Starting phenix.real_space_refine on Tue Aug 4 16:26:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jgz_61467/08_2026/9jgz_61467.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jgz_61467/08_2026/9jgz_61467.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jgz_61467/08_2026/9jgz_61467.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jgz_61467/08_2026/9jgz_61467.map" model { file = "/net/cci-nas-00/data/ceres_data/9jgz_61467/08_2026/9jgz_61467.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jgz_61467/08_2026/9jgz_61467.cif" } resolution = 2.74 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.059 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: 6 Type Number sf(0) Gaussians K 4 8.98 5 P 2 5.49 5 S 36 5.16 5 C 3254 2.51 5 N 776 2.21 5 O 832 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4904 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2285 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 6, 'TRANS': 280} Chain breaks: 2 Chain: "B" Number of atoms: 2285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2285 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 6, 'TRANS': 280} Chain breaks: 2 Chain: "A" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 167 Unusual residues: {' K': 2, 'ACD': 1, 'D21': 1, 'EIC': 1, 'POV': 6} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 235 Unresolved non-hydrogen angles: 283 Unresolved non-hydrogen dihedrals: 211 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'POV:plan-1': 6, 'POV:plan-2': 6} Unresolved non-hydrogen planarities: 48 Chain: "B" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 167 Unusual residues: {' K': 2, 'ACD': 1, 'D21': 1, 'EIC': 1, 'POV': 6} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 235 Unresolved non-hydrogen angles: 283 Unresolved non-hydrogen dihedrals: 211 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'POV:plan-1': 6, 'POV:plan-2': 6} Unresolved non-hydrogen planarities: 48 Time building chain proxies: 0.97, per 1000 atoms: 0.20 Number of scatterers: 4904 At special positions: 0 Unit cell: (69.9, 79.22, 97.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 4 19.00 S 36 16.00 P 2 15.00 O 832 8.00 N 776 7.00 C 3254 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: 0.41 Conformation dependent library (CDL) restraints added in 112.4 milliseconds 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1060 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 0 sheets defined 80.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing helix chain 'A' and resid 14 through 65 removed outlier: 5.892A pdb=" N ALA A 44 " --> pdb=" O ALA A 40 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N HIS A 45 " --> pdb=" O LEU A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 84 removed outlier: 3.862A pdb=" N LEU A 71 " --> pdb=" O SER A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 109 Processing helix chain 'A' and resid 120 through 167 Processing helix chain 'A' and resid 193 through 221 Proline residue: A 218 - end of helix Processing helix chain 'A' and resid 223 through 236 Processing helix chain 'A' and resid 253 through 298 Processing helix chain 'A' and resid 299 through 303 removed outlier: 3.864A pdb=" N CYS A 302 " --> pdb=" O CYS A 299 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N GLN A 303 " --> pdb=" O PRO A 300 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 299 through 303' Processing helix chain 'A' and resid 394 through 398 Processing helix chain 'B' and resid 14 through 65 removed outlier: 5.893A pdb=" N ALA B 44 " --> pdb=" O ALA B 40 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N HIS B 45 " --> pdb=" O LEU B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 84 removed outlier: 3.862A pdb=" N LEU B 71 " --> pdb=" O SER B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 109 Processing helix chain 'B' and resid 120 through 167 Processing helix chain 'B' and resid 193 through 221 Proline residue: B 218 - end of helix Processing helix chain 'B' and resid 223 through 236 Processing helix chain 'B' and resid 253 through 298 Processing helix chain 'B' and resid 299 through 303 removed outlier: 3.864A pdb=" N CYS B 302 " --> pdb=" O CYS B 299 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N GLN B 303 " --> pdb=" O PRO B 300 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 299 through 303' Processing helix chain 'B' and resid 394 through 398 376 hydrogen bonds defined for protein. 