Starting phenix.real_space_refine on Thu Mar 6 05:28:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8szb_40907/03_2025/8szb_40907.cif Found real_map, /net/cci-nas-00/data/ceres_data/8szb_40907/03_2025/8szb_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/cci-nas-00/data/ceres_data/8szb_40907/03_2025/8szb_40907.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8szb_40907/03_2025/8szb_40907.map" model { file = "/net/cci-nas-00/data/ceres_data/8szb_40907/03_2025/8szb_40907.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8szb_40907/03_2025/8szb_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-5624/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: 4.48, per 1000 atoms: 0.90 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: 1.37 Conformation dependent library (CDL) restraints added in 629.2 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: 0.43 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: 1.35 Time building geometry restraints manager: 1.57 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: 0.01 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: 2.040 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: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 17.180 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.800 ------------------------------------------------------------------------------- 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 : 0.515 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: 0.1669 time to fit residues: 39.9770 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 : 0.499 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.165109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.138063 restraints weight = 7208.877| |-----------------------------------------------------------------------------| r_work (start): 0.3907 rms_B_bonded: 2.41 r_work: 0.3784 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 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 : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 LYS cc_start: 0.6614 (mmtt) cc_final: 0.5675 (tmtt) REVERT: A 49 ARG cc_start: 0.8343 (ttm170) cc_final: 0.8077 (ttm170) REVERT: A 51 LYS cc_start: 0.7233 (tptt) cc_final: 0.6918 (tppt) REVERT: D 97 LYS cc_start: 0.5653 (ptpp) cc_final: 0.5223 (pttt) REVERT: B 55 GLU cc_start: 0.8294 (mm-30) cc_final: 0.8055 (mm-30) outliers start: 17 outliers final: 6 residues processed: 145 average time/residue: 0.2339 time to fit residues: 43.4351 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 : 0.467 ------------------------------------------------------------------------------- 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 11 optimal weight: 6.9990 chunk 32 optimal weight: 0.7980 chunk 13 optimal weight: 0.4980 chunk 6 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 20 optimal weight: 5.9990 chunk 27 optimal weight: 0.0370 chunk 43 optimal weight: 5.9990 chunk 8 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 overall best weight: 0.6260 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.164623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.138491 restraints weight = 7278.138| |-----------------------------------------------------------------------------| r_work (start): 0.3899 rms_B_bonded: 2.33 r_work: 0.3774 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.5159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 5052 Z= 0.158 Angle : 0.486 8.079 6912 Z= 0.254 Chirality : 0.035 0.102 906 Planarity : 0.002 0.017 798 Dihedral : 8.172 52.958 1032 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 3.33 % Allowed : 21.85 % Favored : 74.81 % 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: 3.98 (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 161 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 143 time to evaluate : 1.742 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 49 ARG cc_start: 0.7748 (ttp-110) cc_final: 0.7442 (ttp-110) REVERT: A 51 LYS cc_start: 0.7301 (tptt) cc_final: 0.7077 (tppt) REVERT: A 61 HIS cc_start: 0.7588 (OUTLIER) cc_final: 0.7187 (t-90) REVERT: A 103 GLN cc_start: 0.8161 (mm-40) cc_final: 0.7156 (mt0) REVERT: D 49 ARG cc_start: 0.8184 (ttm110) cc_final: 0.7912 (ttm110) outliers start: 18 outliers final: 5 residues processed: 155 average time/residue: 0.2204 time to fit residues: 43.9255 Evaluate side-chains 134 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 128 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 73 SER 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 