Starting phenix.real_space_refine on Sun Dec 29 08:02:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f6r_28889/12_2024/8f6r_28889.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f6r_28889/12_2024/8f6r_28889.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8f6r_28889/12_2024/8f6r_28889.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f6r_28889/12_2024/8f6r_28889.map" model { file = "/net/cci-nas-00/data/ceres_data/8f6r_28889/12_2024/8f6r_28889.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f6r_28889/12_2024/8f6r_28889.cif" } resolution = 4.0 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= 0.003 sd= 0.057 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 12 5.16 5 C 6348 2.51 5 N 1872 2.21 5 O 2058 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 10290 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1715 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 7, 'TRANS': 211} Restraints were copied for chains: C, B, E, D, F Time building chain proxies: 3.50, per 1000 atoms: 0.34 Number of scatterers: 10290 At special positions: 0 Unit cell: (125.073, 129.349, 54.519, 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 12 16.00 O 2058 8.00 N 1872 7.00 C 6348 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: 3.03 Conformation dependent library (CDL) restraints added in 1.3 seconds 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2580 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 0 sheets defined 96.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'A' and resid 3 through 29 Processing helix chain 'A' and resid 30 through 54 removed outlier: 4.072A pdb=" N LEU A 43 " --> pdb=" O GLU A 39 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASP A 54 " --> pdb=" O GLU A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 85 Processing helix chain 'A' and resid 86 through 110 Processing helix chain 'A' and resid 113 through 141 Processing helix chain 'A' and resid 142 through 166 removed outlier: 3.542A pdb=" N ASN A 166 " --> pdb=" O GLU A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 197 Processing helix chain 'A' and resid 198 through 220 removed outlier: 3.940A pdb=" N ARG A 202 " --> pdb=" O ASP A 198 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU A 218 " --> pdb=" O GLU A 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 29 Processing helix chain 'B' and resid 30 through 54 removed outlier: 4.073A pdb=" N LEU B 43 " --> pdb=" O GLU B 39 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASP B 54 " --> pdb=" O GLU B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 85 Processing helix chain 'B' and resid 86 through 110 Processing helix chain 'B' and resid 113 through 141 Processing helix chain 'B' and resid 142 through 166 removed outlier: 3.542A pdb=" N ASN B 166 " --> pdb=" O GLU B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 197 Processing helix chain 'B' and resid 198 through 220 removed outlier: 3.939A pdb=" N ARG B 202 " --> pdb=" O ASP B 198 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU B 218 " --> pdb=" O GLU B 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 29 Processing helix chain 'C' and resid 30 through 54 removed outlier: 4.072A pdb=" N LEU C 43 " --> pdb=" O GLU C 39 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASP C 54 " --> pdb=" O GLU C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 85 Processing helix chain 'C' and resid 86 through 110 Processing helix chain 'C' and resid 113 through 141 Processing helix chain 'C' and resid 142 through 166 removed outlier: 3.543A pdb=" N ASN C 166 " --> pdb=" O GLU C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 197 Processing helix chain 'C' and resid 198 through 220 removed outlier: 3.940A pdb=" N ARG C 202 " --> pdb=" O ASP C 198 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU C 218 " --> pdb=" O GLU C 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 4 through 29 Processing helix chain 'D' and resid 30 through 54 removed outlier: 4.072A pdb=" N LEU D 43 " --> pdb=" O GLU D 39 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASP D 54 " --> pdb=" O GLU D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 85 Processing helix chain 'D' and resid 86 through 110 Processing helix chain 'D' and resid 113 through 141 Processing helix chain 'D' and resid 142 through 166 removed outlier: 3.542A pdb=" N ASN D 166 " --> pdb=" O GLU D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 169 through 197 Processing helix chain 'D' and resid 198 through 220 removed outlier: 3.939A pdb=" N ARG D 202 " --> pdb=" O ASP D 198 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU D 218 " --> pdb=" O GLU D 214 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 29 Processing helix chain 'E' and resid 30 through 54 removed outlier: 4.072A pdb=" N LEU E 43 " --> pdb=" O GLU E 39 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASP E 54 " --> pdb=" O GLU E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 85 Processing helix chain 'E' and resid 86 through 110 Processing helix chain 'E' and resid 113 through 141 Processing helix