Starting phenix.real_space_refine on Thu Nov 14 08:13:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8szb_40907/11_2024/8szb_40907.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8szb_40907/11_2024/8szb_40907.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8szb_40907/11_2024/8szb_40907.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8szb_40907/11_2024/8szb_40907.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8szb_40907/11_2024/8szb_40907.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8szb_40907/11_2024/8szb_40907.cif" } resolution = 3.07 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= 0.002 sd= 0.038 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 18 5.16 5 C 3300 2.51 5 N 792 2.21 5 O 852 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 4962 Number of models: 1 Model: "" Number of chains: 12 Chain: "F" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 799 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 1, 'TRANS': 100} Chain: "A" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 799 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 1, 'TRANS': 100} Chain: "C" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 799 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 1, 'TRANS': 100} Chain: "E" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 799 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 1, 'TRANS': 100} Chain: "D" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 799 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 1, 'TRANS': 100} Chain: "B" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 799 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 1, 'TRANS': 100} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 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: "C" 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: "D" 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} Time building chain proxies: 4.58, per 1000 atoms: 0.92 Number of scatterers: 4962 At special positions: 0 Unit cell: (62.7, 73.26, 95.7, 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 18 16.00 O 852 8.00 N 792 7.00 C 3300 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.40 Conformation dependent library (CDL) restraints added in 642.0 milliseconds 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1188 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 0 sheets defined 90.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'F' and resid 26 through 37 removed outlier: 3.889A pdb=" N MET F 37 " --> pdb=" O VAL F 33 " (cutoff:3.500A) Processing helix chain 'F' and resid 39 through 57 removed outlier: 3.552A pdb=" N GLY F 57 " --> pdb=" O VAL F 53 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 94 removed outlier: 4.493A pdb=" N LEU F 92 " --> pdb=" O ALA F 88 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASN F 93 " --> pdb=" O ARG F 89 " (cutoff:3.500A) Processing helix chain 'F' and resid 98 through 126 Processing helix chain 'A' and resid 26 through 37 removed outlier: 3.645A pdb=" N VAL A 33 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N MET A 37 " --> pdb=" O VAL A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 56 removed outlier: 3.609A pdb=" N SER A 45 " --> pdb=" O ALA A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 94 removed outlier: 3.888A pdb=" N THR A 68 " --> pdb=" O THR A 64 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LEU A 92 " --> pdb=" O ALA A 88 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASN A 93 " --> pdb=" O ARG A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 126 removed outlier: 3.534A pdb=" N THR A 115 " --> pdb=" O LEU A 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 37 removed outlier: 3.638A pdb=" N MET C 37 " --> pdb=" O VAL C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 56 Processing helix chain 'C' and resid 62 through 94 removed outlier: 4.502A pdb=" N LEU C 92 " --> pdb=" O ALA C 88 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASN C 93 " --> pdb=" O ARG C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 126 Processing helix chain 'E' and resid 26 through 36 Processing helix chain 'E' and resid 39 through 57 Processing helix chain 'E' and resid 62 through 94 removed outlier: 4.199A pdb=" N LEU E 92 " --> pdb=" O ALA E 88 