1128 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: 0.71 Time building geometry restraints manager: 0.54 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: 740 1.31 - 1.43: 1417 1.43 - 1.56: 2783 1.56 - 1.68: 2 1.68 - 1.81: 50 Bond restraints: 4992 Sorted by residual: bond pdb="C312 POV A 502 " pdb="C313 POV A 502 " ideal model delta sigma weight residual 1.523 1.191 0.332 2.00e-02 2.50e+03 2.76e+02 bond pdb="C312 POV B 504 " pdb="C313 POV B 504 " ideal model delta sigma weight residual 1.523 1.191 0.332 2.00e-02 2.50e+03 2.75e+02 bond pdb="C312 POV B 509 " pdb="C313 POV B 509 " ideal model delta sigma weight residual 1.523 1.193 0.330 2.00e-02 2.50e+03 2.72e+02 bond pdb="C312 POV A 507 " pdb="C313 POV A 507 " ideal model delta sigma weight residual 1.523 1.193 0.330 2.00e-02 2.50e+03 2.71e+02 bond pdb="C312 POV B 502 " pdb="C313 POV B 502 " ideal model delta sigma weight residual 1.523 1.194 0.329 2.00e-02 2.50e+03 2.71e+02 ... (remaining 4987 not shown) Histogram of bond angle deviations from ideal: 0.00 - 13.25: 6612 13.25 - 26.50: 24 26.50 - 39.75: 0 39.75 - 53.00: 0 53.00 - 66.25: 12 Bond angle restraints: 6648 Sorted by residual: angle pdb="C311 POV B 504 " pdb="C312 POV B 504 " pdb="C313 POV B 504 " ideal model delta sigma weight residual 113.71 179.96 -66.25 3.00e+00 1.11e-01 4.88e+02 angle pdb="C311 POV A 502 " pdb="C312 POV A 502 " pdb="C313 POV A 502 " ideal model delta sigma weight residual 113.71 179.94 -66.23 3.00e+00 1.11e-01 4.87e+02 angle pdb="C311 POV B 501 " pdb="C312 POV B 501 " pdb="C313 POV B 501 " ideal model delta sigma weight residual 113.71 179.73 -66.02 3.00e+00 1.11e-01 4.84e+02 angle pdb="C311 POV A 508 " pdb="C312 POV A 508 " pdb="C313 POV A 508 " ideal model delta sigma weight residual 113.71 179.68 -65.97 3.00e+00 1.11e-01 4.84e+02 angle pdb="C311 POV B 502 " pdb="C312 POV B 502 " pdb="C313 POV B 502 " ideal model delta sigma weight residual 113.71 179.57 -65.86 3.00e+00 1.11e-01 4.82e+02 ... (remaining 6643 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.84: 2781 35.84 - 71.69: 145 71.69 - 107.53: 22 107.53 - 143.38: 2 143.38 - 179.22: 8 Dihedral angle restraints: 2958 sinusoidal: 1304 harmonic: 1654 Sorted by residual: dihedral pdb=" C19 D21 B 507 " pdb=" C20 D21 B 507 " pdb=" O30 D21 B 507 " pdb=" C31 D21 B 507 " ideal model delta sinusoidal sigma weight residual 45.01 -135.77 -179.22 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C19 D21 A 505 " pdb=" C20 D21 A 505 " pdb=" O30 D21 A 505 " pdb=" C31 D21 A 505 " ideal model delta sinusoidal sigma weight residual 45.01 -135.80 -179.19 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C21 D21 A 505 " pdb=" C20 D21 A 505 " pdb=" O30 D21 A 505 " pdb=" C31 D21 A 505 " ideal model delta sinusoidal sigma weight residual 275.84 103.85 171.99 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 2955 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 643 0.064 - 0.128: 51 0.128 - 0.193: 4 0.193 - 0.257: 0 0.257 - 0.321: 2 Chirality restraints: 700 Sorted by residual: chirality pdb=" C20 D21 B 507 " pdb=" C19 D21 B 507 " pdb=" C21 D21 B 507 " pdb=" O30 D21 B 507 " both_signs ideal model delta sigma weight residual False 2.18 2.50 -0.32 2.00e-01 2.50e+01 2.58e+00 chirality pdb=" C20 D21 A 505 " pdb=" C19 D21 A 505 " pdb=" C21 D21 A 505 " pdb=" O30 D21 A 505 " both_signs ideal model delta sigma weight residual False 2.18 2.50 -0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" CA ILE B 396 " pdb=" N ILE B 396 " pdb=" C ILE B 396 " pdb=" CB ILE B 396 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.72e-01 ... (remaining 697 not shown) Planarity restraints: 826 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C11 EIC A 503 " -0.155 2.00e-02 2.50e+03 3.37e-01 1.14e+03 pdb=" C12 EIC A 503 " 0.450 2.00e-02 2.50e+03 pdb=" C13 EIC A 503 " -0.452 