72 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 7 optimal weight: 8.9990 chunk 36 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 23 optimal weight: 9.9990 chunk 24 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 54 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN D 77 GLN B 103 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.162408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.135669 restraints weight = 7372.312| |-----------------------------------------------------------------------------| r_work (start): 0.3871 rms_B_bonded: 2.39 r_work: 0.3747 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.5929 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 : 0.473 7.393 6912 Z= 0.254 Chirality : 0.035 0.110 906 Planarity : 0.002 0.017 798 Dihedral : 8.005 53.789 1032 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 4.07 % Allowed : 22.41 % Favored : 73.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.08 (0.32), residues: 600 helix: 3.15 (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 0.003 0.001 TRP B 99 HIS 0.002 0.001 HIS C 26 PHE 0.009 0.001 PHE D 43 TYR 0.006 0.001 TYR F 63 ARG 0.002 0.000 ARG B 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 157 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 135 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 35 GLU cc_start: 0.8255 (tt0) cc_final: 0.8017 (tm-30) REVERT: A 51 LYS cc_start: 0.7477 (tptt) cc_final: 0.7241 (tppt) REVERT: A 103 GLN cc_start: 0.8223 (mm-40) cc_final: 0.7255 (mt0) REVERT: C 102 ASN cc_start: 0.8019 (t0) cc_final: 0.7674 (m-40) REVERT: B 48 MET cc_start: 0.7216 (mtt) cc_final: 0.6930 (mtt) outliers start: 22 outliers final: 8 residues processed: 148 average time/residue: 0.1899 time to fit residues: 34.8983 Evaluate side-chains 134 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 126 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 102 ASN Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 68 THR 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 41 optimal weight: 0.6980 chunk 30 optimal weight: 4.9990 chunk 15 optimal weight: 0.6980 chunk 10 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 43 optimal weight: 0.4980 chunk 27 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 59 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 54 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 GLN C 119 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.162137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.135483 restraints weight = 7247.302| |-----------------------------------------------------------------------------| r_work (start): 0.3878 rms_B_bonded: 2.39 r_work: 0.3755 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.6253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 5052 Z= 0.163 Angle : 0.463 7.001 6912 Z= 0.244 Chirality : 0.035 0.120 906 Planarity : 0.002 0.025 798 Dihedral : 7.765 56.134 1032 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 3.52 % Allowed : 22.22 % Favored : 74.26 % 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: 4.21 (0.32), residues: 600 helix: 3.24 (0.21), residues: 522 sheet: None (None), residues: 0 loop : -0.89 (0.66), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 99 HIS 0.001 0.000 HIS D 26 PHE 0.008 0.001 PHE F 114 TYR 0.006 0.001 TYR B 62 ARG 0.005 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 153 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 134 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 35 GLU cc_start: 0.8218 (tt0) cc_final: 0.8006 (tm-30) REVERT: F 91 ASN cc_start: 0.7875 (t0) cc_final: 0.7533 (t0) REVERT: A 103 GLN cc_start: 0.8201 (mm-40) cc_final: 0.7337 (mt0) REVERT: C 102 ASN cc_start: 0.8025 (t0) cc_final: 0.7768 (m-40) REVERT: D 91 ASN cc_start: 0.8498 (t0) cc_final: 0.7846 (p0) REVERT: B 44 MET cc_start: 0.8425 (tmm) cc_final: 0.8155 (tmm) REVERT: B 48 MET cc_start: 0.7259 (mtt) cc_final: 0.6996 (mtt) outliers start: 19 outliers final: 12 residues processed: 146 average time/residue: 0.1794 time to fit residues: 33.4585 Evaluate side-chains 139 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 127 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 102 ASN Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 61 HIS 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 43 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 3 optimal weight: 8.9990 chunk 42 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 17 optimal weight: 7.9990 chunk 28 