Starting phenix.real_space_refine on Fri Jun 6 11:31:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fai_28957/06_2025/8fai_28957.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fai_28957/06_2025/8fai_28957.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fai_28957/06_2025/8fai_28957.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fai_28957/06_2025/8fai_28957.map" model { file = "/net/cci-nas-00/data/ceres_data/8fai_28957/06_2025/8fai_28957.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fai_28957/06_2025/8fai_28957.cif" } resolution = 3.0 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= 0.000 sd= 0.002 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: 5 Type Number sf(0) Gaussians P 15 5.49 5 S 60 5.16 5 C 5250 2.51 5 N 1140 2.21 5 O 1380 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 7845 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 472 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 2, 'TRANS': 65} Chain: "G" Number of atoms: 472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 472 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 2, 'TRANS': 65} Chain: "K" Number of atoms: 472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 472 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 2, 'TRANS': 65} Chain: "G" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'XL0': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 102 Unusual residues: {'XL0': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: C, B, E, D, F, I, H, J, M, L, O, N Time building chain proxies: 3.58, per 1000 atoms: 0.46 Number of scatterers: 7845 At special positions: 0 Unit cell: (87.36, 89.024, 93.184, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 60 16.00 P 15 15.00 O 1380 8.00 N 1140 7.00 C 5250 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 64 " - pdb=" SG CYS B 64 " distance=0.00 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 64 " distance=0.00 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=10, symmetry=0 Number of additional bonds: simple=10, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.22 Conformation dependent library (CDL) restraints added in 1.1 seconds 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1620 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 0 sheets defined 91.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'A' and resid 55 through 68 Processing helix chain 'A' and resid 69 through 89 Processing helix chain 'A' and resid 93 through 109 removed outlier: 3.751A pdb=" N VAL A 97 " --> pdb=" O SER A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 118 Processing helix chain 'B' and resid 55 through 68 Processing helix chain 'B' and resid 69 through 89 Processing helix chain 'B' and resid 93 through 109 removed outlier: 3.751A pdb=" N VAL B 97 " --> pdb=" O SER B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 118 Processing helix chain 'C' and resid 55 through 68 Processing helix chain 'C' and resid 69 through 89 Processing helix chain 'C' and resid 93 through 109 removed outlier: 3.751A pdb=" N VAL C 97 " --> pdb=" O SER C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 118 Processing helix chain 'D' and resid 55 through 68 Processing helix chain 'D' and resid 69 through 89 Processing helix chain 'D' and resid 93 through 109 removed outlier: 3.751A pdb=" N VAL D 97 " --> pdb=" O SER D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 118 Processing helix chain 'E' and resid 55 through 68 Processing helix chain 'E' and resid 69 through 89 Processing helix chain 'E' and resid 93 through 109 removed outlier: 3.751A pdb=" N VAL E 97 " --> pdb=" O SER E 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 118 Processing helix chain 'F' and resid 55 through 68 Processing helix chain 'F' and resid 69 through 89 Processing helix chain 'F' and resid 93 through 109 removed outlier: 3.751A pdb=" N VAL F 97 " --> pdb=" O SER F 93 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 118 Processing helix chain 'G' and resid 55 through 68 Processing helix chain 'G' and resid 69 through 89 Processing helix chain 'G' and resid 93 through 109 removed outlier: 3.752A pdb=" N VAL G 97 " --> pdb=" O SER G 93 " (cutoff:3.500A) Processing helix chain 'G' and resid 109 through 118 Processing helix chain 'H' and resid 55 through 68 Processing helix chain 'H' and resid 69 through 89 Processing helix chain 'H' and resid 93 through 109 removed outlier: 3.751A pdb=" N VAL H 97 " --> pdb=" O SER H 93 " (cutoff:3.500A) Processing helix chain 'H' and resid 109 through 118 Processing helix chain 'I' and resid 55 through 68 Processing helix chain 'I' and resid 69 through 89 Processing helix chain 'I' and resid 93 through 109 removed outlier: 3.751A pdb=" N VAL I 97 " --> pdb=" O SER I 93 " (cutoff:3.500A) Processing helix chain 'I' and resid 109 through 118 Processing helix chain 'J' and resid 55 through 68 Processing helix chain 'J' and resid 69 through 89 Processing helix chain 'J' and resid 93 through 109 removed outlier: 3.752A pdb=" N VAL J 97 " --> pdb=" O SER J 93 " (cutoff:3.500A) Processing helix chain 'J' and resid 109 through 118 Processing helix chain 'K' and resid 55 through 68 Processing helix chain 'K' and resid 69 through 89 Processing helix chain 'K' and resid 93 through 109 removed outlier: 3.751A pdb=" N VAL K 97 " --> pdb=" O SER K 93 " (cutoff:3.500A) Processing helix chain 'K' and resid 109 through 118 