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASN E 93 " --> pdb=" O ARG E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 126 Processing helix chain 'D' and resid 26 through 37 removed outlier: 3.629A pdb=" N MET D 37 " --> pdb=" O VAL D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 56 removed outlier: 3.621A pdb=" N SER D 45 " --> pdb=" O ALA D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 94 removed outlier: 4.191A pdb=" N LEU D 92 " --> pdb=" O ALA D 88 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASN D 93 " --> pdb=" O ARG D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 126 Processing helix chain 'B' and resid 26 through 37 removed outlier: 3.563A pdb=" N MET B 37 " --> pdb=" O VAL B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 56 removed outlier: 3.577A pdb=" N MET B 48 " --> pdb=" O MET B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 94 removed outlier: 3.586A pdb=" N THR B 68 " --> pdb=" O THR B 64 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N LEU B 92 " --> pdb=" O ALA B 88 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASN B 93 " --> pdb=" O ARG B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 126 432 hydrogen bonds defined for protein. 1296 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.81 Time building geometry restraints manager: 1.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1504 1.34 - 1.46: 529 1.46 - 1.57: 2983 1.57 - 1.69: 0 1.69 - 1.80: 36 Bond restraints: 5052 Sorted by residual: bond pdb=" CD2 HIS E 26 " pdb=" NE2 HIS E 26 " ideal model delta sigma weight residual 1.374 1.360 0.014 1.10e-02 8.26e+03 1.71e+00 bond pdb=" CD2 HIS D 61 " pdb=" NE2 HIS D 61 " ideal model delta sigma weight residual 1.374 1.360 0.014 1.10e-02 8.26e+03 1.61e+00 bond pdb=" CD2 HIS E 61 " pdb=" NE2 HIS E 61 " ideal model delta sigma weight residual 1.374 1.360 0.014 1.10e-02 8.26e+03 1.60e+00 bond pdb=" CD2 HIS F 26 " pdb=" NE2 HIS F 26 " ideal model delta sigma weight residual 1.374 1.361 0.013 1.10e-02 8.26e+03 1.49e+00 bond pdb=" CG HIS D 61 " pdb=" ND1 HIS D 61 " ideal model delta sigma weight residual 1.378 1.391 -0.013 1.10e-02 8.26e+03 1.43e+00 ... (remaining 5047 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.31: 6731 1.31 - 2.62: 141 2.62 - 3.93: 22 3.93 - 5.24: 15 5.24 - 6.56: 3 Bond angle restraints: 6912 Sorted by residual: angle pdb=" CA VAL B 95 " pdb=" C VAL B 95 " pdb=" N GLU B 96 " ideal model delta sigma weight residual 116.60 119.78 -3.18 1.45e+00 4.76e-01 4.80e+00 angle pdb=" CA HIS E 61 " pdb=" CB HIS E 61 " pdb=" CG HIS E 61 " ideal model delta sigma weight residual 113.80 115.95 -2.15 1.00e+00 1.00e+00 4.61e+00 angle pdb=" CA LYS A 97 " pdb=" CB LYS A 97 " pdb=" CG LYS A 97 " ideal model delta sigma weight residual 114.10 109.96 4.14 2.00e+00 2.50e-01 4.28e+00 angle pdb=" CA LYS E 97 " pdb=" CB LYS E 97 " pdb=" CG LYS E 97 " ideal model delta sigma weight residual 114.10 109.98 4.12 2.00e+00 2.50e-01 4.25e+00 angle pdb=" CA LYS C 97 " pdb=" CB LYS C 97 " pdb=" CG LYS C 97 " ideal model delta sigma weight residual 114.10 110.03 4.07 2.00e+00 2.50e-01 4.13e+00 ... (remaining 6907 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 2890 17.89 - 35.77: 244 35.77 - 53.66: 126 53.66 - 71.54: 25 71.54 - 89.43: 3 Dihedral angle restraints: 3288 sinusoidal: 1476 harmonic: 1812 Sorted by residual: dihedral pdb=" CA ARG B 100 " pdb=" CB ARG B 100 " pdb=" CG ARG B 100 " pdb=" CD ARG B 100 " ideal model delta sinusoidal sigma weight residual 60.00 117.87 -57.87 3 1.50e+01 4.44e-03 9.45e+00 dihedral pdb=" N ASN E 91 " pdb=" CA ASN E 91 " pdb=" CB ASN E 91 " pdb=" CG ASN E 91 " ideal model delta sinusoidal sigma weight residual -180.00 -122.33 -57.67 3 1.50e+01 4.44e-03 9.45e+00 dihedral pdb=" CA ILE D 110 " pdb=" CB ILE D 110 " pdb=" CG1 ILE D 110 " pdb=" CD1 ILE D 110 " ideal model delta sinusoidal sigma weight residual 180.00 122.59 57.41 3 1.50e+01 4.44e-03 9.44e+00 ... (remaining 3285 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 555 0.026 - 0.052: 204 0.052 - 0.078: 129 0.078 - 0.104: 16 0.104 - 0.130: 2 Chirality restraints: 906 Sorted by residual: chirality pdb=" CA TYR E 62 " pdb=" N TYR E 62 " pdb=" C TYR E 62 " pdb=" CB TYR E 62 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.22e-01 chirality pdb=" CB VAL F 112 " pdb=" CA VAL F 112 " pdb=" CG1 VAL F 112 " pdb=" CG2 VAL F 112 " both_signs ideal model delta sigma weight residual False -2.63 -2.52 -0.10 2.00e-01 2.50e+01 2.73e-01 chirality pdb=" CA MET F 37 " pdb=" N MET F 37 " pdb=" C MET F 37 " pdb=" CB MET F 37 " both_signs ideal model delta sigma weight residual False 2.51 2.41 0.10 2.00e-01 2.50e+01 2.31e-01 ... (remaining 903 not shown) Planarity restraints: 798 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 99 " 0.009 2.00e-02 2.50e+03 8.14e-03 1.66e+00 pdb=" CG TRP D 99 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 TRP D 99 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TRP D 99 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP D 99 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 99 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP D 99 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 99 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 99 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP D 99 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 99 " 0.003 2.00e-02 2.50e+03 7.02e-03 1.23e+00 pdb=" CG TRP A 99 " -0.016 2.00e-02 2.50e+03 pdb=" CD1 TRP A 99 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP A 99 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 99 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP A 99 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 99 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 99 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 99 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 99 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 62 " -0.007 2.00e-02 2.50e+03 7.59e-03 1.15e+00 pdb=" CG TYR E 62 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR E 62 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR E 62 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR E 62 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR E 62 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR E 62 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR E 62 " -0.000 2.00e-02 2.50e+03 ... (remaining 795 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 56 2.70 - 3.25: 5223 3.25 - 3.80: 7414 3.80 - 4.35: 9091 4.35 - 4.90: 15549 Nonbonded interactions: 37333 Sorted by model distance: nonbonded pdb=" O VAL C 112 " pdb=" OG1 THR C 115 " model vdw 2.154 3.040 nonbonded pdb=" O VAL A 112 " pdb=" OG1 THR A 115 " model vdw 2.218 3.040 nonbonded pdb=" O VAL B 112 " pdb=" OG1 THR B 115 " model vdw 2.256 3.040 nonbonded pdb=" O VAL B 67 " pdb=" OG SER B 71 " model vdw 2.268 3.040 nonbonded pdb=" O VAL E 67 " pdb=" OG SER E 71 " model vdw 2.277 3.040 ... (remaining 37328 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: 3.230 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: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 18.590 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7137 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 : 0.003 0.027 5052 Z= 0.193 Angle : 0.512 6.556 6912 Z= 0.278 Chirality : 0.034 0.130 906 Planarity : 0.003 0.035 798 Dihedral : 16.774 89.430 2100 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.37 % Allowed : 18.15 % Favored : 81.48 % 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: 2.06 (0.33), residues: 600 helix: 1.73 (0.21), residues: 522 sheet: None (None), residues: 0 loop : -1.00 (0.68), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 99 HIS 0.001 0.000 HIS F 61 PHE 0.009 0.001 PHE F 114 TYR 0.018 0.001 TYR E 62 ARG 0.007 0.001 ARG A 49 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 191 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 49 ARG cc_start: 0.7688 (tpp80) cc_final: 0.6993 (mmm160) REVERT: A 51 LYS cc_start: 0.7105 (tptt) cc_final: 0.6879 (tppt) REVERT: A 61 HIS cc_start: 0.7242 (OUTLIER) cc_final: 0.7024 (t-90) REVERT: A 111 LEU cc_start: 0.8003 (mm) cc_final: 0.7771 (mt) REVERT: E 44 MET cc_start: 0.7474 (tmm) cc_final: 0.7270 (tpt) REVERT: E 64 THR cc_start: 0.7523 (m) cc_final: 0.7245 (p) REVERT: D 76 LEU cc_start: 0.7510 (mp) cc_final: 0.7081 (mp) outliers start: 2 outliers final: 0 residues processed: 191 average time/residue: 0.1794 time to fit residues: 43.1979 Evaluate side-chains 140 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 139 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 30 optimal weight: 5.9990 chunk 24 optimal weight: 0.3980 chunk 47 optimal weight: 0.0170 chunk 18 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 54 optimal weight: 0.