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.161292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.134510 restraints weight = 7318.623| |-----------------------------------------------------------------------------| r_work (start): 0.3862 rms_B_bonded: 2.36 r_work: 0.3741 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.6599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 5052 Z= 0.177 Angle : 0.500 8.615 6912 Z= 0.256 Chirality : 0.036 0.120 906 Planarity : 0.002 0.018 798 Dihedral : 7.771 57.440 1032 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 3.89 % Allowed : 22.22 % 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: 4.21 (0.32), residues: 600 helix: 3.24 (0.21), residues: 522 sheet: None (None), residues: 0 loop : -0.89 (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 0.020 0.001 PHE F 114 TYR 0.005 0.001 TYR F 63 ARG 0.003 0.000 ARG F 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 145 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 124 time to evaluate : 1.045 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 35 GLU cc_start: 0.8278 (tt0) cc_final: 0.8039 (tm-30) REVERT: F 91 ASN cc_start: 0.7891 (t0) cc_final: 0.7594 (t0) REVERT: A 51 LYS cc_start: 0.7640 (tppt) cc_final: 0.6474 (ttmt) REVERT: A 103 GLN cc_start: 0.8172 (mm-40) cc_final: 0.7341 (mt0) REVERT: C 102 ASN cc_start: 0.8057 (t0) cc_final: 0.7837 (m-40) REVERT: D 91 ASN cc_start: 0.8546 (t0) cc_final: 0.7859 (p0) REVERT: D 97 LYS cc_start: 0.6061 (ptpp) cc_final: 0.5572 (pttt) REVERT: B 44 MET cc_start: 0.8403 (tmm) cc_final: 0.7996 (tmm) REVERT: B 48 MET cc_start: 0.7338 (mtt) cc_final: 0.7076 (mtt) outliers start: 21 outliers final: 13 residues processed: 137 average time/residue: 0.3536 time to fit residues: 59.9015 Evaluate side-chains 131 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 118 time to evaluate : 0.900 ------------------------------------------------------------------------------- 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 C residue 40 VAL Chi-restraints excluded: chain C residue 61 HIS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 29 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 57 optimal weight: 6.9990 chunk 19 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 40 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.160338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.133741 restraints weight = 7262.760| |-----------------------------------------------------------------------------| r_work (start): 0.3843 rms_B_bonded: 2.36 r_work: 0.3723 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.6863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 5052 Z= 0.211 Angle : 0.518 7.990 6912 Z= 0.268 Chirality : 0.037 0.126 906 Planarity : 0.002 0.023 798 Dihedral : 7.892 57.610 1032 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % 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: 4.06 (0.32), residues: 600 helix: 3.12 (0.21), residues: 522 sheet: None (None), residues: 0 loop : -0.78 (0.69), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 99 HIS 0.002 0.000 HIS D 26 PHE 0.013 0.001 PHE F 114 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 141 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 123 time to evaluate : 1.028 Fit side-chains revert: symmetry clash REVERT: F 35 GLU cc_start: 0.8320 (tt0) cc_final: 0.8089 (tm-30) REVERT: F 91 ASN cc_start: 0.7964 (t0) cc_final: 0.7700 (t0) REVERT: F 121 PHE cc_start: 0.8532 (OUTLIER) cc_final: 0.8296 (t80) REVERT: A 103 GLN cc_start: 0.8280 (mm-40) cc_final: 0.7430 (mt0) REVERT: D 91 ASN cc_start: 0.8578 (t0) cc_final: 0.7852 (p0) REVERT: D 97 LYS cc_start: 0.6051 (ptpp) cc_final: 0.5597 (pttt) REVERT: B 100 ARG cc_start: 0.7462 (mmt-90) cc_final: 0.6664 (mmt180) outliers start: 18 outliers final: 12 residues processed: 133 average time/residue: 0.2531 time to fit residues: 43.3223 Evaluate side-chains 129 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 116 time to evaluate : 0.969 ------------------------------------------------------------------------------- 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 F residue 121 PHE Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 68 THR 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 34 optimal weight: 0.7980 chunk 49 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 41 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.162056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.134699 restraints weight = 