2.00e-02 2.50e+03 pdb=" C14 EIC A 503 " 0.157 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C11 EIC B 505 " 0.156 2.00e-02 2.50e+03 3.37e-01 1.14e+03 pdb=" C12 EIC B 505 " -0.451 2.00e-02 2.50e+03 pdb=" C13 EIC B 505 " 0.451 2.00e-02 2.50e+03 pdb=" C14 EIC B 505 " -0.156 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C39 D21 B 507 " 0.158 2.00e-02 2.50e+03 3.12e-01 9.74e+02 pdb=" C40 D21 B 507 " -0.415 2.00e-02 2.50e+03 pdb=" C41 D21 B 507 " 0.411 2.00e-02 2.50e+03 pdb=" C42 D21 B 507 " -0.155 2.00e-02 2.50e+03 ... (remaining 823 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.37: 17 2.37 - 3.06: 3319 3.06 - 3.75: 8867 3.75 - 4.45: 13620 4.45 - 5.14: 22071 Nonbonded interactions: 47894 Sorted by model distance: nonbonded pdb=" O MET A 397 " pdb=" NZ LYS B 191 " model vdw 1.675 3.120 nonbonded pdb=" NZ LYS A 191 " pdb=" O MET B 397 " model vdw 1.729 3.120 nonbonded pdb=" OH TYR A 78 " pdb=" OE2 GLU B 79 " model vdw 1.996 3.040 nonbonded pdb=" OH TYR A 273 " pdb=" OH TYR B 273 " model vdw 2.074 3.040 nonbonded pdb=" OE2 GLU A 79 " pdb=" OH TYR B 78 " model vdw 2.097 3.040 ... (remaining 47889 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 9 through 502 or resid 508 through 511)) selection = (chain 'B' and (resid 9 through 502 or resid 508 through 511)) } 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: 1.290 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: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 5.340 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:5.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 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 : 0.021 0.332 4992 Z= 1.032 Angle : 3.133 66.251 6648 Z= 1.069 Chirality : 0.038 0.321 700 Planarity : 0.033 0.337 826 Dihedral : 23.958 179.220 1898 Min Nonbonded Distance : 1.675 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.66 % Allowed : 30.08 % Favored : 68.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.72 (0.34), residues: 562 helix: 3.35 (0.23), residues: 440 sheet: None (None), residues: 0 loop : -1.21 (0.53), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 292 TYR 0.014 0.001 TYR B 78 PHE 0.007 0.001 PHE B 97 TRP 0.014 0.001 TRP A 190 HIS 0.002 0.000 HIS A 12 Details of bonding type rmsd/Z covalent geometry : bond 0.02072 / 1.03 ( 4992) covalent geometry : angle 3.13315 / 1.07 ( 6648) hydrogen bonds : bond 0.10049 / 6.71 ( 376) hydrogen bonds : angle 4.53333 / 3.42 ( 1128) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 99 time to evaluate : 0.109 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 147 GLU cc_start: 0.8380 (tm-30) cc_final: 0.7976 (tm-30) REVERT: A 196 TYR cc_start: 0.8204 (m-80) cc_final: 0.7853 (m-80) REVERT: A 200 ILE cc_start: 0.8735 (OUTLIER) cc_final: 0.8397 (mp) REVERT: A 292 ARG cc_start: 0.8800 (ttm-80) cc_final: 0.8506 (ttp-110) REVERT: B 147 GLU cc_start: 0.8405 (tm-30) cc_final: 0.8047 (tm-30) REVERT: B 200 ILE cc_start: 0.8724 (OUTLIER) cc_final: 0.8418 (mp) REVERT: B 292 ARG cc_start: 0.8761 (ttm-80) cc_final: 0.8417 (ttm110) outliers start: 8 outliers final: 5 residues processed: 105 average time/residue: 0.4311 time to fit residues: 46.9551 Evaluate side-chains 107 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 100 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 397 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 54 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 17 ASN A 254 GLN A 398 ASN B 254 GLN B 398 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.122116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.083638 restraints weight = 6837.076| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 2.28 r_work: 0.2799 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.1199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 4992 Z= 0.147 Angle : 0.586 15.007 6648 Z= 0.272 Chirality : 0.036 0.147 700 Planarity : 0.003 0.023 826 Dihedral : 21.080 160.758 898 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 4.36 % Allowed : 23.24 % Favored : 72.