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 26 HIS F 46 ASN C 119 ASN E 26 HIS E 77 GLN D 105 ASN D 119 ASN B 46 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.3692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5052 Z= 0.168 Angle : 0.513 6.716 6912 Z= 0.268 Chirality : 0.035 0.105 906 Planarity : 0.003 0.019 798 Dihedral : 8.927 58.259 1034 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.15 % Allowed : 21.85 % Favored : 75.00 % 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: 3.51 (0.33), residues: 600 helix: 2.79 (0.21), residues: 522 sheet: None (None), residues: 0 loop : -1.20 (0.64), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 99 HIS 0.002 0.001 HIS A 26 PHE 0.008 0.001 PHE E 43 TYR 0.007 0.001 TYR F 63 ARG 0.005 0.001 ARG F 49 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 137 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 LYS cc_start: 0.6556 (mmtt) cc_final: 0.5651 (tmtt) REVERT: A 49 ARG cc_start: 0.8336 (ttm170) cc_final: 0.8058 (ttm170) REVERT: A 51 LYS cc_start: 0.7201 (tptt) cc_final: 0.6840 (tppt) REVERT: D 97 LYS cc_start: 0.5725 (ptpp) cc_final: 0.5302 (pttt) REVERT: B 55 GLU cc_start: 0.8177 (mm-30) cc_final: 0.7941 (mm-30) outliers start: 17 outliers final: 6 residues processed: 145 average time/residue: 0.2005 time to fit residues: 35.7017 Evaluate side-chains 132 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 126 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 61 HIS Chi-restraints excluded: chain D residue 72 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 30 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 37 optimal weight: 6.9990 chunk 15 optimal weight: 0.6980 chunk 54 optimal weight: 0.8980 chunk 58 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 43 optimal weight: 0.0010 chunk 53 optimal weight: 3.9990 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 119 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.5242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5052 Z= 0.159 Angle : 0.485 8.162 6912 Z= 0.254 Chirality : 0.035 0.108 906 Planarity : 0.002 0.018 798 Dihedral : 8.162 53.066 1032 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 3.52 % Allowed : 21.85 % Favored : 74.63 % 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: 3.99 (0.33), residues: 600 helix: 3.09 (0.21), residues: 522 sheet: None (None), residues: 0 loop : -0.95 (0.66), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 99 HIS 0.003 0.001 HIS B 26 PHE 0.008 0.001 PHE B 43 TYR 0.009 0.001 TYR B 62 ARG 0.002 0.000 ARG E 49 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 144 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 118 ILE cc_start: 0.8399 (OUTLIER) cc_final: 0.8160 (tt) REVERT: A 51 LYS cc_start: 0.7250 (tptt) cc_final: 0.6942 (tppt) REVERT: A 61 HIS cc_start: 0.7443 (OUTLIER) cc_final: 0.6993 (t-90) REVERT: A 103 GLN cc_start: 0.8099 (mm-40) cc_final: 0.7057 (mt0) REVERT: D 49 ARG cc_start: 0.8211 (ttm110) cc_final: 0.7922 (ttm110) REVERT: D 84 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.8076 (mm) REVERT: B 55 GLU cc_start: 0.8234 (mm-30) cc_final: 0.8023 (mm-30) outliers start: 19 outliers final: 4 residues processed: 157 average time/residue: 0.2283 time to fit residues: 44.7344 Evaluate side-chains 135 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 128 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 61 HIS Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain D residue 84 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 41 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 77 GLN B 103 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.6071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 5052 Z= 0.184 Angle : 0.475 8.536 6912 Z= 0.252 Chirality : 0.036 0.103 906 Planarity : 0.002 0.028 798 Dihedral : 8.055 53.638 1032 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 4.81 % Allowed : 21.48 % Favored : 73.70 % 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: 4.04 (0.32), residues: 600 helix: 3.12 (0.20), residues: 522 sheet: None (None), residues: 0 loop : -0.85 (0.66), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 