chain 'E' and resid 142 through 166 removed outlier: 3.542A pdb=" N ASN E 166 " --> pdb=" O GLU E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 169 through 197 Processing helix chain 'E' and resid 198 through 220 removed outlier: 3.939A pdb=" N ARG E 202 " --> pdb=" O ASP E 198 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU E 218 " --> pdb=" O GLU E 214 " (cutoff:3.500A) Processing helix chain 'F' and resid 4 through 29 Processing helix chain 'F' and resid 30 through 54 removed outlier: 4.072A pdb=" N LEU F 43 " --> pdb=" O GLU F 39 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASP F 54 " --> pdb=" O GLU F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 85 Processing helix chain 'F' and resid 86 through 110 Processing helix chain 'F' and resid 113 through 141 Processing helix chain 'F' and resid 142 through 166 removed outlier: 3.542A pdb=" N ASN F 166 " --> pdb=" O GLU F 162 " (cutoff:3.500A) Processing helix chain 'F' and resid 169 through 197 Processing helix chain 'F' and resid 198 through 220 removed outlier: 3.940A pdb=" N ARG F 202 " --> pdb=" O ASP F 198 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU F 218 " --> pdb=" O GLU F 214 " (cutoff:3.500A) 1045 hydrogen bonds defined for protein. 3135 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.21 Time building geometry restraints manager: 3.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3786 1.34 - 1.46: 571 1.46 - 1.57: 5987 1.57 - 1.69: 0 1.69 - 1.80: 24 Bond restraints: 10368 Sorted by residual: bond pdb=" CB TRP C 52 " pdb=" CG TRP C 52 " ideal model delta sigma weight residual 1.498 1.447 0.051 3.10e-02 1.04e+03 2.67e+00 bond pdb=" CB TRP F 52 " pdb=" CG TRP F 52 " ideal model delta sigma weight residual 1.498 1.448 0.050 3.10e-02 1.04e+03 2.64e+00 bond pdb=" CB TRP B 52 " pdb=" CG TRP B 52 " ideal model delta sigma weight residual 1.498 1.448 0.050 3.10e-02 1.04e+03 2.62e+00 bond pdb=" CB TRP E 52 " pdb=" CG TRP E 52 " ideal model delta sigma weight residual 1.498 1.448 0.050 3.10e-02 1.04e+03 2.58e+00 bond pdb=" CB TRP A 52 " pdb=" CG TRP A 52 " ideal model delta sigma weight residual 1.498 1.448 0.050 3.10e-02 1.04e+03 2.57e+00 ... (remaining 10363 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 13621 1.78 - 3.55: 305 3.55 - 5.33: 72 5.33 - 7.11: 24 7.11 - 8.88: 6 Bond angle restraints: 14028 Sorted by residual: angle pdb=" N SER B 58 " pdb=" CA SER B 58 " pdb=" C SER B 58 " ideal model delta sigma weight residual 111.28 120.16 -8.88 1.09e+00 8.42e-01 6.64e+01 angle pdb=" N SER A 58 " pdb=" CA SER A 58 " pdb=" C SER A 58 " ideal model delta sigma weight residual 111.28 120.16 -8.88 1.09e+00 8.42e-01 6.63e+01 angle pdb=" N SER D 58 " pdb=" CA SER D 58 " pdb=" C SER D 58 " ideal model delta sigma weight residual 111.28 120.14 -8.86 1.09e+00 8.42e-01 6.61e+01 angle pdb=" N SER C 58 " pdb=" CA SER C 58 " pdb=" C SER C 58 " ideal model delta sigma weight residual 111.28 120.13 -8.85 1.09e+00 8.42e-01 6.59e+01 angle pdb=" N SER F 58 " pdb=" CA SER F 58 " pdb=" C SER F 58 " ideal model delta sigma weight residual 111.28 120.12 -8.84 1.09e+00 8.42e-01 6.58e+01 ... (remaining 14023 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.27: 5694 13.27 - 26.55: 690 26.55 - 39.82: 198 39.82 - 53.10: 42 53.10 - 66.37: 18 Dihedral angle restraints: 6642 sinusoidal: 2754 harmonic: 3888 Sorted by residual: dihedral pdb=" CA TRP E 52 " pdb=" C TRP E 52 " pdb=" N LEU E 53 " pdb=" CA LEU E 53 " ideal model delta harmonic sigma weight residual -180.00 -163.09 -16.91 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CA TRP A 52 " pdb=" C TRP A 52 " pdb=" N LEU A 53 " pdb=" CA LEU A 53 " ideal model delta harmonic sigma weight residual -180.00 -163.12 -16.88 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CA TRP F 52 " pdb=" C TRP F 52 " pdb=" N LEU F 53 " pdb=" CA LEU F 53 " ideal model delta harmonic sigma weight residual 180.00 -163.14 -16.86 0 5.00e+00 4.00e-02 1.14e+01 ... (remaining 6639 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1473 0.061 - 0.122: 164 0.122 - 0.183: 13 0.183 - 0.244: 6 0.244 - 0.305: 6 Chirality restraints: 1662 Sorted by residual: chirality pdb=" CA SER B 58 " pdb=" N SER B 58 " pdb=" C SER B 58 " pdb=" CB SER B 58 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.32e+00 chirality pdb=" CA SER F 58 " pdb=" N SER F 58 " pdb=" C SER F 58 " pdb=" CB SER F 58 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.32e+00 chirality pdb=" CA SER D 58 " pdb=" N SER D 58 " pdb=" C SER D 58 " pdb=" CB SER D 58 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.31e+00 ... (remaining 1659 not shown) Planarity restraints: 1884 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP C 86 " 0.029 5.00e-02 4.00e+02 4.43e-02 3.14e+00 pdb=" N PRO C 87 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO C 87 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 87 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP E 86 " 0.029 5.00e-02 4.00e+02 4.42e-02 3.12e+00 pdb=" N PRO E 87 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO E 87 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO