Starting phenix.real_space_refine on Thu Jul 2 00:51:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jgz_61467/07_2026/9jgz_61467.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jgz_61467/07_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_61467/07_2026/9jgz_61467.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jgz_61467/07_2026/9jgz_61467.map" model { file = "/net/cci-nas-00/data/ceres_data/9jgz_61467/07_2026/9jgz_61467.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jgz_61467/07_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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/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, 165 Ad-hoc single atom residues: {' K': 2} Unusual residues: {'ACD': 1, 'D21': 1, 'EIC': 1, 'POV': 6} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain breaks: 2 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, 165 Ad-hoc single atom residues: {' K': 2} Unusual residues: {'ACD': 1, 'D21': 1, 'EIC': 1, 'POV': 6} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain breaks: 2 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: 1.12, per 1000 atoms: 0.23 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: 0.30 Conformation dependent library (CDL) restraints added in 115.4 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: 0.66 Time building geometry restraints manager: 0.39 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: 0.790 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: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.210 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:6.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.350 ------------------------------------------------------------------------------- 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 : 0.167 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: 0.4938 time to fit residues: 53.7421 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 : 0.111 ------------------------------------------------------------------------------- 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 = 0.3502 r_free = 0.3502 target = 0.120784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.081668 restraints weight = 6960.368| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 2.38 r_work: 0.2803 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.1274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 4992 Z= 0.151 Angle : 0.591 14.663 6648 Z= 0.276 Chirality : 0.037 0.147 700 Planarity : 0.003 0.024 826 Dihedral : 21.194 161.180 898 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 4.15 % Allowed : 23.86 % 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: 4.11 (0.35), residues: 562 helix: 3.47 (0.22), residues: 440 sheet: None (None), residues: 0 loop : -0.34 (0.61), 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 0.011 0.001 PHE B 232 TRP 0.006 0.001 TRP A 222 HIS 0.003 0.001 HIS A 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 ( 4992) covalent geometry : angle 0.59050 / 0.28 ( 6648) hydrogen bonds : bond 0.04671 / 3.26 ( 376) hydrogen bonds : angle 3.75941 / 2.80 ( 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 117 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 97 time to evaluate : 0.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.8116 (tt0) REVERT: A 147 GLU cc_start: 0.8193 (tm-30) cc_final: 0.7833 (tm-30) REVERT: B 46 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7974 (tt0) REVERT: B 147 GLU cc_start: 0.8233 (tm-30) cc_final: 0.7869 (tm-30) outliers start: 20 outliers final: 8 residues processed: 109 average time/residue: 0.5135 time to fit residues: 58.0075 Evaluate side-chains 100 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 0.185 ------------------------------------------------------------------------------- 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 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 108 VAL 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: 2.9990 chunk 8 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 47 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 44 optimal weight: 0.0980 chunk 17 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 = 0.3504 r_free = 0.3504 target = 0.120934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.082074 restraints weight = 6876.996| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 2.35 r_work: 0.2719 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 4992 Z= 0.141 Angle : 0.502 6.536 6648 Z= 0.258 Chirality : 0.036 0.147 700 Planarity : 0.003 0.040 826 Dihedral : 17.539 144.984 888 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 4.36 % Allowed : 22.82 % Favored : 72.82 % 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: 4.11 (0.34), residues: 562 helix: 3.46 (0.22), residues: 438 sheet: None (None), residues: 0 loop : -0.25 (0.59), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 292 TYR 0.011 0.001 TYR B 78 PHE 0.010 0.001 PHE A 232 TRP 0.009 0.001 TRP A 190 HIS 0.002 0.001 HIS A 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 ( 4992) covalent geometry : angle 0.50208 / 0.26 ( 6648) hydrogen bonds : bond 0.04514 / 3.16 ( 376) hydrogen bonds : angle 3.63962 / 2.71 ( 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 117 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 0.167 