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.98 (0.34), residues: 562 helix: 3.49 (0.22), residues: 440 sheet: None (None), residues: 0 loop : -0.88 (0.55), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 292 TYR 0.008 0.001 TYR A 130 PHE 0.009 0.001 PHE B 232 TRP 0.006 0.001 TRP B 222 HIS 0.003 0.001 HIS A 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 ( 4992) covalent geometry : angle 0.58644 / 0.27 ( 6648) hydrogen bonds : bond 0.04650 / 3.25 ( 376) hydrogen bonds : angle 3.72346 / 2.77 ( 1128) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 97 time to evaluate : 0.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7946 (tt0) REVERT: A 147 GLU cc_start: 0.8147 (tm-30) cc_final: 0.7780 (tm-30) REVERT: B 46 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7958 (tt0) REVERT: B 147 GLU cc_start: 0.8189 (tm-30) cc_final: 0.7825 (tm-30) REVERT: B 397 MET cc_start: 0.7043 (tpt) cc_final: 0.6620 (tpt) outliers start: 21 outliers final: 6 residues processed: 109 average time/residue: 0.4818 time to fit residues: 54.3337 Evaluate side-chains 99 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 91 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 293 LYS Chi-restraints excluded: chain A residue 397 MET Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 280 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 6 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 47 optimal weight: 0.2980 chunk 12 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 44 optimal weight: 0.0570 chunk 17 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 254 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.123545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.084594 restraints weight = 6753.241| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 2.30 r_work: 0.2794 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 4992 Z= 0.122 Angle : 0.486 5.718 6648 Z= 0.250 Chirality : 0.035 0.139 700 Planarity : 0.003 0.031 826 Dihedral : 16.876 142.345 886 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 4.36 % Allowed : 22.61 % Favored : 73.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.08 (0.34), residues: 562 helix: 3.52 (0.22), residues: 438 sheet: None (None), residues: 0 loop : -0.60 (0.56), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 62 TYR 0.009 0.001 TYR B 78 PHE 0.008 0.001 PHE B 232 TRP 0.010 0.001 TRP A 190 HIS 0.002 0.000 HIS A 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 ( 4992) covalent geometry : angle 0.48596 / 0.25 ( 6648) hydrogen bonds : bond 0.04370 / 3.06 ( 376) hydrogen bonds : angle 3.55338 / 2.65 ( 1128) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 99 time to evaluate : 0.171 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7860 (tt0) REVERT: A 147 GLU cc_start: 0.8130 (tm-30) cc_final: 0.7773 (tm-30) REVERT: A 292 ARG cc_start: 0.8760 (ttm-80) cc_final: 0.8452 (ttm110) REVERT: B 46 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7867 (tt0) REVERT: B 147 GLU cc_start: 0.8153 (tm-30) cc_final: 0.7794 (tm-30) REVERT: B 292 ARG cc_start: 0.8739 (ttm-80) cc_final: 0.8440 (ttm110) outliers start: 21 outliers final: 7 residues processed: 113 average time/residue: 0.5554 time to fit residues: 64.9376 Evaluate side-chains 99 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 90 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 286 SER Chi-restraints excluded: chain B residue 287 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 55 optimal weight: 0.4980 chunk 20 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 32 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 254 GLN B 254 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.122447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.083110 restraints weight = 6826.718| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 2.33 r_work: 0.2776 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4992 Z= 0.130 Angle : 0.491 6.449 6648 Z= 0.255 Chirality : 0.035 0.144 700 Planarity : 0.003 0.036 826 Dihedral : 15.902 145.017 886 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 3.11 % Allowed : 24.90 % Favored : 71.