E 87 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 86 " -0.029 5.00e-02 4.00e+02 4.41e-02 3.11e+00 pdb=" N PRO A 87 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 87 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 87 " -0.025 5.00e-02 4.00e+02 ... (remaining 1881 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 42 2.58 - 3.16: 9766 3.16 - 3.74: 17399 3.74 - 4.32: 20508 4.32 - 4.90: 33156 Nonbonded interactions: 80871 Sorted by model distance: nonbonded pdb=" OE2 GLU F 11 " pdb=" NH2 ARG F 15 " model vdw 1.997 3.120 nonbonded pdb=" OE2 GLU B 11 " pdb=" NH2 ARG B 15 " model vdw 1.998 3.120 nonbonded pdb=" OE2 GLU D 11 " pdb=" NH2 ARG D 15 " model vdw 1.998 3.120 nonbonded pdb=" OE2 GLU C 11 " pdb=" NH2 ARG C 15 " model vdw 1.998 3.120 nonbonded pdb=" OE2 GLU A 11 " pdb=" NH2 ARG A 15 " model vdw 1.998 3.120 ... (remaining 80866 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 group one per residue 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: 0.700 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: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 22.970 Find NCS groups from input model: 0.350 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 10368 Z= 0.331 Angle : 0.751 8.883 14028 Z= 0.474 Chirality : 0.043 0.305 1662 Planarity : 0.005 0.044 1884 Dihedral : 12.985 66.374 4062 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 17.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % 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: -1.46 (0.20), residues: 1302 helix: -0.69 (0.13), residues: 1248 sheet: None (None), residues: 0 loop : -2.81 (0.56), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 52 PHE 0.002 0.000 PHE B 185 ARG 0.002 0.000 ARG F 76 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 364 time to evaluate : 1.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.8003 (tm-30) cc_final: 0.7800 (tm-30) REVERT: A 110 ASN cc_start: 0.8677 (m110) cc_final: 0.8269 (t0) REVERT: A 121 LYS cc_start: 0.9440 (mttt) cc_final: 0.9078 (mtpp) REVERT: A 142 ASP cc_start: 0.8086 (t0) cc_final: 0.7856 (t0) REVERT: A 183 ILE cc_start: 0.9127 (mt) cc_final: 0.8831 (tp) REVERT: B 121 LYS cc_start: 0.9445 (mttt) cc_final: 0.9042 (mtpp) REVERT: B 142 ASP cc_start: 0.8038 (t0) cc_final: 0.7561 (t0) REVERT: B 185 PHE cc_start: 0.8784 (t80) cc_final: 0.8562 (t80) REVERT: C 110 ASN cc_start: 0.8679 (m110) cc_final: 0.8089 (t0) REVERT: C 121 LYS cc_start: 0.9417 (mttt) cc_final: 0.9041 (mtpt) REVERT: C 142 ASP cc_start: 0.8128 (t0) cc_final: 0.7719 (t0) REVERT: C 183 ILE cc_start: 0.9199 (mt) cc_final: 0.8981 (tp) REVERT: C 185 PHE cc_start: 0.8818 (t80) cc_final: 0.8171 (t80) REVERT: D 12 GLU cc_start: 0.8658 (tp30) cc_final: 0.8448 (tp30) REVERT: D 110 ASN cc_start: 0.8653 (m110) cc_final: 0.8405 (m110) REVERT: D 121 LYS cc_start: 0.9431 (mttt) cc_final: 0.9120 (mtpp) REVERT: D 183 ILE cc_start: 0.9079 (mt) cc_final: 0.8811 (tp) REVERT: D 185 PHE cc_start: 0.8747 (t80) cc_final: 0.8460 (t80) REVERT: E 110 ASN cc_start: 0.8714 (m110) cc_final: 0.8275 (t0) REVERT: E 121 LYS cc_start: 0.9412 (mttt) cc_final: 0.9132 (mtpp) REVERT: E 142 ASP cc_start: 0.7971 (t0) cc_final: 0.7522 (t0) REVERT: E 183 ILE cc_start: 0.9170 (mt) cc_final: 0.8923 (tp) REVERT: F 110 ASN cc_start: 0.8649 (m110) cc_final: 0.8260 (t0) REVERT: F 121 LYS cc_start: 0.9451 (mttt) cc_final: 0.9048 (mtpt) REVERT: F 185 PHE cc_start: 0.9000 (t80) cc_final: 0.8268 (t80) outliers start: 0 outliers final: 0 residues processed: 364 average time/residue: 0.2548 time to fit residues: 124.1382 Evaluate side-chains 205 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 205 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 0.9990 chunk 95 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 32 optimal weight: 7.9990 chunk 64 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 98 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 73 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 ASN B 117 ASN B 173 ASN ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 ASN D 173 ASN E 173 ASN ** F 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 173 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10368 Z= 0.232 Angle : 0.609 9.680 14028 Z= 0.319 Chirality : 0.040 0.345 1662 Planarity : 0.005 0.034 1884 Dihedral : 3.452 13.250 1458 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.76 % Allowed : 12.95 % Favored : 84.29 % 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: 2.20 (0.21), residues: 1302 helix: 1.69 (0.13), residues: 1248 sheet: None (None), residues: 0 loop : -3.75 (0.60), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 201 PHE 0.025 0.002 PHE A 185 ARG 0.004 0.000 ARG C 165 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 278 time to evaluate : 1.241 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 110 ASN cc_start: 0.8607 (m110) cc_final: 0.8038 (t0) REVERT: A 121 LYS cc_start: 0.9425 (mttt) cc_final: 0.9134 (mtpp) REVERT: A 142 ASP cc_start: 0.8288 (t0) cc_final: 0.7899 (t0) REVERT: A 152 LEU cc_start: 0.9333 (pp) cc_final: 0.8896 (tp) REVERT: A 