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7824 (tt0) REVERT: A 147 GLU cc_start: 0.8105 (tm-30) cc_final: 0.7741 (tm-30) REVERT: A 292 ARG cc_start: 0.8758 (ttm-80) cc_final: 0.8447 (ttm110) REVERT: B 46 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7805 (tt0) REVERT: B 147 GLU cc_start: 0.8131 (tm-30) cc_final: 0.7757 (tm-30) REVERT: B 292 ARG cc_start: 0.8729 (ttm-80) cc_final: 0.8422 (ttm110) outliers start: 21 outliers final: 5 residues processed: 110 average time/residue: 0.4973 time to fit residues: 56.6951 Evaluate side-chains 96 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 89 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU 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 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: 4.9990 chunk 20 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 32 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3499 r_free = 0.3499 target = 0.120272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.082289 restraints weight = 6925.083| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 2.33 r_work: 0.2786 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4992 Z= 0.148 Angle : 0.503 6.549 6648 Z= 0.262 Chirality : 0.036 0.151 700 Planarity : 0.003 0.038 826 Dihedral : 16.347 144.466 886 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 3.73 % Allowed : 25.31 % Favored : 70.95 % 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: 3.46 (0.22), residues: 438 sheet: None (None), residues: 0 loop : -0.19 (0.60), 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 0.010 0.001 PHE A 97 TRP 0.005 0.001 TRP B 222 HIS 0.003 0.001 HIS B 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 ( 4992) covalent geometry : angle 0.50278 / 0.26 ( 6648) hydrogen bonds : bond 0.04525 / 3.17 ( 376) hydrogen bonds : angle 3.61850 / 2.69 ( 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 115 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 97 time to evaluate : 0.139 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7941 (tt0) REVERT: A 51 GLN cc_start: 0.8488 (tp40) cc_final: 0.8269 (tp40) REVERT: A 147 GLU cc_start: 0.8198 (tm-30) cc_final: 0.7778 (tm-30) REVERT: B 46 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7982 (tt0) REVERT: B 147 GLU cc_start: 0.8202 (tm-30) cc_final: 0.7778 (tm-30) outliers start: 18 outliers final: 7 residues processed: 108 average time/residue: 0.4542 time to fit residues: 50.7074 Evaluate side-chains 102 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 93 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 66 LEU 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 223 SER 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: 2.9990 chunk 15 optimal weight: 10.0000 chunk 13 optimal weight: 0.6980 chunk 43 optimal weight: 9.9990 chunk 14 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.3486 r_free = 0.3486 target = 0.119176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.080393 restraints weight = 6980.456| |-----------------------------------------------------------------------------| r_work (start): 0.2839 rms_B_bonded: 2.35 r_work: 0.2680 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 4992 Z= 0.178 Angle : 0.525 6.084 6648 Z= 0.276 Chirality : 0.037 0.163 700 Planarity : 0.003 0.026 826 Dihedral : 15.686 143.607 886 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 3.73 % Allowed : 24.48 % 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: 4.05 (0.34), residues: 562 helix: 3.40 (0.22), residues: 436 sheet: None (None), residues: 0 loop : -0.10 (0.59), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 292 TYR 0.014 0.001 TYR B 78 PHE 0.011 0.001 PHE A 232 TRP 0.005 0.001 TRP A 190 HIS 0.003 0.001 HIS B 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.18 ( 4992) covalent geometry : angle 0.52519 / 0.28 ( 6648) hydrogen bonds : bond 0.04694 / 3.28 ( 376) hydrogen bonds : angle 3.68039 / 2.74 ( 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 108 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 0.105 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7887 (tt0) REVERT: A 51 GLN cc_start: 0.8440 (tp40) cc_final: 0.8157 (tp40) REVERT: A 147 GLU cc_start: 0.8193 (tm-30) cc_final: 0.7756 (tm-30) REVERT: A 292 ARG cc_start: 0.8782 (ttm-80) cc_final: 0.8491 (ttm110) REVERT: B 46 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7871 (tt0) REVERT: B 147 GLU cc_start: 0.8177 (tm-30) cc_final: 0.7734 (tm-30) REVERT: B 292 ARG cc_start: 0.8740 (ttm-80) cc_final: 0.8431 (ttm110) outliers start: 18 outliers final: 12 residues processed: 102 average time/residue: 0.5035 time to fit residues: 53.0963 Evaluate side-chains 101 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 223 SER 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 223 SER Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 286 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: 5.9990 chunk 47 optimal weight: 0.7980 chunk 52 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 39 optimal weight: 0.4980 chunk 54 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3515 r_free = 0.3515 target = 0.121341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.083384 restraints weight = 7011.566| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 2.33 r_work: 0.2772 