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.12 (0.34), residues: 562 helix: 3.53 (0.22), residues: 438 sheet: None (None), residues: 0 loop : -0.51 (0.57), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 62 TYR 0.012 0.001 TYR B 78 PHE 0.009 0.001 PHE A 97 TRP 0.005 0.001 TRP B 53 HIS 0.002 0.001 HIS A 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 ( 4992) covalent geometry : angle 0.49130 / 0.26 ( 6648) hydrogen bonds : bond 0.04400 / 3.08 ( 376) hydrogen bonds : angle 3.53600 / 2.63 ( 1128) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 98 time to evaluate : 0.180 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7880 (tt0) REVERT: A 51 GLN cc_start: 0.8399 (tp40) cc_final: 0.8153 (tp40) REVERT: A 147 GLU cc_start: 0.8153 (tm-30) cc_final: 0.7784 (tm-30) REVERT: B 46 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7888 (tt0) REVERT: B 147 GLU cc_start: 0.8169 (tm-30) cc_final: 0.7793 (tm-30) outliers start: 15 outliers final: 5 residues processed: 106 average time/residue: 0.5169 time to fit residues: 56.6289 Evaluate side-chains 100 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 93 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 287 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 9 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 43 optimal weight: 9.9990 chunk 14 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 254 GLN B 254 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.121820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.082532 restraints weight = 6865.736| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 2.32 r_work: 0.2759 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4992 Z= 0.147 Angle : 0.503 6.650 6648 Z= 0.264 Chirality : 0.036 0.152 700 Planarity : 0.003 0.026 826 Dihedral : 14.867 144.657 886 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 3.73 % Allowed : 25.10 % Favored : 71.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.08 (0.34), residues: 562 helix: 3.48 (0.22), residues: 438 sheet: None (None), residues: 0 loop : -0.41 (0.58), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 292 TYR 0.013 0.001 TYR B 78 PHE 0.010 0.001 PHE B 97 TRP 0.006 0.001 TRP A 190 HIS 0.002 0.001 HIS B 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 ( 4992) covalent geometry : angle 0.50285 / 0.26 ( 6648) hydrogen bonds : bond 0.04504 / 3.15 ( 376) hydrogen bonds : angle 3.56352 / 2.65 ( 1128) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 94 time to evaluate : 0.143 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7917 (tt0) REVERT: A 51 GLN cc_start: 0.8451 (tp40) cc_final: 0.8176 (tp40) REVERT: A 147 GLU cc_start: 0.8194 (tm-30) cc_final: 0.7765 (tm-30) REVERT: A 292 ARG cc_start: 0.8794 (ttm-80) cc_final: 0.8511 (ttm110) REVERT: B 46 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7897 (tt0) REVERT: B 51 GLN cc_start: 0.8322 (tp40) cc_final: 0.8024 (tp40) REVERT: B 147 GLU cc_start: 0.8181 (tm-30) cc_final: 0.7760 (tm-30) REVERT: B 292 ARG cc_start: 0.8735 (ttm-80) cc_final: 0.8444 (ttm110) outliers start: 18 outliers final: 6 residues processed: 105 average time/residue: 0.5120 time to fit residues: 55.6782 Evaluate side-chains 93 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 293 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 55 optimal weight: 2.9990 chunk 47 optimal weight: 0.0870 chunk 52 optimal weight: 0.7980 chunk 22 optimal weight: 0.3980 chunk 21 optimal weight: 0.5980 chunk 35 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 26 optimal weight: 0.5980 chunk 39 optimal weight: 0.7980 chunk 54 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 254 GLN B 254 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.123927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.085871 restraints weight = 6864.461| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 2.28 r_work: 0.2834 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 4992 Z= 0.119 Angle : 0.482 6.870 6648 Z= 0.252 Chirality : 0.035 0.134 700 Planarity : 0.003 0.025 826 Dihedral : 13.867 142.733 886 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 2.90 % Allowed : 25.31 % Favored : 71.