190 LEU cc_start: 0.9246 (mt) cc_final: 0.8944 (mt) REVERT: B 118 GLU cc_start: 0.8658 (mm-30) cc_final: 0.7960 (mt-10) REVERT: B 121 LYS cc_start: 0.9422 (mttt) cc_final: 0.9208 (mtpp) REVERT: B 142 ASP cc_start: 0.7865 (t0) cc_final: 0.7577 (t0) REVERT: B 164 GLN cc_start: 0.8498 (tt0) cc_final: 0.8225 (tt0) REVERT: C 110 ASN cc_start: 0.8714 (m110) cc_final: 0.7996 (t0) REVERT: C 121 LYS cc_start: 0.9406 (mttt) cc_final: 0.9130 (mtpt) REVERT: C 142 ASP cc_start: 0.8163 (t0) cc_final: 0.7879 (t0) REVERT: D 58 SER cc_start: 0.8672 (m) cc_final: 0.8274 (p) REVERT: D 110 ASN cc_start: 0.8483 (m110) cc_final: 0.7880 (t0) REVERT: D 121 LYS cc_start: 0.9428 (mttt) cc_final: 0.9147 (mtpp) REVERT: D 152 LEU cc_start: 0.9291 (pp) cc_final: 0.8900 (tp) REVERT: E 110 ASN cc_start: 0.8615 (m110) cc_final: 0.8050 (t0) REVERT: E 142 ASP cc_start: 0.7960 (t0) cc_final: 0.7655 (t0) REVERT: E 152 LEU cc_start: 0.9326 (pp) cc_final: 0.8860 (tp) REVERT: E 164 GLN cc_start: 0.8547 (tt0) cc_final: 0.8338 (tt0) REVERT: F 110 ASN cc_start: 0.8675 (m110) cc_final: 0.8025 (t0) REVERT: F 121 LYS cc_start: 0.9424 (mttt) cc_final: 0.9116 (mtpt) REVERT: F 142 ASP cc_start: 0.7813 (t0) cc_final: 0.7528 (t0) REVERT: F 185 PHE cc_start: 0.8753 (t80) cc_final: 0.8173 (t80) outliers start: 29 outliers final: 20 residues processed: 293 average time/residue: 0.2140 time to fit residues: 88.5955 Evaluate side-chains 238 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 218 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 59 ASP Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 59 ASP Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain E residue 22 ILE Chi-restraints excluded: chain E residue 59 ASP Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 180 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 63 optimal weight: 9.9990 chunk 35 optimal weight: 0.7980 chunk 95 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 chunk 31 optimal weight: 6.9990 chunk 114 optimal weight: 0.9980 chunk 123 optimal weight: 0.6980 chunk 102 optimal weight: 0.7980 chunk 113 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 164 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10368 Z= 0.200 Angle : 0.583 10.078 14028 Z= 0.302 Chirality : 0.039 0.382 1662 Planarity : 0.004 0.032 1884 Dihedral : 3.429 12.901 1458 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.76 % Allowed : 17.62 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.91 (0.22), residues: 1302 helix: 2.18 (0.14), residues: 1242 sheet: None (None), residues: 0 loop : -3.95 (0.58), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 201 PHE 0.017 0.003 PHE A 185 ARG 0.005 0.000 ARG D 27 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 237 time to evaluate : 1.213 Fit side-chains REVERT: A 16 GLU cc_start: 0.8575 (mm-30) cc_final: 0.8322 (mm-30) REVERT: A 58 SER cc_start: 0.8743 (m) cc_final: 0.8312 (p) REVERT: A 110 ASN cc_start: 0.8602 (m110) cc_final: 0.7902 (t0) REVERT: A 121 LYS cc_start: 0.9451 (mttt) cc_final: 0.9162 (mtpp) REVERT: A 142 ASP cc_start: 0.8329 (t0) cc_final: 0.8047 (t0) REVERT: A 178 LYS cc_start: 0.9313 (mttm) cc_final: 0.8948 (tppp) REVERT: B 121 LYS cc_start: 0.9466 (mttt) cc_final: 0.9257 (mtpp) REVERT: B 142 ASP cc_start: 0.7856 (t0) cc_final: 0.7512 (t0) REVERT: B 164 GLN cc_start: 0.8605 (tt0) cc_final: 0.8305 (tp40) REVERT: C 110 ASN cc_start: 0.8771 (m110) cc_final: 0.7919 (t0) REVERT: C 121 LYS cc_start: 0.9401 (mttt) cc_final: 0.9163 (mtpt) REVERT: C 142 ASP cc_start: 0.8081 (t0) cc_final: 0.7772 (t0) REVERT: C 152 LEU cc_start: 0.9434 (OUTLIER) cc_final: 0.8944 (tt) REVERT: C 181 LYS cc_start: 0.9513 (ttmt) cc_final: 0.9307 (mmmt) REVERT: D 58 SER cc_start: 0.8711 (m) cc_final: 0.8237 (p) REVERT: D 121 LYS cc_start: 0.9429 (mttt) cc_final: 0.9173 (mtpp) REVERT: D 188 MET cc_start: 0.9135 (mtp) cc_final: 0.8865 (mtp) REVERT: E 110 ASN cc_start: 0.8588 (m110) cc_final: 0.7995 (t0) REVERT: E 142 ASP cc_start: 0.7819 (t0) cc_final: 0.7538 (t0) REVERT: E 164 GLN cc_start: 0.8591 (tt0) cc_final: 0.8353 (tt0) REVERT: E 183 ILE cc_start: 0.9105 (mt) cc_final: 0.8755 (tp) REVERT: F 110 ASN cc_start: 0.8684 (m110) cc_final: 0.7938 (t0) REVERT: F 118 GLU cc_start: 0.8650 (mm-30) cc_final: 0.7973 (mt-10) REVERT: F 121 LYS cc_start: 0.9450 (mttt) cc_final: 0.9197 (mtpt) REVERT: F 142 ASP cc_start: 0.7895 (t0) cc_final: 0.7545 (t0) REVERT: F 185 PHE cc_start: 0.8709 (t80) cc_final: 0.8139 (t80) REVERT: F 204 MET cc_start: 0.8590 (ttm) cc_final: 0.8341 (ttm) outliers start: 29 outliers final: 17 residues processed: 252 average time/residue: 0.2110 time to fit residues: 76.1107 Evaluate side-chains 235 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 217 time to evaluate : 1.