Processing helix chain 'L' and resid 55 through 68 Processing helix chain 'L' and resid 69 through 89 Processing helix chain 'L' and resid 93 through 109 removed outlier: 3.751A pdb=" N VAL L 97 " --> pdb=" O SER L 93 " (cutoff:3.500A) Processing helix chain 'L' and resid 109 through 118 Processing helix chain 'M' and resid 55 through 68 Processing helix chain 'M' and resid 69 through 89 Processing helix chain 'M' and resid 93 through 109 removed outlier: 3.751A pdb=" N VAL M 97 " --> pdb=" O SER M 93 " (cutoff:3.500A) Processing helix chain 'M' and resid 109 through 118 Processing helix chain 'N' and resid 55 through 68 Processing helix chain 'N' and resid 69 through 89 Processing helix chain 'N' and resid 93 through 109 removed outlier: 3.751A pdb=" N VAL N 97 " --> pdb=" O SER N 93 " (cutoff:3.500A) Processing helix chain 'N' and resid 109 through 118 Processing helix chain 'O' and resid 55 through 68 Processing helix chain 'O' and resid 69 through 89 Processing helix chain 'O' and resid 93 through 109 removed outlier: 3.751A pdb=" N VAL O 97 " --> pdb=" O SER O 93 " (cutoff:3.500A) Processing helix chain 'O' and resid 109 through 118 675 hydrogen bonds defined for protein. 2025 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: 2.11 Time building geometry restraints manager: 2.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1125 1.31 - 1.43: 1909 1.43 - 1.56: 4631 1.56 - 1.68: 180 1.68 - 1.81: 105 Bond restraints: 7950 Sorted by residual: bond pdb=" C31 XL0 L 202 " pdb=" O31 XL0 L 202 " ideal model delta sigma weight residual 1.333 1.440 -0.107 2.00e-02 2.50e+03 2.86e+01 bond pdb=" C31 XL0 I 200 " pdb=" O31 XL0 I 200 " ideal model delta sigma weight residual 1.333 1.440 -0.107 2.00e-02 2.50e+03 2.85e+01 bond pdb=" C31 XL0 M 202 " pdb=" O31 XL0 M 202 " ideal model delta sigma weight residual 1.333 1.440 -0.107 2.00e-02 2.50e+03 2.84e+01 bond pdb=" C31 XL0 N 202 " pdb=" O31 XL0 N 202 " ideal model delta sigma weight residual 1.333 1.440 -0.107 2.00e-02 2.50e+03 2.84e+01 bond pdb=" C31 XL0 N 201 " pdb=" O31 XL0 N 201 " ideal model delta sigma weight residual 1.333 1.440 -0.107 2.00e-02 2.50e+03 2.84e+01 ... (remaining 7945 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.47: 10249 4.47 - 8.94: 311 8.94 - 13.41: 15 13.41 - 17.88: 0 17.88 - 22.36: 15 Bond angle restraints: 10590 Sorted by residual: angle pdb=" O13 XL0 M 202 " pdb=" P XL0 M 202 " pdb=" O14 XL0 M 202 " ideal model delta sigma weight residual 123.28 100.92 22.36 3.00e+00 1.11e-01 5.55e+01 angle pdb=" O13 XL0 K 202 " pdb=" P XL0 K 202 " pdb=" O14 XL0 K 202 " ideal model delta sigma weight residual 123.28 100.93 22.35 3.00e+00 1.11e-01 5.55e+01 angle pdb=" O13 XL0 K 201 " pdb=" P XL0 K 201 " pdb=" O14 XL0 K 201 " ideal model delta sigma weight residual 123.28 100.94 22.34 3.00e+00 1.11e-01 5.54e+01 angle pdb=" O13 XL0 H 200 " pdb=" P XL0 H 200 " pdb=" O14 XL0 H 200 " ideal model delta sigma weight residual 123.28 100.94 22.34 3.00e+00 1.11e-01 5.54e+01 angle pdb=" O13 XL0 N 202 " pdb=" P XL0 N 202 " pdb=" O14 XL0 N 202 " ideal model delta sigma weight residual 123.28 100.95 22.33 3.00e+00 1.11e-01 5.54e+01 ... (remaining 10585 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.75: 3655 10.75 - 21.50: 481 21.50 - 32.26: 443 32.26 - 43.01: 150 43.01 - 53.76: 45 Dihedral angle restraints: 4774 sinusoidal: 2149 harmonic: 2625 Sorted by residual: dihedral pdb=" CB MET N 59 " pdb=" CG MET N 59 " pdb=" SD MET N 59 " pdb=" CE MET N 59 " ideal model delta sinusoidal sigma weight residual 180.00 141.01 38.99 3 1.50e+01 4.44e-03 6.89e+00 dihedral pdb=" CB MET B 59 " pdb=" CG MET B 59 " pdb=" SD MET B 59 " pdb=" CE MET B 59 " ideal model delta sinusoidal sigma weight residual 180.00 141.01 38.99 3 1.50e+01 4.44e-03 6.89e+00 dihedral pdb=" CB MET I 59 " pdb=" CG MET I 59 " pdb=" SD MET I 59 " pdb=" CE MET I 59 " ideal model delta sinusoidal sigma weight residual 180.00 141.02 38.98 3 1.50e+01 4.44e-03 6.89e+00 ... (remaining 4771 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 705 0.027 - 0.053: 284 0.053 - 0.080: 211 0.080 - 0.106: 15 0.106 - 0.133: 15 Chirality restraints: 1230 Sorted by residual: chirality pdb=" C12 XL0 L 201 " pdb=" C11 XL0 L 201 " pdb=" C13 XL0 L 201 " pdb=" OC2 XL0 L 201 " both_signs ideal model delta sigma weight residual False -2.38 -2.52 0.13 2.00e-01 2.50e+01 4.40e-01 chirality pdb=" C12 XL0 F 200 " pdb=" C11 XL0 F 200 " pdb=" C13 XL0 F 200 " pdb=" OC2 XL0 F 200 " both_signs ideal model delta sigma weight residual False -2.38 -2.52 0.13 2.00e-01 2.50e+01 4.33e-01 chirality pdb=" C12 XL0 O 201 " pdb=" C11 XL0 O 201 " pdb=" C13 XL0 O 201 " pdb=" OC2 XL0 O 201 " both_signs ideal model delta sigma weight residual False -2.38 -2.51 0.13 2.00e-01 2.50e+01 4.23e-01 ... (remaining 1227 not shown) Planarity restraints: 1260 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C38 XL0 L 202 " -0.012 2.00e-02 2.50e+03 2.12e-02 4.51e+00 pdb=" C39 XL0 L 202 " 0.027 2.00e-02 2.50e+03 pdb="C310 XL0 L 202 " -0.027 2.00e-02 2.50e+03 pdb="C311 XL0 L 202 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C38 XL0 N 201 " 0.012 2.00e-02 2.50e+03 2.12e-02 4.49e+00 pdb=" C39 XL0 N 201 " -0.027 2.00e-02 2.50e+03 pdb="C310 XL0 N 201 " 0.027 2.00e-02 2.50e+03 pdb="C311 XL0 N 201 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C38 XL0 G 200 " -0.012 2.00e-02 2.50e+03 2.08e-02 4.32e+00 pdb=" C39 XL0 G 200 " 0.027 2.00e-02 2.50e+03 pdb="C310 XL0 