99 HIS 0.002 0.001 HIS C 26 PHE 0.011 0.001 PHE F 114 TYR 0.006 0.001 TYR F 63 ARG 0.005 0.000 ARG F 49 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 134 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 35 GLU cc_start: 0.8328 (tt0) cc_final: 0.7994 (tm-30) REVERT: A 51 LYS cc_start: 0.7517 (tptt) cc_final: 0.7315 (tppt) REVERT: A 61 HIS cc_start: 0.7522 (OUTLIER) cc_final: 0.7129 (t-90) REVERT: A 77 GLN cc_start: 0.7791 (OUTLIER) cc_final: 0.7548 (mp10) REVERT: A 103 GLN cc_start: 0.8207 (mm-40) cc_final: 0.7223 (mt0) REVERT: D 97 LYS cc_start: 0.5965 (ptpp) cc_final: 0.5515 (pttt) REVERT: D 102 ASN cc_start: 0.8210 (m-40) cc_final: 0.8002 (m-40) REVERT: B 48 MET cc_start: 0.7222 (mtt) cc_final: 0.6968 (mtt) outliers start: 26 outliers final: 13 residues processed: 147 average time/residue: 0.1907 time to fit residues: 35.1286 Evaluate side-chains 140 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 125 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 102 ASN Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 61 HIS Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 77 GLN Chi-restraints excluded: chain C residue 61 HIS Chi-restraints excluded: chain C residue 102 ASN Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 61 HIS Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 118 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 0 optimal weight: 5.9990 chunk 43 optimal weight: 0.2980 chunk 23 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 chunk 40 optimal weight: 5.9990 chunk 29 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 19 optimal weight: 0.1980 chunk 11 optimal weight: 5.9990 chunk 34 optimal weight: 0.4980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.6321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 5052 Z= 0.151 Angle : 0.457 7.210 6912 Z= 0.241 Chirality : 0.034 0.105 906 Planarity : 0.002 0.018 798 Dihedral : 7.720 55.973 1032 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 3.15 % Allowed : 22.96 % Favored : 73.89 % 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: 4.31 (0.32), residues: 600 helix: 3.32 (0.21), residues: 522 sheet: None (None), residues: 0 loop : -0.91 (0.66), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 99 HIS 0.001 0.000 HIS D 26 PHE 0.010 0.001 PHE F 113 TYR 0.006 0.001 TYR F 63 ARG 0.003 0.000 ARG F 49 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 125 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 91 ASN cc_start: 0.7878 (t0) cc_final: 0.7529 (t0) REVERT: A 103 GLN cc_start: 0.8180 (mm-40) cc_final: 0.7296 (mt0) REVERT: D 91 ASN cc_start: 0.8499 (t0) cc_final: 0.7869 (p0) REVERT: D 102 ASN cc_start: 0.8234 (m-40) cc_final: 0.7999 (m-40) REVERT: B 44 MET cc_start: 0.8334 (tmm) cc_final: 0.8018 (tmm) REVERT: B 48 MET cc_start: 0.7282 (mtt) cc_final: 0.6975 (mtt) outliers start: 17 outliers final: 11 residues processed: 137 average time/residue: 0.2441 time to fit residues: 41.4394 Evaluate side-chains 129 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 118 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 102 ASN Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 121 PHE Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 61 HIS Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain B residue 40 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 14 optimal weight: 0.8980 chunk 58 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 4 optimal weight: 0.0770 chunk 19 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.6664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 5052 Z= 0.160 Angle : 0.489 8.861 6912 Z= 0.250 Chirality : 0.035 0.108 906 Planarity : 0.002 0.024 798 Dihedral : 7.639 58.560 1032 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 3.89 % Allowed : 22.41 % Favored : 73.70 % 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: 4.34 (0.32), residues: 600 helix: 3.33 (0.21), residues: 522 sheet: None (None), residues: 0 loop : -0.85 (0.66), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 99 HIS 0.001 0.000 HIS D 26 PHE 0.007 0.001 PHE D 43 TYR 0.007 0.001 TYR B 62 ARG 0.006 0.001 ARG A 49 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 120 time to evaluate : 0.584 Fit side-chains revert: symmetry clash REVERT: F 35 GLU cc_start: 0.8284 (tt0) cc_final: 0.7979 (tm-30) REVERT: F 91 ASN cc_start: 0.7896 (t0) cc_final: 0.7574 (t0) REVERT: A 51 LYS cc_start: 0.7627 (tppt) cc_final: 0.6444 (ttmt) REVERT: A 77 GLN cc_start: 0.7709 (OUTLIER) cc_final: 0.7065 (mt0) REVERT: A 103 GLN cc_start: 0.8158 (mm-40) cc_final: 0.7311 (mt0) REVERT: E 84 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8156 (mm) REVERT: D 91 ASN cc_start: 0.8551 (t0) cc_final: 0.7860 (p0) REVERT: D 97 LYS cc_start: 0.6158 (ptpp) cc_final: 0.5680 (pttt) REVERT: D 102 ASN cc_start: 0.8238 (m-40) cc_final: 0.7984 (m-40) REVERT: B 44 MET cc_start: 0.8333 (tmm) cc_final: 0.7884 (tmm) REVERT: B 48 MET cc_start: 0.7371 (mtt) cc_final: 0.7059 (mtt) outliers start: 21 outliers final: 12 residues processed: 135 average time/residue: 0.2019 time to fit residues: 34.4507 Evaluate side-chains 130 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 116 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 102 ASN Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 77 GLN Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 121 PHE Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 61 HIS Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain B residue 40 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 32 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 26 optimal weight: 0.0980 chunk 23 optimal weight: 6.9990 chunk 34 optimal weight: 0.7980 chunk 17 optimal weight: 7.9990 chunk 11 optimal weight: 5.9990 chunk 39 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.6818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 5052 Z= 0.161 Angle : 0.490 8.084 6912 Z= 0.253 Chirality : 0.035 0.112 906 Planarity : 0.002 0.025 798 Dihedral : 7.526 59.153 1032 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 3.33 % Allowed : 22.59 % Favored : 74.07 % 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: 4.35 (0.33), residues: 600 helix: 3.32 (0.21), residues: 522 sheet: None (None), residues: 0 loop : -0.72 (0.68), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 99 HIS 0.001 0.000 HIS D 26 PHE 0.015 0.001 PHE F 113 TYR 0.005 0.001 TYR F 63 ARG 0.007 0.001 ARG F 49 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 124 time to evaluate : 0.578 Fit side-chains revert: symmetry clash REVERT: F 35 GLU cc_start: 0.8265 (tt0) cc_final: 0.7960 (tm-30) REVERT: F 91 ASN cc_start: 0.7931 (t0) cc_final: 0.7626 (t0) REVERT: F 121 PHE cc_start: 0.8477 (OUTLIER) cc_final: 0.8256 (t80) REVERT: A 51 LYS cc_start: 0.7554 (tppt) cc_final: 0.6412 (ttmt) REVERT: A 77 GLN cc_start: 0.7752 (OUTLIER) cc_final: 0.7196 (mt0) REVERT: A 103 GLN cc_start: 0.8246 (mm-40) cc_final: 0.7362 (mt0) REVERT: C 102 ASN cc_start: 0.8077 (t0) cc_final: 0.7602 (m-40) REVERT: D 91 ASN cc_start: 0.8564 (t0) cc_final: 0.7812 (p0) REVERT: D 97 LYS cc_start: 0.6132 (ptpp) cc_final: 0.5631 (pttt) REVERT: D 102 ASN cc_start: 0.8245 (m-40) cc_final: 0.7967 (m-40) REVERT: B 44 MET cc_start: 0.8343 (tmm) cc_final: 0.7829 (tmm) REVERT: B 48 MET cc_start: 0.7323 (mtt) cc_final: 0.7031 (mtt) outliers start: 18 outliers final: 11 residues processed: 135 average time/residue: 0.1898 time to fit residues: 32.0574 Evaluate side-chains 132 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 119 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 121 PHE Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 77 GLN Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 121 PHE Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 61 HIS Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain B residue 40 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 28 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 chunk 45 optimal weight: 0.1980 chunk 52 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN ** B 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.6910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 5052 Z= 0.166 Angle : 0.490 7.622 6912 Z= 0.254 Chirality : 0.036 0.170 906 Planarity : 0.002 0.023 798 Dihedral : 7.475 57.595 1032 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 3.70 % Allowed : 22.41 % Favored : 73.89 % 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: 4.37 (0.33), residues: 600 helix: 3.34 (0.21), residues: 522 sheet: None (None), residues: 0 loop : -0.73 (0.68), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 99 HIS 0.001 0.000 