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain E residue 22 ILE Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 51 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 6.9990 chunk 86 optimal weight: 6.9990 chunk 59 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 115 optimal weight: 1.9990 chunk 121 optimal weight: 5.9990 chunk 60 optimal weight: 0.6980 chunk 109 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 164 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.3725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10368 Z= 0.192 Angle : 0.580 11.381 14028 Z= 0.298 Chirality : 0.037 0.368 1662 Planarity : 0.004 0.029 1884 Dihedral : 3.424 13.098 1458 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 3.52 % Allowed : 16.67 % Favored : 79.81 % 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: 3.03 (0.22), residues: 1302 helix: 2.24 (0.14), residues: 1248 sheet: None (None), residues: 0 loop : -3.93 (0.66), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 201 PHE 0.006 0.001 PHE A 185 ARG 0.004 0.000 ARG C 27 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 245 time to evaluate : 1.310 Fit side-chains revert: symmetry clash REVERT: A 16 GLU cc_start: 0.8594 (mm-30) cc_final: 0.8309 (mm-30) REVERT: A 58 SER cc_start: 0.8673 (m) cc_final: 0.8218 (p) REVERT: A 121 LYS cc_start: 0.9465 (mttt) cc_final: 0.9210 (mtpp) REVERT: A 142 ASP cc_start: 0.8303 (t0) cc_final: 0.7989 (t0) REVERT: A 178 LYS cc_start: 0.9294 (mttm) cc_final: 0.9040 (mmmm) REVERT: A 182 LEU cc_start: 0.9361 (mt) cc_final: 0.8792 (tt) REVERT: A 196 ILE cc_start: 0.8988 (tp) cc_final: 0.8694 (tp) REVERT: B 142 ASP cc_start: 0.7768 (t0) cc_final: 0.7292 (t0) REVERT: B 164 GLN cc_start: 0.8486 (tt0) cc_final: 0.8244 (tt0) REVERT: C 12 GLU cc_start: 0.8713 (tp30) cc_final: 0.8502 (tp30) REVERT: C 110 ASN cc_start: 0.8742 (m110) cc_final: 0.7952 (t0) REVERT: C 121 LYS cc_start: 0.9433 (mttt) cc_final: 0.9216 (mtpp) REVERT: C 142 ASP cc_start: 0.8149 (t0) cc_final: 0.7820 (t0) REVERT: D 58 SER cc_start: 0.8800 (m) cc_final: 0.8332 (p) REVERT: D 121 LYS cc_start: 0.9447 (mttt) cc_final: 0.9206 (mtpp) REVERT: D 152 LEU cc_start: 0.9350 (OUTLIER) cc_final: 0.8956 (tt) REVERT: D 188 MET cc_start: 0.9143 (mtp) cc_final: 0.8842 (mtp) REVERT: E 142 ASP cc_start: 0.7888 (t0) cc_final: 0.7490 (t0) REVERT: F 110 ASN cc_start: 0.8794 (m110) cc_final: 0.7855 (t0) REVERT: F 121 LYS cc_start: 0.9472 (mttt) cc_final: 0.9220 (mtpt) REVERT: F 142 ASP cc_start: 0.7618 (t0) cc_final: 0.7313 (t0) REVERT: F 185 PHE cc_start: 0.8689 (t80) cc_final: 0.8106 (t80) outliers start: 37 outliers final: 17 residues processed: 271 average time/residue: 0.2175 time to fit residues: 83.4524 Evaluate side-chains 241 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 223 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain E residue 22 ILE Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 51 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 chunk 1 optimal weight: 10.0000 chunk 90 optimal weight: 5.9990 chunk 50 optimal weight: 0.9990 chunk 103 optimal weight: 10.0000 chunk 84 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 62 optimal weight: 7.9990 chunk 109 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN C 220 GLN D 220 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.3815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10368 Z= 0.289 Angle : 0.659 12.289 14028 Z= 0.336 Chirality : 0.040 0.391 1662 Planarity : 0.004 0.025 1884 Dihedral : 3.435 13.594 1458 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 3.14 % Allowed : 19.52 % Favored : 77.33 % 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: 2.66 (0.22), residues: 1302 helix: 1.98 (0.13), residues: 1254 sheet: None (None), residues: 0 loop : -4.31 (0.67), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 201 PHE 0.014 0.003 PHE C 185 ARG 0.004 0.000 ARG C 15 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 212 time to evaluate : 1.309 Fit side-chains REVERT: A 58 SER cc_start: 0.8869 (m) cc_final: 0.8459 (p) REVERT: A 121 LYS cc_start: 0.9473 (mttt) cc_final: 0.9159 (mtpp) REVERT: A 142 ASP cc_start: 0.8154 (t0) cc_final: 0.7828 (t0) REVERT: A 178 LYS cc_start: 0.9330 (mttm) cc_final: 0.8952 (tppp) REVERT: B 142 ASP cc_start: 0.7832 (t0) cc_final: 0.7456 (t0) REVERT: B 164 GLN cc_start: 0.8578 (tt0) cc_final: 0.8270 (tt0) REVERT: C 121 LYS cc_start: 0.9436 (mttt) cc_final: 0.9172 (mtpt) REVERT: C 142 ASP cc_start: 0.8032 (t0) cc_final: 0.7668 (t0) REVERT: D 58 SER cc_start: 0.8863 (m) cc_final: 0.8388 (p) REVERT: D 121 LYS cc_start: 0.9452 (mttt) cc_final: 0.9202 (mtpp) REVERT: E 142 ASP cc_start: 0.7938 (t0) cc_final: 0.7529 (t0) REVERT: E 178 LYS cc_start: 0.9199 (mtpp) cc_final: 0.8968 (tppp) REVERT: E 181 LYS cc_start: 0.9516 (mmtp) cc_final: 0.9126 (mmtt) REVERT: F 110 ASN cc_start: 0.8806 (m110) cc_final: 0.7868 (t0) REVERT: F 121 LYS cc_start: 0.9473 (mttt) cc_final: 0.9133 (mtpt) REVERT: F 142 ASP cc_start: 0.7613 (t0) cc_final: 0.7295 (t0) outliers start: 33 outliers final: 26 residues processed: 233 average time/residue: 0.2079 time to fit residues: 69.9228 Evaluate side-chains 227 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 201 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain E residue 22 ILE Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 204 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 10.0000 chunk 109 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 