G 200 " -0.027 2.00e-02 2.50e+03 pdb="C311 XL0 G 200 " 0.012 2.00e-02 2.50e+03 ... (remaining 1257 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 2815 2.90 - 3.40: 8045 3.40 - 3.90: 13421 3.90 - 4.40: 15033 4.40 - 4.90: 23836 Nonbonded interactions: 63150 Sorted by model distance: nonbonded pdb=" O LEU B 117 " pdb=" OG1 THR B 118 " model vdw 2.395 3.040 nonbonded pdb=" O LEU N 117 " pdb=" OG1 THR N 118 " model vdw 2.395 3.040 nonbonded pdb=" O LEU G 117 " pdb=" OG1 THR G 118 " model vdw 2.396 3.040 nonbonded pdb=" O LEU A 117 " pdb=" OG1 THR A 118 " model vdw 2.396 3.040 nonbonded pdb=" O LEU K 117 " pdb=" OG1 THR K 118 " model vdw 2.396 3.040 ... (remaining 63145 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' } ncs_group { reference = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'K' selection = chain 'M' selection = chain 'L' selection = chain 'O' selection = chain 'N' } 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: 6.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 19.930 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 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:11.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 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 : 0.011 0.107 7960 Z= 0.553 Angle : 1.627 22.356 10592 Z= 0.588 Chirality : 0.038 0.133 1230 Planarity : 0.004 0.022 1260 Dihedral : 15.884 53.761 3150 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 3.16 (0.27), residues: 990 helix: 2.50 (0.17), residues: 885 sheet: None (None), residues: 0 loop : -1.82 (0.48), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP N 87 PHE 0.007 0.001 PHE D 71 ARG 0.001 0.000 ARG O 91 Details of bonding type rmsd hydrogen bonds : bond 0.13819 ( 675) hydrogen bonds : angle 5.78682 ( 2025) SS BOND : angle 0.00000 ( 2) covalent geometry : bond 0.01111 ( 7950) covalent geometry : angle 1.62692 (10590) Misc. bond : bond 0.00104 ( 10) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 271 time to evaluate : 1.533 Fit side-chains REVERT: A 74 SER cc_start: 0.8716 (m) cc_final: 0.8398 (p) REVERT: B 74 SER cc_start: 0.8818 (m) cc_final: 0.8539 (p) REVERT: B 94 LEU cc_start: 0.8697 (tp) cc_final: 0.8410 (tp) REVERT: C 74 SER cc_start: 0.8697 (m) cc_final: 0.8425 (p) REVERT: D 74 SER cc_start: 0.8707 (m) cc_final: 0.8443 (p) REVERT: E 74 SER cc_start: 0.8792 (m) cc_final: 0.8483 (p) REVERT: F 74 SER cc_start: 0.8656 (m) cc_final: 0.8425 (p) REVERT: H 74 SER cc_start: 0.8705 (m) cc_final: 0.8496 (p) outliers start: 0 outliers final: 1 residues processed: 271 average time/residue: 0.7617 time to fit residues: 225.6428 Evaluate side-chains 189 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 188 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 107 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 75 optimal weight: 0.6980 chunk 68 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 46 optimal weight: 0.5980 chunk 36 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 42 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3445 r_free = 0.3445 target = 0.123746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.114463 restraints weight = 10757.015| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 1.26 r_work: 0.3220 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7960 Z= 0.156 Angle : 0.657 8.382 10592 Z= 0.321 Chirality : 0.038 0.211 1230 Planarity : 0.005 0.044 1260 Dihedral : 12.494 45.850 1818 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Rotamer: Outliers : 6.81 % Allowed : 22.08 % Favored : 71.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.76 (0.26), residues: 990 helix: 2.88 (0.17), residues: 885 sheet: None (None), residues: 0 loop : -1.42 (0.45), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP L 87 PHE 0.012 0.001 PHE L 112 ARG 0.014 0.003 ARG N 91 Details of bonding type rmsd hydrogen bonds : bond 0.03649 ( 675) hydrogen bonds : angle 4.42548 ( 2025) SS BOND : angle 0.00000 ( 2) covalent geometry : bond 0.00367 ( 7950) covalent geometry : angle 0.65750 (10590) Misc. bond : bond 0.00630 ( 10) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 202 time to evaluate : 0.941 Fit side-chains REVERT: A 54 THR cc_start: 0.8364 (OUTLIER) cc_final: 0.7999 (t) REVERT: A 91 ARG cc_start: 0.6726 (ppt170) cc_final: 0.6511 (ppt170) REVERT: B 74 SER cc_start: 0.8973 (m) cc_final: 0.8516 (p) REVERT: C 54 THR cc_start: 0.8268 (OUTLIER) cc_final: 0.7979 (t) REVERT: C 74 SER cc_start: 0.8991 (m) cc_final: 0.8571 (p) REVERT: D 74 SER cc_start: 0.8976 (m) cc_final: 0.8603 (p) REVERT: F 54 THR cc_start: 0.8460 (OUTLIER) cc_final: 0.8099 (t) REVERT: G 54 THR cc_start: 0.8323 (OUTLIER) cc_final: 0.7952 (t) REVERT: H 54 THR cc_start: 0.8268 (p) cc_final: 0.7898 (t) REVERT: J 54 THR cc_start: 0.8299 (OUTLIER) cc_final: 0.7943 (t) REVERT: K 54 THR cc_start: 0.8092 (OUTLIER) cc_final: 0.7854 (t) REVERT: L 54 THR cc_start: 0.8217 (p) cc_final: 0.7918 (t) REVERT: M 54 THR cc_start: 0.8219 (OUTLIER) cc_final: 0.7960 (t) REVERT: N 54 THR cc_start: 0.8054 (OUTLIER) cc_final: 0.7827 (t) REVERT: N 60 VAL cc_start: 0.8536 (t) cc_final: 0.7841 (m) REVERT: O 54 THR cc_start: 0.8191 (OUTLIER) cc_final: 0.7930 (t) outliers start: 49 outliers final: 28 residues processed: 223 average time/residue: 0.7699 time to fit residues: 189.8179 Evaluate side-chains 208 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 171 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 