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4992 Z= 0.137 Angle : 0.498 6.862 6648 Z= 0.262 Chirality : 0.036 0.142 700 Planarity : 0.003 0.025 826 Dihedral : 14.532 143.577 886 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 3.53 % Allowed : 24.48 % 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: 3.45 (0.22), residues: 436 sheet: None (None), residues: 0 loop : -0.10 (0.58), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 292 TYR 0.012 0.001 TYR A 78 PHE 0.009 0.001 PHE A 232 TRP 0.006 0.001 TRP B 53 HIS 0.002 0.000 HIS A 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 ( 4992) covalent geometry : angle 0.49826 / 0.26 ( 6648) hydrogen bonds : bond 0.04450 / 3.12 ( 376) hydrogen bonds : angle 3.58813 / 2.67 ( 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 112 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 95 time to evaluate : 0.103 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7736 (tt0) REVERT: A 51 GLN cc_start: 0.8409 (tp40) cc_final: 0.8123 (tp40) REVERT: A 70 GLU cc_start: 0.8473 (mp0) cc_final: 0.7950 (pm20) REVERT: A 147 GLU cc_start: 0.8139 (tm-30) cc_final: 0.7741 (tm-30) REVERT: A 292 ARG cc_start: 0.8774 (ttm-80) cc_final: 0.8477 (ttm110) REVERT: B 46 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7758 (tt0) REVERT: B 70 GLU cc_start: 0.8465 (mp0) cc_final: 0.7942 (pm20) REVERT: B 147 GLU cc_start: 0.8137 (tm-30) cc_final: 0.7755 (tm-30) REVERT: B 196 TYR cc_start: 0.7926 (m-80) cc_final: 0.7619 (m-80) REVERT: B 292 ARG cc_start: 0.8717 (ttm-80) cc_final: 0.8426 (ttm110) outliers start: 17 outliers final: 9 residues processed: 107 average time/residue: 0.5081 time to fit residues: 56.3705 Evaluate side-chains 98 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 87 time to evaluate : 0.114 ------------------------------------------------------------------------------- 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 193 SER Chi-restraints excluded: chain A residue 223 SER 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 223 SER 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: 0.8980 chunk 10 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 48 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3507 r_free = 0.3507 target = 0.120658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.081893 restraints weight = 6835.648| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 2.32 r_work: 0.2754 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 4992 Z= 0.153 Angle : 0.515 7.211 6648 Z= 0.274 Chirality : 0.036 0.150 700 Planarity : 0.003 0.025 826 Dihedral : 13.976 141.210 886 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 3.53 % Allowed : 24.90 % Favored : 71.58 % 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: 4.09 (0.34), residues: 562 helix: 3.42 (0.22), residues: 436 sheet: None (None), residues: 0 loop : -0.06 (0.58), residues: 126 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 0.010 0.001 PHE B 97 TRP 0.004 0.001 TRP B 53 HIS 0.002 0.001 HIS B 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 ( 4992) covalent geometry : angle 0.51465 / 0.27 ( 6648) hydrogen bonds : bond 0.04558 / 3.18 ( 376) hydrogen bonds : angle 3.64860 / 2.72 ( 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 103 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 86 time to evaluate : 0.109 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7898 (tt0) REVERT: A 51 GLN cc_start: 0.8447 (tp40) cc_final: 0.8146 (tp40) REVERT: A 147 GLU cc_start: 0.8177 (tm-30) cc_final: 0.7730 (tm-30) REVERT: A 200 ILE cc_start: 0.8349 (OUTLIER) cc_final: 0.8066 (mp) REVERT: A 292 ARG cc_start: 0.8785 (ttm-80) cc_final: 0.8490 (ttm110) REVERT: B 46 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7865 (tt0) REVERT: B 51 GLN cc_start: 0.8316 (tp40) cc_final: 0.8036 (tp40) REVERT: B 147 GLU cc_start: 0.8168 (tm-30) cc_final: 0.7737 (tm-30) REVERT: B 292 ARG cc_start: 0.8773 (ttm-80) cc_final: 0.8479 (ttm110) outliers start: 17 outliers final: 10 residues processed: 100 average time/residue: 0.5445 time to fit residues: 56.3661 Evaluate side-chains 94 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 81 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 193 SER 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 223 SER 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: 1.9990 chunk 16 optimal weight: 3.9990 chunk 37 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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 = 0.3483 r_free = 0.3483 target = 0.119005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.080456 restraints weight = 7011.683| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 2.30 r_work: 0.2738 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 4992 Z= 0.203 Angle : 0.564 7.541 6648 Z= 0.293 Chirality : 0.038 0.167 700 Planarity : 0.004 0.028 826 Dihedral : 14.057 138.572 886 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 3.32 % Allowed : 24.90 % 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: 3.98 (0.34), residues: 562 helix: 3.38 (0.22), residues: 432 sheet: None (None), residues: 0 loop : -0.14 (0.58), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 292 TYR 0.016 0.002 TYR B 78 PHE 0.012 0.001 PHE B 97 TRP 0.004 0.001 TRP B 222 HIS 0.003 0.001 HIS B 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.20 ( 