4821 (OUTLIER) cc_final: 0.4512 (ptpp) outliers start: 22 outliers final: 11 residues processed: 221 average time/residue: 0.3549 time to fit residues: 97.9996 Evaluate side-chains 206 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 194 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 201 CYS Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain D residue 201 CYS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 111 optimal weight: 7.9990 chunk 13 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 84 optimal weight: 9.9990 chunk 65 optimal weight: 6.9990 chunk 97 optimal weight: 3.9990 chunk 64 optimal weight: 7.9990 chunk 115 optimal weight: 8.9990 chunk 72 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10344 Z= 0.247 Angle : 0.522 6.960 14130 Z= 0.270 Chirality : 0.039 0.117 1680 Planarity : 0.004 0.042 1656 Dihedral : 3.328 12.647 1728 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.55 % Allowed : 12.39 % Favored : 85.06 % 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: 3.68 (0.25), residues: 1206 helix: 3.68 (0.15), residues: 924 sheet: -2.76 (0.57), residues: 60 loop : -1.92 (0.44), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 44 HIS 0.002 0.001 HIS E 123 PHE 0.008 0.001 PHE D 190 TYR 0.016 0.001 TYR B 211 ARG 0.010 0.001 ARG E 142 *********************** 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 224 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 196 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 20 residues processed: 216 average time/residue: 0.3489 time to fit residues: 94.6334 Evaluate side-chains 214 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 194 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain B residue 71 ILE 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 71 ILE Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 201 CYS Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 71 optimal weight: 7.9990 chunk 46 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 90 optimal weight: 8.9990 chunk 105 optimal weight: 5.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 205 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10344 Z= 0.234 Angle : 0.533 8.112 14130 Z= 0.273 Chirality : 0.039 0.121 1680 Planarity : 0.004 0.041 1656 Dihedral : 3.334 12.744 1728 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.09 % Allowed : 12.48 % 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: 3.57 (0.25), residues: 1206 helix: 3.59 (0.15), residues: 924 sheet: -2.79 (0.56), residues: 60 loop : -1.91 (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 B 73 PHE 0.007 0.001 PHE D 51 TYR 0.017 0.001 TYR C 211 ARG 0.009 0.001 ARG E 142 *********************** 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 220 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 197 time to evaluate : 1.194 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 MET cc_start: 0.5000 (mpp) cc_final: 0.4792 (mpp) outliers start: 23 outliers final: 22 residues processed: 215 average time/residue: 0.3604 time to fit residues: 96.5386 Evaluate side-chains 216 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 194 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 71 ILE 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 42 SER Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 201 CYS Chi-restraints excluded: chain E residue 71 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 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 110 optimal weight: 0.9990 chunk 101 optimal weight: 0.0970 chunk 107 optimal weight: 0.9990 chunk 64 optimal weight: 9.9990 chunk 46 optimal weight: 3.9990 chunk 84 optimal weight: 9.9990 chunk 33 optimal weight: 0.8980 chunk 97 optimal weight: 0.7980 chunk 70 optimal weight: 3.9990 chunk 113 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 205 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10344 Z= 0.167 Angle : 0.516 8.358 14130 Z= 0.264 Chirality : 0.038 0.124 1680 Planarity : 0.004 0.036 1656 Dihedral : 3.278 11.935 1728 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.64 % Allowed : 13.21 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.61 (0.24), residues: 1206 helix: 3.62 (0.15), residues: 924 sheet: -2.87 (0.55), residues: 60 loop : -1.87 (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 A 73 PHE 0.007 0.001 PHE F 31 TYR 0.016 0.001 TYR E 211 ARG 0.009 0.001 ARG D 142 *********************** 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 226 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 208 time to evaluate : 1.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 17 residues processed: 222 average time/residue: 0.3512 time to fit residues: 97.7830 Evaluate side-chains 214 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 197 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 71 ILE 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 42 SER Chi-restraints excluded: chain C residue 71 ILE 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 71 ILE Chi-restraints excluded: chain E residue 83 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 54 optimal weight: 10.0000 chunk 79 optimal weight: 5.9990 chunk 119 optimal weight: 5.9990 chunk 110 optimal weight: 3.9990 chunk 95 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 chunk 75 optimal weight: 6.9990 chunk 101 optimal weight: 1.9990 chunk 29 optimal weight: 6.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 ASN ** C 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 10344 Z= 0.219 Angle : 0.545 9.248 14130 Z= 0.279 Chirality : 0.039 0.132 1680 Planarity : 0.004 0.046 1656 Dihedral : 3.296 12.499 1728 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.91 % Allowed : 13.30 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.60 (0.25), residues: 1206 helix: 3.61 (0.15), residues: 924 sheet: -2.87 (0.54), residues: 60 loop : -1.85 (0.45), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 44 HIS 0.002 0.000 HIS C 73 PHE 0.008 0.001 PHE F 190 TYR 0.018 0.001 TYR C 211 ARG 0.009 0.001 ARG B 142 ********************** 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 216 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 195 time to evaluate : 1.218 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 20 residues processed: 211 average time/residue: 0.3431 time to fit residues: 91.1480 Evaluate side-chains 216 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 196 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain B residue 71 ILE 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 42 SER Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 201 CYS Chi-restraints excluded: chain E residue 71 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 165 LEU 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 87 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 95 optimal weight: 7.9990 chunk 39 optimal weight: 5.9990 chunk 97 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 68 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3050 r_free = 0.3050 target = 0.064631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.052147 restraints weight = 27393.460| |-----------------------------------------------------------------------------| r_work (start): 0.2726 rms_B_bonded: 2.60 r_work: 0.2589 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8949 moved from start: 0.2888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10344 Z= 0.175 Angle : 0.536 9.010 14130 Z= 0.275 Chirality : 0.038 0.129 1680 Planarity : 0.004 0.041 1656 Dihedral : 3.285 12.546 1728 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.73 % Allowed : 13.57 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.60 (0.25), residues: 1206 helix: 3.65 (0.15), residues: 918 sheet: -2.89 (0.54), residues: 60 loop : -1.89 (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 C 73 PHE 0.009 0.001 PHE F 149 TYR 0.017 0.001 TYR A 211 ARG 0.009 0.001 ARG D 142 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2510.86 seconds wall clock time: 46 minutes 26.70 seconds (2786.70 seconds total)