67 ILE Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 93 SER Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain K residue 54 THR Chi-restraints excluded: chain K residue 67 ILE Chi-restraints excluded: chain K residue 93 SER Chi-restraints excluded: chain K residue 97 VAL Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain M residue 54 THR Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain N residue 54 THR Chi-restraints excluded: chain N residue 93 SER Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain O residue 54 THR Chi-restraints excluded: chain O residue 67 ILE Chi-restraints excluded: chain O residue 97 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 62 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 12 optimal weight: 8.9990 chunk 84 optimal weight: 5.9990 chunk 41 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 71 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 62 ASN L 61 ASN L 62 ASN M 62 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.123103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.114301 restraints weight = 10733.952| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 1.16 r_work: 0.3220 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7960 Z= 0.143 Angle : 0.597 8.448 10592 Z= 0.290 Chirality : 0.037 0.209 1230 Planarity : 0.003 0.027 1260 Dihedral : 11.759 49.090 1815 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 7.08 % Allowed : 24.72 % Favored : 68.19 % 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: 3.78 (0.25), residues: 990 helix: 2.90 (0.16), residues: 885 sheet: None (None), residues: 0 loop : -1.50 (0.36), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP J 87 PHE 0.010 0.001 PHE K 112 ARG 0.007 0.002 ARG N 91 Details of bonding type rmsd hydrogen bonds : bond 0.03619 ( 675) hydrogen bonds : angle 4.25764 ( 2025) SS BOND : angle 0.00000 ( 2) covalent geometry : bond 0.00342 ( 7950) covalent geometry : angle 0.59735 (10590) Misc. bond : bond 0.00327 ( 10) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 173 time to evaluate : 0.831 Fit side-chains REVERT: A 54 THR cc_start: 0.8331 (OUTLIER) cc_final: 0.7989 (t) REVERT: B 54 THR cc_start: 0.8276 (OUTLIER) cc_final: 0.7914 (t) REVERT: D 65 THR cc_start: 0.8543 (OUTLIER) cc_final: 0.8151 (p) REVERT: E 59 MET cc_start: 0.7965 (mtt) cc_final: 0.7636 (mtp) REVERT: E 94 LEU cc_start: 0.8884 (tp) cc_final: 0.8643 (tp) REVERT: F 54 THR cc_start: 0.8530 (OUTLIER) cc_final: 0.8163 (t) REVERT: G 54 THR cc_start: 0.8377 (OUTLIER) cc_final: 0.8018 (t) REVERT: H 54 THR cc_start: 0.8306 (p) cc_final: 0.7960 (t) REVERT: H 74 SER cc_start: 0.8910 (m) cc_final: 0.8643 (p) REVERT: J 54 THR cc_start: 0.8542 (OUTLIER) cc_final: 0.8179 (t) REVERT: K 54 THR cc_start: 0.8427 (OUTLIER) cc_final: 0.8213 (t) REVERT: L 54 THR cc_start: 0.8311 (p) cc_final: 0.8074 (t) REVERT: M 54 THR cc_start: 0.8241 (OUTLIER) cc_final: 0.7929 (t) REVERT: N 54 THR cc_start: 0.8275 (OUTLIER) cc_final: 0.8021 (t) REVERT: N 60 VAL cc_start: 0.8486 (t) cc_final: 0.8097 (m) REVERT: O 54 THR cc_start: 0.8340 (OUTLIER) cc_final: 0.8061 (t) outliers start: 51 outliers final: 29 residues processed: 194 average time/residue: 0.6568 time to fit residues: 140.5212 Evaluate side-chains 206 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 167 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 88 MET Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain K residue 54 THR Chi-restraints excluded: chain K residue 67 ILE Chi-restraints excluded: chain K residue 93 SER Chi-restraints excluded: chain K residue 97 VAL Chi-restraints excluded: chain L residue 67 ILE Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain M residue 54 THR Chi-restraints excluded: chain M residue 86 SER Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain M residue 111 SER Chi-restraints excluded: chain N residue 54 THR Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain O residue 54 THR Chi-restraints excluded: chain O residue 67 ILE Chi-restraints excluded: chain O residue 97 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 89 optimal weight: 0.9980 chunk 22 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 chunk 16 optimal weight: 6.9990 chunk 69 optimal weight: 0.5980 chunk 75 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 chunk 31 optimal weight: 0.5980 chunk 39 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 62 ASN L 61 ASN L 62 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.124566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.115332 restraints weight = 10712.190| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 1.24 r_work: 0.3230 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7960 Z= 0.128 Angle : 0.545 8.185 10592 Z= 0.268 Chirality : 0.035 0.145 1230 Planarity : 0.003 0.023 1260 Dihedral : 11.251 48.872 1815 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 8.33 % Allowed : 24.72 % Favored : 66.94 % 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: 3.92 (0.25), residues: 990 helix: 3.01 (0.16), residues: 885 sheet: None (None), residues: 0 loop : -1.68 (0.31), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP H 87 PHE 0.008 0.001 PHE M 112 ARG 0.005 0.001 ARG N 91 Details of bonding type rmsd hydrogen bonds : bond 0.03279 ( 675) hydrogen bonds : angle 4.12817 ( 2025) SS BOND : angle 0.00000 ( 2) covalent geometry : bond 0.00306 ( 7950) covalent