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.14 (0.34), residues: 562 helix: 3.52 (0.22), residues: 438 sheet: None (None), residues: 0 loop : -0.41 (0.58), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 292 TYR 0.014 0.001 TYR B 78 PHE 0.008 0.001 PHE A 232 TRP 0.005 0.001 TRP A 53 HIS 0.002 0.000 HIS A 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.12 ( 4992) covalent geometry : angle 0.48241 / 0.25 ( 6648) hydrogen bonds : bond 0.04292 / 3.01 ( 376) hydrogen bonds : angle 3.47833 / 2.58 ( 1128) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 99 time to evaluate : 0.130 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7831 (tt0) REVERT: A 51 GLN cc_start: 0.8479 (tp40) cc_final: 0.8172 (tp40) REVERT: A 70 GLU cc_start: 0.8521 (mp0) cc_final: 0.8012 (pm20) REVERT: A 147 GLU cc_start: 0.8177 (tm-30) cc_final: 0.7805 (tm-30) REVERT: A 200 ILE cc_start: 0.8422 (OUTLIER) cc_final: 0.8136 (mp) REVERT: A 292 ARG cc_start: 0.8776 (ttm-80) cc_final: 0.8483 (ttm110) REVERT: B 46 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7850 (tt0) REVERT: B 70 GLU cc_start: 0.8523 (mp0) cc_final: 0.8015 (pm20) REVERT: B 147 GLU cc_start: 0.8214 (tm-30) cc_final: 0.7819 (tm-30) REVERT: B 195 TYR cc_start: 0.7724 (m-80) cc_final: 0.7490 (m-80) REVERT: B 200 ILE cc_start: 0.8435 (OUTLIER) cc_final: 0.8139 (mp) REVERT: B 292 ARG cc_start: 0.8730 (ttm-80) cc_final: 0.8442 (ttm110) outliers start: 14 outliers final: 5 residues processed: 107 average time/residue: 0.5409 time to fit residues: 59.8615 Evaluate side-chains 97 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 88 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 286 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 38 optimal weight: 0.0980 chunk 10 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 chunk 42 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 254 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.122909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.083605 restraints weight = 6735.919| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 2.30 r_work: 0.2761 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4992 Z= 0.129 Angle : 0.496 7.233 6648 Z= 0.260 Chirality : 0.035 0.143 700 Planarity : 0.003 0.025 826 Dihedral : 13.329 139.346 886 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 3.32 % Allowed : 25.31 % Favored : 71.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.12 (0.34), residues: 562 helix: 3.50 (0.22), residues: 436 sheet: None (None), residues: 0 loop : -0.30 (0.57), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 292 TYR 0.014 0.001 TYR B 78 PHE 0.009 0.001 PHE A 97 TRP 0.005 0.001 TRP A 222 HIS 0.002 0.000 HIS B 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 ( 4992) covalent geometry : angle 0.49602 / 0.26 ( 6648) hydrogen bonds : bond 0.04366 / 3.06 ( 376) hydrogen bonds : angle 3.49371 / 2.59 ( 1128) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 0.109 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7898 (tt0) REVERT: A 51 GLN cc_start: 0.8457 (tp40) cc_final: 0.8155 (tp40) REVERT: A 147 GLU cc_start: 0.8138 (tm-30) cc_final: 0.7756 (tm-30) REVERT: A 292 ARG cc_start: 0.8780 (ttm-80) cc_final: 0.8491 (ttm110) REVERT: B 46 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7882 (tt0) REVERT: B 54 GLU cc_start: 0.8608 (tm-30) cc_final: 0.8176 (tp30) REVERT: B 147 GLU cc_start: 0.8142 (tm-30) cc_final: 0.7728 (tm-30) REVERT: B 195 TYR cc_start: 0.7685 (m-80) cc_final: 0.7441 (m-80) REVERT: B 292 ARG cc_start: 0.8770 (ttm-80) cc_final: 0.8481 (ttm110) outliers start: 16 outliers final: 5 residues processed: 102 average time/residue: 0.4476 time to fit residues: 47.2090 Evaluate side-chains 94 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 87 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 286 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 0 optimal weight: 7.9990 chunk 1 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.2980 chunk 10 optimal weight: 0.7980 chunk 2 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 36 optimal weight: 0.0470 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 254 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.124411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.086010 restraints weight = 6840.398| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 2.29 r_work: 0.2877 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4992 Z= 0.122 Angle : 0.497 7.672 6648 Z= 0.256 Chirality : 0.035 0.135 700 Planarity : 0.003 0.027 826 Dihedral : 12.825 135.804 886 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 2.90 % Allowed : 25.31 % Favored : 71.