71 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 121 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 64 optimal weight: 7.9990 chunk 117 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 164 GLN F 220 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.4087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10368 Z= 0.205 Angle : 0.671 12.735 14028 Z= 0.325 Chirality : 0.042 0.400 1662 Planarity : 0.003 0.024 1884 Dihedral : 3.453 13.631 1458 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.76 % Allowed : 20.48 % Favored : 76.76 % 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: 2.90 (0.22), residues: 1302 helix: 2.14 (0.14), residues: 1254 sheet: None (None), residues: 0 loop : -4.19 (0.69), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 201 PHE 0.019 0.002 PHE F 185 ARG 0.002 0.000 ARG C 15 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 227 time to evaluate : 1.300 Fit side-chains REVERT: A 16 GLU cc_start: 0.8579 (mm-30) cc_final: 0.8338 (mm-30) REVERT: A 58 SER cc_start: 0.8895 (m) cc_final: 0.8511 (p) REVERT: A 142 ASP cc_start: 0.8120 (t0) cc_final: 0.7764 (t0) REVERT: A 178 LYS cc_start: 0.9279 (mttm) cc_final: 0.8876 (tppp) REVERT: A 181 LYS cc_start: 0.9471 (tppt) cc_final: 0.9042 (mmtt) REVERT: A 196 ILE cc_start: 0.9006 (tp) cc_final: 0.8711 (tp) REVERT: B 142 ASP cc_start: 0.7823 (t0) cc_final: 0.7500 (t0) REVERT: B 164 GLN cc_start: 0.8586 (tt0) cc_final: 0.8252 (tt0) REVERT: C 110 ASN cc_start: 0.8767 (m-40) cc_final: 0.7864 (t0) REVERT: C 142 ASP cc_start: 0.7791 (t0) cc_final: 0.7527 (t0) REVERT: D 58 SER cc_start: 0.8829 (m) cc_final: 0.8362 (p) REVERT: D 121 LYS cc_start: 0.9457 (mttt) cc_final: 0.9194 (mtpp) REVERT: E 142 ASP cc_start: 0.7901 (t0) cc_final: 0.7583 (t0) REVERT: E 181 LYS cc_start: 0.9442 (mmtp) cc_final: 0.8990 (mmtt) REVERT: E 196 ILE cc_start: 0.8684 (tp) cc_final: 0.8474 (tp) REVERT: F 110 ASN cc_start: 0.8740 (m110) cc_final: 0.7786 (t0) REVERT: F 142 ASP cc_start: 0.7527 (t0) cc_final: 0.7243 (t0) REVERT: F 204 MET cc_start: 0.8563 (OUTLIER) cc_final: 0.8328 (ttm) outliers start: 29 outliers final: 18 residues processed: 247 average time/residue: 0.2121 time to fit residues: 76.3462 Evaluate side-chains 222 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 203 time to evaluate : 1.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain E residue 22 ILE Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 144 GLU Chi-restraints excluded: chain F residue 204 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 0.6980 chunk 69 optimal weight: 0.9980 chunk 89 optimal weight: 7.9990 chunk 68 optimal weight: 0.9990 chunk 102 optimal weight: 0.5980 chunk 121 optimal weight: 2.9990 chunk 76 optimal weight: 0.0670 chunk 74 optimal weight: 6.9990 chunk 56 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN E 166 ASN E 220 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.4306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10368 Z= 0.199 Angle : 0.690 13.304 14028 Z= 0.334 Chirality : 0.043 0.408 1662 Planarity : 0.003 0.024 1884 Dihedral : 3.480 13.548 1458 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.29 % Allowed : 22.00 % Favored : 75.71 % 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: 2.90 (0.22), residues: 1302 helix: 2.13 (0.14), residues: 1254 sheet: None (None), residues: 0 loop : -4.13 (0.69), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 201 PHE 0.020 0.003 PHE F 185 ARG 0.003 0.000 ARG B 139 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 218 time to evaluate : 1.250 Fit side-chains revert: symmetry clash REVERT: A 16 GLU cc_start: 0.8592 (mm-30) cc_final: 0.8342 (mm-30) REVERT: A 58 SER cc_start: 0.8874 (m) cc_final: 0.8494 (p) REVERT: A 142 ASP cc_start: 0.8053 (t0) cc_final: 0.7740 (t0) REVERT: A 178 LYS cc_start: 0.9271 (mttm) cc_final: 0.8888 (tppp) REVERT: A 181 LYS cc_start: 0.9414 (tppt) cc_final: 0.8983 (mmtt) REVERT: A 188 MET cc_start: 0.8956 (mtp) cc_final: 0.8723 (mtp) REVERT: A 196 ILE cc_start: 0.8915 (tp) cc_final: 0.8619 (tp) REVERT: B 142 ASP cc_start: 0.7821 (t0) cc_final: 0.7470 (t0) REVERT: B 164 GLN cc_start: 0.8553 (tt0) cc_final: 0.8240 (tt0) REVERT: C 110 ASN cc_start: 0.8707 (m-40) cc_final: 0.7793 (t0) REVERT: C 142 ASP cc_start: 0.7891 (t0) cc_final: 0.7577 (t0) REVERT: D 58 SER cc_start: 0.8874 (m) cc_final: 0.8410 (p) REVERT: D 121 LYS cc_start: 0.9434 (mttt) cc_final: 0.9214 (mtpp) REVERT: E 142 ASP cc_start: 0.7924 (t0) cc_final: 0.7579 (t0) REVERT: E 181 LYS cc_start: 0.9314 (mmtp) cc_final: 0.8871 (mmtm) REVERT: F 110 ASN cc_start: 0.8768 (m110) cc_final: 0.7940 (t0) REVERT: F 142 ASP cc_start: 0.7590 (t0) cc_final: 0.7255 (t0) REVERT: F 204 MET cc_start: 0.8552 (OUTLIER) cc_final: 0.8329 (ttm) outliers start: 24 outliers final: 16 residues processed: 233 average time/residue: 0.1938 time to fit residues: 65.8129 Evaluate side-chains 218 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 201 time to evaluate : 1.