geometry : angle 0.54537 (10590) Misc. bond : bond 0.00241 ( 10) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 173 time to evaluate : 0.729 Fit side-chains revert: symmetry clash REVERT: B 54 THR cc_start: 0.8326 (OUTLIER) cc_final: 0.7982 (t) REVERT: D 65 THR cc_start: 0.8529 (OUTLIER) cc_final: 0.8201 (p) REVERT: E 59 MET cc_start: 0.7980 (mtt) cc_final: 0.7740 (mtp) REVERT: E 94 LEU cc_start: 0.8876 (tp) cc_final: 0.8645 (tp) REVERT: E 115 LYS cc_start: 0.7806 (ttmm) cc_final: 0.7503 (mttp) REVERT: G 54 THR cc_start: 0.8377 (OUTLIER) cc_final: 0.7992 (t) REVERT: G 88 MET cc_start: 0.7673 (ttm) cc_final: 0.7450 (ttp) REVERT: H 74 SER cc_start: 0.8864 (m) cc_final: 0.8602 (p) REVERT: K 54 THR cc_start: 0.8424 (OUTLIER) cc_final: 0.8185 (t) REVERT: L 54 THR cc_start: 0.8277 (OUTLIER) cc_final: 0.8039 (t) REVERT: M 54 THR cc_start: 0.8277 (OUTLIER) cc_final: 0.7963 (t) REVERT: N 54 THR cc_start: 0.8353 (OUTLIER) cc_final: 0.8082 (t) REVERT: N 60 VAL cc_start: 0.8485 (t) cc_final: 0.8095 (m) REVERT: O 54 THR cc_start: 0.8304 (OUTLIER) cc_final: 0.8040 (t) outliers start: 60 outliers final: 33 residues processed: 202 average time/residue: 0.6216 time to fit residues: 138.9688 Evaluate side-chains 203 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 162 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 67 ILE Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 65 THR Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain K residue 54 THR Chi-restraints excluded: chain K residue 67 ILE Chi-restraints excluded: chain K residue 93 SER Chi-restraints excluded: chain K residue 97 VAL Chi-restraints excluded: chain L residue 54 THR Chi-restraints excluded: chain L residue 67 ILE Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain M residue 54 THR Chi-restraints excluded: chain M residue 86 SER Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain N residue 54 THR Chi-restraints excluded: chain N residue 93 SER Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain O residue 54 THR Chi-restraints excluded: chain O residue 67 ILE Chi-restraints excluded: chain O residue 97 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 74 optimal weight: 0.9980 chunk 64 optimal weight: 4.9990 chunk 48 optimal weight: 7.9990 chunk 83 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 chunk 88 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 chunk 54 optimal weight: 7.9990 chunk 16 optimal weight: 4.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 62 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.122064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.112944 restraints weight = 10688.583| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 1.24 r_work: 0.3200 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.3126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7960 Z= 0.152 Angle : 0.599 9.326 10592 Z= 0.288 Chirality : 0.037 0.108 1230 Planarity : 0.003 0.025 1260 Dihedral : 12.241 54.339 1815 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 9.58 % Allowed : 26.25 % Favored : 64.17 % 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: 3.73 (0.25), residues: 990 helix: 2.89 (0.16), residues: 885 sheet: None (None), residues: 0 loop : -1.78 (0.28), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 87 PHE 0.009 0.001 PHE B 108 ARG 0.007 0.001 ARG N 91 Details of bonding type rmsd hydrogen bonds : bond 0.03671 ( 675) hydrogen bonds : angle 4.26840 ( 2025) SS BOND : angle 0.00000 ( 2) covalent geometry : bond 0.00369 ( 7950) covalent geometry : angle 0.59931 (10590) Misc. bond : bond 0.00285 ( 10) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 171 time to evaluate : 0.814 Fit side-chains REVERT: D 65 THR cc_start: 0.8563 (OUTLIER) cc_final: 0.8191 (p) REVERT: E 59 MET cc_start: 0.8020 (mtt) cc_final: 0.7740 (mtp) REVERT: E 94 LEU cc_start: 0.8860 (tp) cc_final: 0.8640 (tp) REVERT: G 54 THR cc_start: 0.8428 (OUTLIER) cc_final: 0.7987 (t) REVERT: K 54 THR cc_start: 0.8453 (OUTLIER) cc_final: 0.8222 (t) REVERT: L 54 THR cc_start: 0.8267 (OUTLIER) cc_final: 0.8009 (t) REVERT: M 54 THR cc_start: 0.8278 (OUTLIER) cc_final: 0.7936 (t) REVERT: N 54 THR cc_start: 0.8364 (OUTLIER) cc_final: 0.8092 (t) REVERT: N 60 VAL cc_start: 0.8546 (t) cc_final: 0.8149 (m) outliers start: 69 outliers final: 42 residues processed: 213 average time/residue: 0.7905 time to fit residues: 183.2411 Evaluate side-chains 208 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 160 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 67 ILE Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 93 SER Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 93 SER Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain H residue 67 ILE Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 67 ILE Chi-restraints excluded: chain I residue 97 VAL Chi-restraints excluded: chain J residue 67 ILE Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain K residue 54 THR Chi-restraints excluded: chain K residue 67 ILE Chi-restraints excluded: chain K residue 93 SER Chi-restraints excluded: chain K residue 97 VAL Chi-restraints excluded: chain L residue 54 THR Chi-restraints excluded: chain L residue 67 ILE Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain M residue 54 THR Chi-restraints excluded: chain M residue 67 ILE Chi-restraints excluded: chain M residue 86 SER Chi-restraints excluded: chain M residue 93 