HIS D 26 PHE 0.006 0.001 PHE A 125 TYR 0.006 0.001 TYR F 63 ARG 0.006 0.000 ARG F 49 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 118 time to evaluate : 0.576 Fit side-chains revert: symmetry clash REVERT: F 35 GLU cc_start: 0.8247 (tt0) cc_final: 0.7947 (tm-30) REVERT: F 91 ASN cc_start: 0.7948 (t0) cc_final: 0.7660 (t0) REVERT: F 121 PHE cc_start: 0.8496 (OUTLIER) cc_final: 0.8279 (t80) REVERT: A 77 GLN cc_start: 0.7758 (OUTLIER) cc_final: 0.7266 (mt0) REVERT: A 103 GLN cc_start: 0.8256 (mm-40) cc_final: 0.7437 (mt0) REVERT: C 72 LEU cc_start: 0.7863 (OUTLIER) cc_final: 0.7513 (mt) REVERT: C 98 GLN cc_start: 0.8311 (mp10) cc_final: 0.7797 (mp10) REVERT: C 102 ASN cc_start: 0.8054 (t0) cc_final: 0.7619 (m-40) REVERT: D 48 MET cc_start: 0.7642 (OUTLIER) cc_final: 0.7314 (mtt) REVERT: D 84 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7831 (mm) REVERT: D 91 ASN cc_start: 0.8595 (t0) cc_final: 0.7873 (p0) REVERT: D 97 LYS cc_start: 0.6087 (ptpp) cc_final: 0.5665 (pttt) REVERT: D 102 ASN cc_start: 0.8250 (m-40) cc_final: 0.8017 (m-40) REVERT: B 44 MET cc_start: 0.8324 (tmm) cc_final: 0.7760 (tmm) REVERT: B 48 MET cc_start: 0.7385 (mtt) cc_final: 0.7086 (mtt) REVERT: B 100 ARG cc_start: 0.7472 (mmt-90) cc_final: 0.6641 (mmt180) outliers start: 20 outliers final: 13 residues processed: 129 average time/residue: 0.1997 time to fit residues: 32.2969 Evaluate side-chains 133 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 115 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 121 PHE Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 77 GLN Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 61 HIS Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 121 PHE Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 48 MET Chi-restraints excluded: chain D residue 61 HIS Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain B residue 40 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 27 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.7080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5052 Z= 0.169 Angle : 0.523 8.903 6912 Z= 0.265 Chirality : 0.036 0.150 906 Planarity : 0.002 0.025 798 Dihedral : 7.442 56.825 1032 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 3.89 % Allowed : 22.41 % Favored : 73.70 % 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: 4.42 (0.33), residues: 600 helix: 3.37 (0.21), residues: 522 sheet: None (None), residues: 0 loop : -0.70 (0.69), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 99 HIS 0.001 0.000 HIS D 26 PHE 0.011 0.001 PHE A 125 TYR 0.016 0.001 TYR A 62 ARG 0.006 0.000 ARG F 49 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 117 time to evaluate : 0.632 Fit side-chains revert: symmetry clash REVERT: F 35 GLU cc_start: 0.8269 (tt0) cc_final: 0.7960 (tm-30) REVERT: F 91 ASN cc_start: 0.7982 (t0) cc_final: 0.7709 (t0) REVERT: F 121 PHE cc_start: 0.8500 (OUTLIER) cc_final: 0.8259 (t80) REVERT: A 51 LYS cc_start: 0.7911 (tppt) cc_final: 0.6673 (ttmt) REVERT: A 77 GLN cc_start: 0.7670 (OUTLIER) cc_final: 0.7104 (mt0) REVERT: A 103 GLN cc_start: 0.8245 (mm-40) cc_final: 0.7432 (mt0) REVERT: C 48 MET cc_start: 0.8528 (mmm) cc_final: 0.8034 (mmm) REVERT: C 72 LEU cc_start: 0.7855 (OUTLIER) cc_final: 0.7532 (mt) REVERT: C 98 GLN cc_start: 0.8328 (mp10) cc_final: 0.7815 (mp10) REVERT: C 102 ASN cc_start: 0.8053 (t0) cc_final: 0.7652 (m-40) REVERT: D 42 LEU cc_start: 0.8146 (tt) cc_final: 0.7932 (tp) REVERT: D 48 MET cc_start: 0.7675 (OUTLIER) cc_final: 0.7224 (mtt) REVERT: D 84 LEU cc_start: 0.8058 (OUTLIER) cc_final: 0.7839 (mm) REVERT: D 91 ASN cc_start: 0.8610 (t0) cc_final: 0.7823 (p0) REVERT: D 97 LYS cc_start: 0.6081 (ptpp) cc_final: 0.5671 (pttt) REVERT: D 102 ASN cc_start: 0.8259 (m-40) cc_final: 0.8055 (m-40) REVERT: B 44 MET cc_start: 0.8314 (tmm) cc_final: 0.7727 (tmm) REVERT: B 48 MET cc_start: 0.7385 (mtt) cc_final: 0.7105 (mtt) outliers start: 21 outliers final: 15 residues processed: 129 average time/residue: 0.2052 time to fit residues: 33.0056 Evaluate side-chains 136 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 116 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 121 PHE Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 61 HIS Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 77 GLN Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 