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain E residue 22 ILE Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 144 GLU Chi-restraints excluded: chain F residue 204 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 23 optimal weight: 7.9990 chunk 77 optimal weight: 6.9990 chunk 82 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 chunk 11 optimal weight: 7.9990 chunk 95 optimal weight: 3.9990 chunk 110 optimal weight: 9.9990 chunk 116 optimal weight: 0.8980 chunk 106 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 GLN B 166 ASN C 166 ASN D 166 ASN F 220 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.4326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10368 Z= 0.231 Angle : 0.700 13.232 14028 Z= 0.344 Chirality : 0.043 0.415 1662 Planarity : 0.003 0.029 1884 Dihedral : 3.448 14.097 1458 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.19 % Allowed : 22.76 % Favored : 75.05 % 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: 2.80 (0.22), residues: 1302 helix: 2.07 (0.14), residues: 1254 sheet: None (None), residues: 0 loop : -4.11 (0.66), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 201 PHE 0.021 0.003 PHE F 185 ARG 0.002 0.000 ARG C 15 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 208 time to evaluate : 1.461 Fit side-chains REVERT: A 16 GLU cc_start: 0.8624 (mm-30) cc_final: 0.8354 (mm-30) REVERT: A 58 SER cc_start: 0.8920 (m) cc_final: 0.8553 (p) REVERT: A 142 ASP cc_start: 0.8121 (t0) cc_final: 0.7764 (t0) REVERT: A 178 LYS cc_start: 0.9275 (mttm) cc_final: 0.8900 (tppp) REVERT: A 196 ILE cc_start: 0.8933 (tp) cc_final: 0.8658 (tp) REVERT: A 220 GLN cc_start: 0.8150 (OUTLIER) cc_final: 0.7931 (tm-30) REVERT: B 142 ASP cc_start: 0.7962 (t0) cc_final: 0.7557 (t70) REVERT: B 164 GLN cc_start: 0.8598 (tt0) cc_final: 0.8229 (tt0) REVERT: C 110 ASN cc_start: 0.8758 (m-40) cc_final: 0.7784 (t0) REVERT: C 142 ASP cc_start: 0.7902 (t0) cc_final: 0.7555 (t0) REVERT: C 164 GLN cc_start: 0.8572 (tt0) cc_final: 0.8351 (mt0) REVERT: D 58 SER cc_start: 0.8942 (m) cc_final: 0.8489 (p) REVERT: E 142 ASP cc_start: 0.8045 (t0) cc_final: 0.7672 (t0) REVERT: E 178 LYS cc_start: 0.9204 (mtpp) cc_final: 0.8978 (tppt) REVERT: E 182 LEU cc_start: 0.9255 (mt) cc_final: 0.8612 (tt) REVERT: F 110 ASN cc_start: 0.8784 (m110) cc_final: 0.7917 (t0) REVERT: F 142 ASP cc_start: 0.7630 (t0) cc_final: 0.7332 (t0) REVERT: F 204 MET cc_start: 0.8577 (OUTLIER) cc_final: 0.8375 (ttm) outliers start: 23 outliers final: 18 residues processed: 221 average time/residue: 0.2039 time to fit residues: 65.3773 Evaluate side-chains 220 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 200 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 220 GLN Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain E residue 22 ILE Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 204 MET Chi-restraints excluded: chain F residue 215 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 5.9990 chunk 116 optimal weight: 7.9990 chunk 68 optimal weight: 0.0770 chunk 49 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 102 optimal weight: 0.7980 chunk 107 optimal weight: 0.8980 chunk 112 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 chunk 119 optimal weight: 0.9990 overall best weight: 0.7540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN D 166 ASN E 220 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.4472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 10368 Z= 0.205 Angle : 0.708 13.536 14028 Z= 0.348 Chirality : 0.043 0.417 1662 Planarity : 0.003 0.028 1884 Dihedral : 3.488 13.975 1458 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.00 % Allowed : 22.86 % Favored : 75.14 % 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: 2.85 (0.22), residues: 1302 helix: 2.10 (0.14), residues: 1254 sheet: None (None), residues: 0 loop : -4.13 (0.67), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 201 PHE 0.021 0.003 PHE F 185 ARG 0.002 0.000 ARG A 221 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 215 time to evaluate : 1.435 Fit side-chains REVERT: A 16 GLU cc_start: 0.8610 (mm-30) cc_final: 0.8337 (mm-30) REVERT: A 58 SER cc_start: 0.8880 (m) cc_final: 0.8494 (p) REVERT: A 142 ASP cc_start: 0.8099 (t0) cc_final: 0.7744 (t0) REVERT: A 178 LYS cc_start: 0.9268 (mttm) cc_final: 0.8924 (tppp) REVERT: A 188 MET cc_start: 0.8976 (mtp) cc_final: 0.8751 (mtp) REVERT: A 196 ILE cc_start: 0.8851 (tp) cc_final: 0.8566 (tp) REVERT: B 142 ASP cc_start: 0.7928 (t0) cc_final: 0.7526 (t0) REVERT: B 164 GLN cc_start: 0.8605 (tt0) cc_final: 0.8213 (tt0) REVERT: C 110 ASN cc_start: 0.8721 (m-40) cc_final: 0.7707 (t0) REVERT: C 125 ILE cc_start: 0.9158 (mm) cc_final: 0.8855 (mm) REVERT: C 142 ASP cc_start: 0.7843 (t0) cc_final: 0.7541 (t0) REVERT: C 164 GLN cc_start: 0.8577 (tt0) cc_final: 0.8356 (mt0) REVERT: D 58 SER cc_start: 0.8914 (m) cc_final: 0.8473 (p) REVERT: E 142 ASP cc_start: 0.7952 (t0) cc_final: 0.7592 (t0) REVERT: E 178 LYS cc_start: 0.9167 (mtpp) cc_final: 0.8953 (tppt) REVERT: E 181 LYS cc_start: 0.9368 (mmtp) cc_final: 0.8880 (mmtt) REVERT: E 182 LEU cc_start: 0.9209 (mt) cc_final: 0.8635 (tt) REVERT: F 79 GLU cc_start: 0.7777 (tm-30) cc_final: 0.7539 (tm-30) REVERT: F 110 ASN cc_start: 0.8782 (m110) cc_final: 0.7805 (t0) REVERT: F 142 ASP cc_start: 0.7641 (t0) cc_final: 0.7328 (t0) REVERT: F 204 MET cc_start: 0.8567 (OUTLIER) cc_final: 0.8323 (ttm) outliers start: 21 outliers final: 18 residues processed: 227 average time/residue: 0.2281 time to fit residues: 75.1629 Evaluate side-chains 220 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 201 time to evaluate : 1.