SER Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain N residue 54 THR Chi-restraints excluded: chain N residue 93 SER Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain O residue 67 ILE Chi-restraints excluded: chain O residue 97 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 83 optimal weight: 0.7980 chunk 12 optimal weight: 9.9990 chunk 29 optimal weight: 1.9990 chunk 63 optimal weight: 0.0980 chunk 69 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN C 62 ASN E 62 ASN G 62 ASN L 62 ASN M 62 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.125597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.117319 restraints weight = 10709.813| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 1.10 r_work: 0.3255 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.3352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7960 Z= 0.145 Angle : 0.621 8.594 10592 Z= 0.302 Chirality : 0.036 0.093 1230 Planarity : 0.005 0.075 1260 Dihedral : 12.072 53.652 1815 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 8.19 % Allowed : 28.61 % Favored : 63.19 % 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: 3.84 (0.24), residues: 990 helix: 2.98 (0.16), residues: 885 sheet: None (None), residues: 0 loop : -1.90 (0.27), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 87 PHE 0.009 0.001 PHE F 89 ARG 0.017 0.004 ARG M 91 Details of bonding type rmsd hydrogen bonds : bond 0.03266 ( 675) hydrogen bonds : angle 4.14302 ( 2025) SS BOND : angle 0.00000 ( 2) covalent geometry : bond 0.00343 ( 7950) covalent geometry : angle 0.62134 (10590) Misc. bond : bond 0.00612 ( 10) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 181 time to evaluate : 0.813 Fit side-chains REVERT: D 65 THR cc_start: 0.8505 (OUTLIER) cc_final: 0.8180 (p) REVERT: E 59 MET cc_start: 0.7931 (mtt) cc_final: 0.7694 (mtp) REVERT: E 94 LEU cc_start: 0.8842 (tp) cc_final: 0.8634 (tp) REVERT: G 54 THR cc_start: 0.8408 (OUTLIER) cc_final: 0.7985 (t) REVERT: H 74 SER cc_start: 0.8862 (m) cc_final: 0.8637 (p) REVERT: N 54 THR cc_start: 0.8355 (OUTLIER) cc_final: 0.8087 (t) REVERT: N 60 VAL cc_start: 0.8499 (t) cc_final: 0.7968 (m) outliers start: 59 outliers final: 43 residues processed: 211 average time/residue: 0.5996 time to fit residues: 141.5712 Evaluate side-chains 214 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 168 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 93 SER Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 97 VAL Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain K residue 67 ILE Chi-restraints excluded: chain K residue 93 SER Chi-restraints excluded: chain K residue 97 VAL Chi-restraints excluded: chain L residue 67 ILE Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain M residue 67 ILE Chi-restraints excluded: chain M residue 86 SER Chi-restraints excluded: chain M residue 93 SER Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain N residue 54 THR Chi-restraints excluded: chain N residue 86 SER Chi-restraints excluded: chain N residue 93 SER Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain O residue 67 ILE Chi-restraints excluded: chain O residue 97 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 59 optimal weight: 2.9990 chunk 60 optimal weight: 6.9990 chunk 84 optimal weight: 6.9990 chunk 39 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 chunk 3 optimal weight: 0.0060 chunk 31 optimal weight: 0.6980 chunk 55 optimal weight: 0.5980 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 ASN F 62 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.126301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.117049 restraints weight = 10708.922| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 1.23 r_work: 0.3257 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.3461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7960 Z= 0.134 Angle : 0.590 8.133 10592 Z= 0.289 Chirality : 0.035 0.097 1230 Planarity : 0.004 0.043 1260 Dihedral : 11.530 51.498 1815 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 7.08 % Allowed : 30.83 % Favored : 62.08 % 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 (0.24), residues: 990 helix: 3.08 (0.16), residues: 885 sheet: None (None), residues: 0 loop : -1.94 (0.27), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP M 87 PHE 0.008 0.001 PHE O 112 ARG 0.012 0.003 ARG M 91 Details of bonding type rmsd hydrogen bonds : bond 0.03209 ( 675) hydrogen bonds : angle 4.05435 ( 2025) SS BOND : angle 0.00000 ( 2) covalent geometry : bond 0.00317 ( 7950) covalent geometry : angle 0.58967 (10590) Misc. bond : bond 0.00486 ( 10) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 170 time to evaluate : 1.080 Fit side-chains REVERT: E 59 MET cc_start: 0.7969 (mtt) cc_final: 0.7729 (mtp) REVERT: G 54 THR cc_start: 0.8409 (OUTLIER) cc_final: 0.7978 (t) REVERT: H 74 SER cc_start: 0.8816 (m) cc_final: 0.8608 (p) REVERT: N 60 VAL cc_start: 0.8451 (t) cc_final: 0.8063 (m) outliers start: 51 outliers final: 41 residues processed: 198 average time/residue: 0.8860 time to fit residues: 195.1788 Evaluate side-chains 204 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 162 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 88 MET Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 93 SER Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 97 VAL Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain K residue 67 ILE Chi-restraints excluded: chain K residue 93 SER Chi-restraints excluded: chain K residue 97 VAL Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain M residue 67 ILE Chi-restraints excluded: chain M residue 86 SER Chi-restraints excluded: chain M residue 93 SER Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain N residue 86 SER Chi-restraints excluded: chain N residue 93 SER Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain O residue 67 ILE Chi-restraints excluded: chain O residue 97 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 26 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 chunk 72 optimal weight: 7.9990 chunk 89 optimal weight: 0.6980 chunk 4 optimal weight: 3.9990 chunk 54 optimal weight: 7.9990 chunk 29 optimal weight: 0.7980 chunk 66 optimal weight: 6.