7217.488| |-----------------------------------------------------------------------------| r_work (start): 0.3841 rms_B_bonded: 2.53 r_work: 0.3707 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.7102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5052 Z= 0.178 Angle : 0.503 6.801 6912 Z= 0.265 Chirality : 0.037 0.170 906 Planarity : 0.002 0.027 798 Dihedral : 7.754 59.419 1032 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 3.52 % Allowed : 22.41 % 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: 4.12 (0.32), residues: 600 helix: 3.16 (0.21), residues: 522 sheet: None (None), residues: 0 loop : -0.73 (0.70), 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 0.006 0.001 PHE F 113 TYR 0.008 0.001 TYR B 62 ARG 0.006 0.001 ARG A 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 144 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 125 time to evaluate : 0.574 Fit side-chains revert: symmetry clash REVERT: F 35 GLU cc_start: 0.8346 (tt0) cc_final: 0.8048 (tm-30) REVERT: F 91 ASN cc_start: 0.7954 (t0) cc_final: 0.7703 (t0) REVERT: F 121 PHE cc_start: 0.8500 (OUTLIER) cc_final: 0.8263 (t80) REVERT: F 123 THR cc_start: 0.7735 (m) cc_final: 0.7511 (p) REVERT: A 51 LYS cc_start: 0.7719 (tppt) cc_final: 0.6618 (ttmt) REVERT: A 103 GLN cc_start: 0.8239 (mm-40) cc_final: 0.7455 (mt0) REVERT: C 72 LEU cc_start: 0.7723 (OUTLIER) cc_final: 0.7475 (mt) REVERT: D 84 LEU cc_start: 0.8059 (OUTLIER) cc_final: 0.7842 (mm) REVERT: D 97 LYS cc_start: 0.6153 (ptpp) cc_final: 0.5683 (pttt) REVERT: B 44 MET cc_start: 0.8489 (tmm) cc_final: 0.8054 (tmm) REVERT: B 48 MET cc_start: 0.7330 (mtt) cc_final: 0.6923 (mtt) REVERT: B 100 ARG cc_start: 0.7421 (mmt-90) cc_final: 0.6645 (tpt90) outliers start: 19 outliers final: 13 residues processed: 137 average time/residue: 0.2098 time to fit residues: 35.8281 Evaluate side-chains 133 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 117 time to evaluate : 0.547 ------------------------------------------------------------------------------- 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 F residue 121 PHE Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 72 LEU 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 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 23 optimal weight: 0.0870 chunk 10 optimal weight: 4.9990 chunk 46 optimal weight: 0.0970 chunk 29 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 chunk 36 optimal weight: 0.0050 chunk 34 optimal weight: 0.7980 overall best weight: 0.3570 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.163648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.137604 restraints weight = 7195.170| |-----------------------------------------------------------------------------| r_work (start): 0.3897 rms_B_bonded: 2.35 r_work: 0.3776 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.7243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 5052 Z= 0.149 Angle : 0.513 9.131 6912 Z= 0.266 Chirality : 0.036 0.147 906 Planarity : 0.002 0.030 798 Dihedral : 7.281 55.456 1032 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 3.33 % Allowed : 23.15 % Favored : 73.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.31 (0.32), residues: 600 helix: 3.30 (0.21), residues: 522 sheet: None (None), residues: 0 loop : -0.74 (0.68), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 99 HIS 0.001 0.000 HIS D 26 PHE 0.007 0.001 PHE E 114 TYR 0.005 0.001 TYR F 63 ARG 0.008 0.001 ARG A 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 143 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 125 time to evaluate : 0.608 Fit side-chains revert: symmetry clash REVERT: F 35 GLU cc_start: 0.8230 (tt0) cc_final: 0.7982 (tm-30) REVERT: F 91 ASN cc_start: 0.8011 (t0) cc_final: 0.7749 (t0) REVERT: F 121 PHE cc_start: 0.8509 (OUTLIER) cc_final: 0.8292 (t80) REVERT: F 123 THR cc_start: 0.7727 (m) cc_final: 0.7515 (p) REVERT: A 51 LYS cc_start: 0.7689 (tppt) cc_final: 0.6614 (ttmt) REVERT: A 103 GLN cc_start: 0.8241 (mm-40) cc_final: 0.7479 (mt0) REVERT: A 114 PHE cc_start: 0.8123 (m-80) cc_final: 0.7884 (m-10) REVERT: C 48 MET cc_start: 0.8618 (mmm) cc_final: 0.8179 (mmm) REVERT: C 53 VAL cc_start: 0.8006 (t) cc_final: 0.7716 (p) REVERT: C 72 LEU cc_start: 0.7733 (OUTLIER) cc_final: 0.7430 (mt) REVERT: C 121 PHE cc_start: 0.8284 (OUTLIER) cc_final: 0.8013 (t80) REVERT: D 48 MET cc_start: 0.7732 (OUTLIER) cc_final: 0.7270 (mtt) REVERT: D 84 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7647 (mm) REVERT: D 97 LYS cc_start: 0.6008 (ptpp) cc_final: 0.5795 (pttt) REVERT: B 44 MET cc_start: 