61 HIS Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 121 PHE Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 48 MET Chi-restraints excluded: chain D residue 61 HIS Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain B residue 40 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 4 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 50 optimal weight: 0.0980 chunk 14 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN ** B 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.7157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 5052 Z= 0.162 Angle : 0.525 8.495 6912 Z= 0.267 Chirality : 0.036 0.146 906 Planarity : 0.002 0.030 798 Dihedral : 7.359 55.890 1032 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 3.70 % Allowed : 22.59 % Favored : 73.70 % 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: 4.46 (0.32), residues: 600 helix: 3.39 (0.21), residues: 522 sheet: None (None), residues: 0 loop : -0.67 (0.69), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 99 HIS 0.001 0.000 HIS D 26 PHE 0.014 0.001 PHE A 125 TYR 0.018 0.001 TYR A 62 ARG 0.007 0.001 ARG A 49 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 119 time to evaluate : 0.831 Fit side-chains revert: symmetry clash REVERT: F 35 GLU cc_start: 0.8250 (tt0) cc_final: 0.7949 (tm-30) REVERT: F 91 ASN cc_start: 0.7998 (t0) cc_final: 0.7728 (t0) REVERT: F 121 PHE cc_start: 0.8520 (OUTLIER) cc_final: 0.8287 (t80) REVERT: A 51 LYS cc_start: 0.7898 (tppt) cc_final: 0.6663 (ttmt) REVERT: A 77 GLN cc_start: 0.7583 (OUTLIER) cc_final: 0.6943 (mt0) REVERT: A 103 GLN cc_start: 0.8245 (mm-40) cc_final: 0.7447 (mt0) REVERT: C 48 MET cc_start: 0.8543 (mmm) cc_final: 0.8061 (mmm) REVERT: C 72 LEU cc_start: 0.7857 (OUTLIER) cc_final: 0.7549 (mt) REVERT: C 98 GLN cc_start: 0.8321 (mp10) cc_final: 0.7796 (mp10) REVERT: C 102 ASN cc_start: 0.8040 (t0) cc_final: 0.7646 (m-40) REVERT: C 121 PHE cc_start: 0.8273 (OUTLIER) cc_final: 0.8001 (t80) REVERT: D 42 LEU cc_start: 0.8154 (tt) cc_final: 0.7944 (tp) REVERT: D 48 MET cc_start: 0.7707 (OUTLIER) cc_final: 0.7175 (mtt) REVERT: D 84 LEU cc_start: 0.8048 (OUTLIER) cc_final: 0.7841 (mm) REVERT: D 97 LYS cc_start: 0.6104 (ptpp) cc_final: 0.5739 (pttt) REVERT: B 44 MET cc_start: 0.8305 (tmm) cc_final: 0.7701 (tmm) REVERT: B 48 MET cc_start: 0.7420 (mtt) cc_final: 0.7128 (mtt) REVERT: B 100 ARG cc_start: 0.7339 (mmt180) cc_final: 0.6794 (tpt170) outliers start: 20 outliers final: 13 residues processed: 130 average time/residue: 0.2176 time to fit residues: 35.8872 Evaluate side-chains 136 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 117 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 121 PHE Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 61 HIS Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 77 GLN Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 61 HIS Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 97 LYS Chi-restraints excluded: chain C residue 121 PHE Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 48 MET Chi-restraints excluded: chain D residue 61 HIS Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain B residue 40 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 41 optimal weight: 0.0050 chunk 2 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.163688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.137728 restraints weight = 7045.079| |-----------------------------------------------------------------------------| r_work (start): 0.3892 rms_B_bonded: 2.30 r_work: 0.3765 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.7307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5052 Z= 0.173 Angle : 0.529 8.110 6912 Z= 0.270 Chirality : 0.036 0.147 906 Planarity : 0.002 0.031 798 Dihedral : 7.347 55.639 1032 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 3.70 % Allowed : 23.33 % Favored : 72.96 % 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: 4.41 (0.32), residues: 600 helix: 3.37 (0.21), residues: 522 sheet: None (None), residues: 0 loop : -0.71 (0.68), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 99 HIS 0.001 0.000 HIS D 26 PHE 0.013 0.001 PHE A 125 TYR 0.019 0.001 TYR A 62 ARG 0.008 0.001 ARG A 49 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1613.31 seconds wall clock time: 30 minutes 57.79 seconds (1857.79 seconds total)