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 62 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.124083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.114943 restraints weight = 10790.420| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.25 r_work: 0.3226 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.3447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 7960 Z= 0.148 Angle : 0.624 9.008 10592 Z= 0.302 Chirality : 0.037 0.116 1230 Planarity : 0.003 0.036 1260 Dihedral : 11.961 52.935 1815 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 7.36 % Allowed : 30.69 % Favored : 61.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.87 (0.24), residues: 990 helix: 3.01 (0.16), residues: 885 sheet: None (None), residues: 0 loop : -1.96 (0.27), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP O 87 PHE 0.009 0.001 PHE B 108 ARG 0.010 0.003 ARG M 91 Details of bonding type rmsd hydrogen bonds : bond 0.03445 ( 675) hydrogen bonds : angle 4.14858 ( 2025) SS BOND : angle 0.00000 ( 2) covalent geometry : bond 0.00360 ( 7950) covalent geometry : angle 0.62418 (10590) Misc. bond : bond 0.00429 ( 10) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 162 time to evaluate : 0.760 Fit side-chains REVERT: A 65 THR cc_start: 0.8431 (OUTLIER) cc_final: 0.8087 (p) REVERT: E 59 MET cc_start: 0.7975 (mtp) cc_final: 0.7724 (mtp) REVERT: G 54 THR cc_start: 0.8477 (OUTLIER) cc_final: 0.8043 (t) REVERT: H 74 SER cc_start: 0.8887 (m) cc_final: 0.8636 (p) REVERT: N 60 VAL cc_start: 0.8527 (t) cc_final: 0.8123 (m) outliers start: 53 outliers final: 46 residues processed: 196 average time/residue: 0.6090 time to fit residues: 132.6432 Evaluate side-chains 209 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 161 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 93 SER Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 93 SER Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 97 VAL Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain K residue 54 THR Chi-restraints excluded: chain K residue 67 ILE Chi-restraints excluded: chain K residue 93 SER Chi-restraints excluded: chain K residue 97 VAL Chi-restraints excluded: chain L residue 59 MET Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain M residue 54 THR Chi-restraints excluded: chain M residue 67 ILE Chi-restraints excluded: chain M residue 86 SER Chi-restraints excluded: chain M residue 93 SER Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain N residue 86 SER Chi-restraints excluded: chain N residue 93 SER Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain O residue 67 ILE Chi-restraints excluded: chain O residue 97 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 73 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 68 optimal weight: 0.9990 chunk 63 optimal weight: 0.3980 chunk 9 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 54 optimal weight: 7.9990 chunk 2 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.3453 r_free = 0.3453 target = 0.124196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.115071 restraints weight = 10785.223| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 1.25 r_work: 0.3227 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.3468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 7960 Z= 0.147 Angle : 0.629 11.613 10592 Z= 0.303 Chirality : 0.037 0.138 1230 Planarity : 0.004 0.037 1260 Dihedral : 12.098 51.676 1815 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 7.36 % Allowed : 31.11 % Favored : 61.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.85 (0.24), residues: 990 helix: 2.99 (0.16), residues: 885 sheet: None (None), residues: 0 loop : -1.99 (0.27), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 87 PHE 0.008 0.001 PHE G 108 ARG 0.009 0.002 ARG O 91 Details of bonding type rmsd hydrogen bonds : bond 0.03447 ( 675) hydrogen bonds : angle 4.15850 ( 2025) SS BOND : angle 0.00000 ( 2) covalent geometry : bond 0.00357 ( 7950) covalent geometry : angle 0.62878 (10590) Misc. bond : bond 0.00402 ( 10) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 164 time to evaluate : 0.727 Fit side-chains revert: symmetry clash REVERT: A 65 THR cc_start: 0.8446 (OUTLIER) cc_final: 0.8101 (p) REVERT: E 59 MET cc_start: 0.8000 (mtp) cc_final: 0.7740 (mtp) REVERT: G 54 THR cc_start: 0.8484 (OUTLIER) cc_final: 0.8052 (t) REVERT: H 74 SER cc_start: 0.8838 (m) cc_final: 0.8630 (p) REVERT: N 60 VAL cc_start: 0.8482 (t) cc_final: 0.8078 (m) outliers start: 53 outliers final: 45 residues processed: 197 average time/residue: 0.6370 time to fit residues: 138.3993 Evaluate side-chains 207 