0.8486 (tmm) cc_final: 0.8103 (tmm) REVERT: B 48 MET cc_start: 0.7388 (mtt) cc_final: 0.6951 (mtt) REVERT: B 100 ARG cc_start: 0.7359 (mmt-90) cc_final: 0.6636 (tpt90) outliers start: 18 outliers final: 11 residues processed: 136 average time/residue: 0.2630 time to fit residues: 45.1403 Evaluate side-chains 134 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 118 time to evaluate : 0.774 ------------------------------------------------------------------------------- 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 F residue 121 PHE Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 72 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 29 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 27 optimal weight: 0.0470 chunk 54 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN A 77 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.164846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.138782 restraints weight = 7166.571| |-----------------------------------------------------------------------------| r_work (start): 0.3886 rms_B_bonded: 2.31 r_work: 0.3763 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.7302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 5052 Z= 0.173 Angle : 0.538 8.433 6912 Z= 0.276 Chirality : 0.037 0.151 906 Planarity : 0.002 0.031 798 Dihedral : 7.251 54.960 1032 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.96 % Allowed : 24.44 % Favored : 72.59 % 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: 4.25 (0.32), residues: 600 helix: 3.25 (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 0.013 0.002 TRP D 99 HIS 0.001 0.000 HIS D 26 PHE 0.019 0.001 PHE C 114 TYR 0.013 0.001 TYR B 62 ARG 0.008 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 135 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 119 time to evaluate : 0.642 Fit side-chains revert: symmetry clash REVERT: F 35 GLU cc_start: 0.8231 (tt0) cc_final: 0.7975 (tm-30) REVERT: F 91 ASN cc_start: 0.8025 (t0) cc_final: 0.7782 (t0) REVERT: F 121 PHE cc_start: 0.8525 (OUTLIER) cc_final: 0.8279 (t80) REVERT: A 51 LYS cc_start: 0.7684 (tppt) cc_final: 0.6621 (ttmt) REVERT: C 48 MET cc_start: 0.8641 (mmm) cc_final: 0.8190 (mmm) REVERT: C 72 LEU cc_start: 0.7744 (OUTLIER) cc_final: 0.7406 (mt) REVERT: C 121 PHE cc_start: 0.8276 (OUTLIER) cc_final: 0.8014 (t80) REVERT: E 55 GLU cc_start: 0.8117 (tm-30) cc_final: 0.7882 (tm-30) REVERT: D 48 MET cc_start: 0.7566 (OUTLIER) cc_final: 0.7175 (mtt) REVERT: D 84 LEU cc_start: 0.8092 (OUTLIER) cc_final: 0.7839 (mm) REVERT: D 97 LYS cc_start: 0.5917 (ptpp) cc_final: 0.5582 (pttt) REVERT: B 44 MET cc_start: 0.8485 (tmm) cc_final: 0.8280 (tpp) REVERT: B 48 MET cc_start: 0.7394 (mtt) cc_final: 0.7031 (mtt) REVERT: B 100 ARG cc_start: 0.7362 (mmt-90) cc_final: 0.6635 (tpt90) outliers start: 16 outliers final: 10 residues processed: 129 average time/residue: 0.2305 time to fit residues: 37.5505 Evaluate side-chains 133 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 118 time to evaluate : 0.479 ------------------------------------------------------------------------------- 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 F residue 121 PHE Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 72 LEU 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 72 LEU 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 40 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 14 optimal weight: 0.5980 chunk 59 optimal weight: 0.6980 chunk 42 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.163879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.137691 restraints weight = 7135.140| |-----------------------------------------------------------------------------| r_work (start): 0.3890 rms_B_bonded: 2.33 r_work: 0.3760 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.7397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 5052 Z= 0.183 Angle : 0.545 7.757 6912 Z= 0.280 Chirality : 0.038 0.151 906 Planarity : 0.002 0.031 798 Dihedral : 7.317 55.347 1032 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.78 % Allowed : 24.81 % Favored : 72.41 % 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: 4.21 (0.32), residues: 600 helix: 3.22 (0.21), residues: 522 sheet: None (None), residues: 0 loop : -0.66 (0.69), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 99 HIS 0.001 0.000 HIS D 26 PHE 0.028 0.001 PHE F 114 TYR 0.010 0.001 TYR E 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: 2959.31 seconds wall clock time: 56 minutes 21.74 seconds (3381.74 seconds total)