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain E residue 22 ILE Chi-restraints excluded: chain E residue 43 LEU Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 204 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 0.0670 chunk 56 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 125 optimal weight: 4.9990 chunk 115 optimal weight: 3.9990 chunk 99 optimal weight: 0.6980 chunk 10 optimal weight: 0.2980 chunk 77 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 79 optimal weight: 8.9990 chunk 106 optimal weight: 0.9980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 166 ASN D 166 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.4564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 10368 Z= 0.211 Angle : 0.724 13.687 14028 Z= 0.355 Chirality : 0.043 0.417 1662 Planarity : 0.003 0.028 1884 Dihedral : 3.497 14.141 1458 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.62 % Allowed : 23.81 % Favored : 74.57 % 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: 2.86 (0.22), residues: 1302 helix: 2.11 (0.14), residues: 1254 sheet: None (None), residues: 0 loop : -4.19 (0.69), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 201 PHE 0.022 0.002 PHE F 185 ARG 0.002 0.000 ARG E 221 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 216 time to evaluate : 1.173 Fit side-chains REVERT: A 58 SER cc_start: 0.8893 (m) cc_final: 0.8543 (p) REVERT: A 142 ASP cc_start: 0.8061 (t0) cc_final: 0.7729 (t0) REVERT: A 178 LYS cc_start: 0.9259 (mttm) cc_final: 0.8891 (tppp) REVERT: A 188 MET cc_start: 0.8939 (mtp) cc_final: 0.8732 (mtp) REVERT: A 196 ILE cc_start: 0.8779 (tp) cc_final: 0.8494 (tp) REVERT: B 142 ASP cc_start: 0.7943 (t0) cc_final: 0.7556 (t70) REVERT: B 164 GLN cc_start: 0.8634 (tt0) cc_final: 0.8267 (tt0) REVERT: B 182 LEU cc_start: 0.9306 (mt) cc_final: 0.8672 (tt) REVERT: C 110 ASN cc_start: 0.8604 (m-40) cc_final: 0.7653 (t0) REVERT: C 125 ILE cc_start: 0.9182 (mm) cc_final: 0.8891 (mm) REVERT: C 142 ASP cc_start: 0.7836 (t0) cc_final: 0.7548 (t0) REVERT: C 164 GLN cc_start: 0.8621 (tt0) cc_final: 0.8367 (mt0) REVERT: D 58 SER cc_start: 0.8902 (m) cc_final: 0.8461 (p) REVERT: D 196 ILE cc_start: 0.8940 (tp) cc_final: 0.8690 (tp) REVERT: E 110 ASN cc_start: 0.8527 (m-40) cc_final: 0.7978 (t0) REVERT: E 142 ASP cc_start: 0.7896 (t0) cc_final: 0.7567 (t0) REVERT: E 178 LYS cc_start: 0.9162 (mtpp) cc_final: 0.8938 (tppt) REVERT: E 181 LYS cc_start: 0.9342 (mmtp) cc_final: 0.8819 (mmtt) REVERT: E 182 LEU cc_start: 0.9215 (mt) cc_final: 0.8665 (tt) REVERT: F 110 ASN cc_start: 0.8749 (m110) cc_final: 0.7767 (t0) REVERT: F 142 ASP cc_start: 0.7610 (t0) cc_final: 0.7262 (t0) REVERT: F 185 PHE cc_start: 0.8710 (t80) cc_final: 0.8218 (t80) REVERT: F 204 MET cc_start: 0.8555 (OUTLIER) cc_final: 0.8326 (ttm) outliers start: 17 outliers final: 15 residues processed: 226 average time/residue: 0.1995 time to fit residues: 65.3997 Evaluate side-chains 226 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 210 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain E residue 22 ILE Chi-restraints excluded: chain E residue 43 LEU Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 144 GLU Chi-restraints excluded: chain F residue 204 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 0.8980 chunk 92 optimal weight: 0.8980 chunk 14 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 100 optimal weight: 9.9990 chunk 41 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 chunk 87 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 166 ASN D 166 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.104261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.080612 restraints weight = 25252.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.083926 restraints weight = 16851.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.086256 restraints weight = 12835.403| |-----------------------------------------------------------------------------| r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.4680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 10368 Z= 0.212 Angle : 0.714 13.765 14028 Z= 0.352 Chirality : 0.043 0.417 1662 Planarity : 0.003 0.028 1884 Dihedral : 3.487 14.311 1458 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.71 % Allowed : 24.29 % Favored : 74.00 % 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: 2.89 (0.22), residues: 1302 helix: 2.15 (0.14), residues: 1248 sheet: None (None), residues: 0 loop : -4.14 (0.64), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 201 PHE 0.021 0.003 PHE F 185 ARG 0.002 0.000 ARG E 15 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2075.24 seconds wall clock time: 38 minutes 43.20 seconds (2323.20 seconds total)