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 160 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 93 SER Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 91 ARG Chi-restraints excluded: chain G residue 93 SER Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 97 VAL Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain K residue 54 THR Chi-restraints excluded: chain K residue 67 ILE Chi-restraints excluded: chain K residue 93 SER Chi-restraints excluded: chain K residue 97 VAL Chi-restraints excluded: chain M residue 54 THR Chi-restraints excluded: chain M residue 67 ILE Chi-restraints excluded: chain M residue 86 SER Chi-restraints excluded: chain M residue 93 SER Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain N residue 86 SER Chi-restraints excluded: chain N residue 93 SER Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain O residue 67 ILE Chi-restraints excluded: chain O residue 97 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 4 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 30 optimal weight: 6.9990 chunk 60 optimal weight: 6.9990 chunk 50 optimal weight: 0.6980 chunk 59 optimal weight: 0.9990 chunk 55 optimal weight: 0.6980 chunk 68 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3434 r_free = 0.3434 target = 0.123138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.114455 restraints weight = 10945.945| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 1.22 r_work: 0.3225 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.3520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 7960 Z= 0.147 Angle : 0.633 10.689 10592 Z= 0.306 Chirality : 0.037 0.147 1230 Planarity : 0.003 0.035 1260 Dihedral : 12.202 52.282 1815 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 6.67 % Allowed : 31.81 % Favored : 61.53 % 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: 3.84 (0.24), residues: 990 helix: 2.99 (0.16), residues: 885 sheet: None (None), residues: 0 loop : -2.03 (0.26), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 87 PHE 0.008 0.001 PHE G 108 ARG 0.009 0.002 ARG O 91 Details of bonding type rmsd hydrogen bonds : bond 0.03445 ( 675) hydrogen bonds : angle 4.15855 ( 2025) SS BOND : angle 0.00000 ( 2) covalent geometry : bond 0.00359 ( 7950) covalent geometry : angle 0.63301 (10590) Misc. bond : bond 0.00408 ( 10) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 161 time to evaluate : 0.736 Fit side-chains revert: symmetry clash REVERT: A 65 THR cc_start: 0.8473 (OUTLIER) cc_final: 0.8134 (p) REVERT: D 65 THR cc_start: 0.8552 (OUTLIER) cc_final: 0.8223 (p) REVERT: E 59 MET cc_start: 0.8004 (mtp) cc_final: 0.7744 (mtp) REVERT: G 54 THR cc_start: 0.8481 (OUTLIER) cc_final: 0.8028 (t) REVERT: H 74 SER cc_start: 0.8842 (m) cc_final: 0.8591 (p) REVERT: N 60 VAL cc_start: 0.8406 (t) cc_final: 0.7995 (m) outliers start: 48 outliers final: 44 residues processed: 194 average time/residue: 0.6434 time to fit residues: 138.1957 Evaluate side-chains 207 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 160 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 65 THR Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 93 SER Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 91 ARG Chi-restraints excluded: chain G residue 93 SER Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 97 VAL Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain K residue 54 THR Chi-restraints excluded: chain K residue 67 ILE Chi-restraints excluded: chain K residue 93 SER Chi-restraints excluded: chain K residue 97 VAL Chi-restraints excluded: chain L residue 67 ILE Chi-restraints excluded: chain M residue 54 THR Chi-restraints excluded: chain M residue 67 ILE Chi-restraints excluded: chain M residue 86 SER Chi-restraints excluded: chain M residue 93 SER Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain O residue 67 ILE Chi-restraints excluded: chain O residue 97 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 28 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 63 optimal weight: 0.5980 chunk 88 optimal weight: 0.7980 chunk 18 optimal weight: 7.9990 chunk 55 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 6 optimal weight: 7.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3448 r_free = 0.3448 target = 0.124103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.115391 restraints weight = 10885.047| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.23 r_work: 0.3239 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.3566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 7960 Z= 0.140 Angle : 0.615 9.060 10592 Z= 0.299 Chirality : 0.037 0.140 1230 Planarity : 0.003 0.033 1260 Dihedral : 11.927 51.922 1815 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 7.22 % Allowed : 31.39 % Favored : 61.39 % 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: 3.88 (0.24), residues: 990 helix: 3.03 (0.16), residues: 885 sheet: None (None), residues: 0 loop : -2.08 (0.26), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 87 PHE 0.007 0.001 PHE E 108 ARG 0.008 0.002 ARG M 91 Details of bonding type rmsd hydrogen bonds : bond 0.03333 ( 675) hydrogen bonds : angle 4.10507 ( 2025) SS BOND : angle 0.00000 ( 2) covalent geometry : bond 0.00340 ( 7950) covalent geometry : angle 0.61514 (10590) Misc. bond : bond 0.00390 ( 10) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5013.78 seconds wall clock time: 89 minutes 6.68 seconds (5346.68 seconds total)