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.18 (0.34), residues: 562 helix: 3.53 (0.22), residues: 436 sheet: None (None), residues: 0 loop : -0.24 (0.58), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 292 TYR 0.014 0.001 TYR B 78 PHE 0.008 0.001 PHE A 232 TRP 0.005 0.001 TRP A 53 HIS 0.002 0.001 HIS A 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 ( 4992) covalent geometry : angle 0.49694 / 0.26 ( 6648) hydrogen bonds : bond 0.04271 / 2.99 ( 376) hydrogen bonds : angle 3.45747 / 2.57 ( 1128) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 95 time to evaluate : 0.132 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7884 (tt0) REVERT: A 51 GLN cc_start: 0.8457 (tp40) cc_final: 0.8120 (tp40) REVERT: A 70 GLU cc_start: 0.8534 (mp0) cc_final: 0.7930 (pm20) REVERT: A 147 GLU cc_start: 0.8185 (tm-30) cc_final: 0.7793 (tm-30) REVERT: A 200 ILE cc_start: 0.8411 (OUTLIER) cc_final: 0.8127 (mp) REVERT: A 292 ARG cc_start: 0.8796 (ttm-80) cc_final: 0.8520 (ttm110) REVERT: B 46 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7842 (tt0) REVERT: B 70 GLU cc_start: 0.8539 (mp0) cc_final: 0.7937 (pm20) REVERT: B 147 GLU cc_start: 0.8182 (tm-30) cc_final: 0.7808 (tm-30) REVERT: B 195 TYR cc_start: 0.7730 (m-80) cc_final: 0.7498 (m-80) REVERT: B 200 ILE cc_start: 0.8431 (OUTLIER) cc_final: 0.8140 (mp) REVERT: B 292 ARG cc_start: 0.8777 (ttm-80) cc_final: 0.8502 (ttm110) outliers start: 14 outliers final: 5 residues processed: 105 average time/residue: 0.4421 time to fit residues: 48.0903 Evaluate side-chains 101 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 92 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 286 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 50 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 6 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 55 optimal weight: 0.0070 chunk 33 optimal weight: 0.7980 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 254 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.123824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.084513 restraints weight = 6817.885| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 2.33 r_work: 0.2869 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4992 Z= 0.132 Angle : 0.520 7.275 6648 Z= 0.269 Chirality : 0.035 0.141 700 Planarity : 0.003 0.027 826 Dihedral : 12.652 133.305 886 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 2.49 % Allowed : 25.73 % Favored : 71.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.16 (0.34), residues: 562 helix: 3.50 (0.22), residues: 434 sheet: None (None), residues: 0 loop : -0.13 (0.58), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 292 TYR 0.016 0.001 TYR A 78 PHE 0.009 0.001 PHE B 97 TRP 0.004 0.001 TRP A 222 HIS 0.002 0.000 HIS B 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 ( 4992) covalent geometry : angle 0.52008 / 0.27 ( 6648) hydrogen bonds : bond 0.04359 / 3.04 ( 376) hydrogen bonds : angle 3.48919 / 2.59 ( 1128) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 92 time to evaluate : 0.107 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7943 (tt0) REVERT: A 51 GLN cc_start: 0.8505 (tp40) cc_final: 0.8200 (tp40) REVERT: A 70 GLU cc_start: 0.8517 (mp0) cc_final: 0.7916 (pm20) REVERT: A 147 GLU cc_start: 0.8186 (tm-30) cc_final: 0.7761 (tm-30) REVERT: A 200 ILE cc_start: 0.8429 (OUTLIER) cc_final: 0.8140 (mp) REVERT: A 292 ARG cc_start: 0.8795 (ttm-80) cc_final: 0.8522 (ttm110) REVERT: B 46 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7951 (tt0) REVERT: B 54 GLU cc_start: 0.8599 (tm-30) cc_final: 0.8265 (tp30) REVERT: B 70 GLU cc_start: 0.8534 (mp0) cc_final: 0.7958 (pm20) REVERT: B 147 GLU cc_start: 0.8195 (tm-30) cc_final: 0.7770 (tm-30) REVERT: B 195 TYR cc_start: 0.7741 (m-80) cc_final: 0.7502 (m-80) REVERT: B 200 ILE cc_start: 0.8429 (OUTLIER) cc_final: 0.8142 (mp) REVERT: B 292 ARG cc_start: 0.8786 (ttm-80) cc_final: 0.8514 (ttm110) outliers start: 12 outliers final: 5 residues processed: 100 average time/residue: 0.4813 time to fit residues: 49.8080 Evaluate side-chains 95 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 286 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 32 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 51 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 chunk 16 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.123379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.084192 restraints weight = 6780.256| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 2.32 r_work: 0.2772 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4992 Z= 0.133 Angle : 0.513 7.467 6648 Z= 0.267 Chirality : 0.035 0.141 700 Planarity : 0.003 0.027 826 Dihedral : 12.487 130.912 886 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 2.49 % Allowed : 25.73 % Favored : 71.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.13 (0.34), residues: 562 helix: 3.48 (0.22), residues: 434 sheet: None (None), residues: 0 loop : -0.14 (0.58), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 292 TYR 0.015 0.001 TYR A 78 PHE 0.009 0.001 PHE B 97 TRP 0.004 0.001 TRP A 222 HIS 0.002 0.000 HIS B 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 ( 4992) covalent geometry : angle 0.51320 / 0.27 ( 6648) hydrogen bonds : bond 0.04365 / 3.05 ( 376) hydrogen bonds : angle 3.49352 / 2.59 ( 1128) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 0.104 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7888 (tt0) REVERT: A 51 GLN cc_start: 0.8458 (tp40) cc_final: 0.8162 (tp40) REVERT: A 70 GLU cc_start: 0.8482 (mp0) cc_final: 0.7887 (pm20) REVERT: A 147 GLU cc_start: 0.8145 (tm-30) cc_final: 0.7721 (tm-30) REVERT: A 200 ILE cc_start: 0.8348 (OUTLIER) cc_final: 0.8068 (mp) REVERT: A 292 ARG cc_start: 0.8782 (ttm-80) cc_final: 0.8510 (ttm110) REVERT: B 46 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7860 (tt0) REVERT: B 54 GLU cc_start: 0.8539 (tm-30) cc_final: 0.8234 (tp30) REVERT: B 70 GLU cc_start: 0.8507 (mp0) cc_final: 0.7933 (pm20) REVERT: B 147 GLU cc_start: 0.8140 (tm-30) cc_final: 0.7712 (tm-30) REVERT: B 195 TYR cc_start: 0.7674 (m-80) cc_final: 0.7443 (m-80) REVERT: B 200 ILE cc_start: 0.8357 (OUTLIER) cc_final: 0.8082 (mp) REVERT: B 292 ARG cc_start: 0.8786 (ttm-80) cc_final: 0.8509 (ttm110) outliers start: 12 outliers final: 6 residues processed: 94 average time/residue: 0.4712 time to fit residues: 45.7341 Evaluate side-chains 96 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 86 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 286 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 5 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 8 optimal weight: 0.2980 chunk 21 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.121492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.082934 restraints weight = 6938.406| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 2.29 r_work: 0.2768 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4992 Z= 0.164 Angle : 0.540 7.425 6648 Z= 0.282 Chirality : 0.037 0.156 700 Planarity : 0.003 0.027 826 Dihedral : 12.626 127.990 886 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 2.28 % Allowed : 25.73 % Favored : 71.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.07 (0.34), residues: 562 helix: 3.43 (0.22), residues: 434 sheet: None (None), residues: 0 loop : -0.11 (0.58), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 292 TYR 0.015 0.001 TYR A 78 PHE 0.010 0.001 PHE B 97 TRP 0.005 0.001 TRP A 222 HIS 0.002 0.001 HIS B 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.16 ( 4992) covalent geometry : angle 0.54006 / 0.28 ( 6648) hydrogen bonds : bond 0.04618 / 3.22 ( 376) hydrogen bonds : angle 3.58900 / 2.66 ( 1128) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1517.55 seconds wall clock time: 26 minutes 30.81 seconds (1590.81 seconds total)