4992) covalent geometry : angle 0.56385 / 0.29 ( 6648) hydrogen bonds : bond 0.04877 / 3.40 ( 376) hydrogen bonds : angle 3.74150 / 2.79 ( 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 96 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 0.247 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.8014 (tt0) REVERT: A 51 GLN cc_start: 0.8480 (tp40) cc_final: 0.8243 (tp40) REVERT: A 147 GLU cc_start: 0.8240 (tm-30) cc_final: 0.7730 (tm-30) REVERT: B 46 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7998 (tt0) REVERT: B 147 GLU cc_start: 0.8238 (tm-30) cc_final: 0.7759 (tm-30) outliers start: 16 outliers final: 12 residues processed: 94 average time/residue: 0.5271 time to fit residues: 51.3277 Evaluate side-chains 93 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 223 SER 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 66 LEU Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 223 SER 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: 0.9980 chunk 0 optimal weight: 7.9990 chunk 6 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 54 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 53 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3505 r_free = 0.3505 target = 0.120809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.081729 restraints weight = 6879.383| |-----------------------------------------------------------------------------| r_work (start): 0.2862 rms_B_bonded: 2.34 r_work: 0.2706 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 4992 Z= 0.154 Angle : 0.548 7.195 6648 Z= 0.285 Chirality : 0.036 0.145 700 Planarity : 0.004 0.052 826 Dihedral : 13.470 136.868 886 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 3.32 % Allowed : 26.76 % Favored : 69.92 % 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: 3.39 (0.22), residues: 434 sheet: None (None), residues: 0 loop : 0.04 (0.58), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 292 TYR 0.014 0.001 TYR B 78 PHE 0.010 0.001 PHE B 97 TRP 0.006 0.001 TRP B 53 HIS 0.002 0.000 HIS B 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 ( 4992) covalent geometry : angle 0.54824 / 0.28 ( 6648) hydrogen bonds : bond 0.04603 / 3.21 ( 376) hydrogen bonds : angle 3.64695 / 2.72 ( 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 101 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 85 time to evaluate : 0.116 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7915 (tt0) REVERT: A 51 GLN cc_start: 0.8458 (tp40) cc_final: 0.8217 (tp40) REVERT: A 147 GLU cc_start: 0.8202 (tm-30) cc_final: 0.7753 (tm-30) REVERT: A 200 ILE cc_start: 0.8355 (OUTLIER) cc_final: 0.8091 (mp) REVERT: A 292 ARG cc_start: 0.8801 (ttm-80) cc_final: 0.8480 (ttp-110) REVERT: B 46 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7891 (tt0) REVERT: B 54 GLU cc_start: 0.8555 (tm-30) cc_final: 0.8166 (tp30) REVERT: B 147 GLU cc_start: 0.8196 (tm-30) cc_final: 0.7755 (tm-30) REVERT: B 292 ARG cc_start: 0.8788 (ttm-80) cc_final: 0.8469 (ttp-110) outliers start: 16 outliers final: 11 residues processed: 97 average time/residue: 0.5198 time to fit residues: 52.1339 Evaluate side-chains 96 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 223 SER 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 66 LEU Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 223 SER 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: 3.9990 chunk 34 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 51 optimal weight: 0.5980 chunk 35 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3505 r_free = 0.3505 target = 0.120739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.082341 restraints weight = 6906.087| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 2.30 r_work: 0.2709 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 4992 Z= 0.159 Angle : 0.553 7.742 6648 Z= 0.288 Chirality : 0.036 0.146 700 Planarity : 0.004 0.047 826 Dihedral : 13.166 134.267 886 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 2.90 % Allowed : 27.18 % Favored : 69.92 % 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: 4.02 (0.34), residues: 562 helix: 3.35 (0.22), residues: 436 sheet: None (None), residues: 0 loop : -0.04 (0.59), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 292 TYR 0.016 0.002 TYR B 78 PHE 0.010 0.001 PHE B 97 TRP 0.005 0.001 TRP A 53 HIS 0.002 0.000 HIS A 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 ( 4992) covalent geometry : angle 0.55306 / 0.29 ( 6648) hydrogen bonds : bond 0.04601 / 3.21 ( 376) hydrogen bonds : angle 3.65551 / 2.72 ( 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 93 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 0.160 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7887 (tt0) REVERT: A 51 GLN cc_start: 0.8473 (tp40) cc_final: 0.8232 (tp40) REVERT: A 70 GLU cc_start: 0.8469 (mp0) cc_final: 0.8056 (pm20) REVERT: A 147 GLU cc_start: 0.8203 (tm-30) cc_final: 0.7754 (tm-30) REVERT: A 200 ILE cc_start: 0.8365 (OUTLIER) cc_final: 0.8097 (mp) REVERT: A 292 ARG cc_start: 0.8781 (ttm-80) cc_final: 0.8473 (ttp-110) REVERT: B 46 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7947 (tt0) REVERT: B 54 GLU cc_start: 0.8553 (tm-30) cc_final: 0.8193 (tp30) REVERT: B 70 GLU cc_start: 0.8467 (mp0) cc_final: 0.8058 (pm20) REVERT: B 147 GLU cc_start: 0.8204 (tm-30) cc_final: 0.7752 (tm-30) REVERT: B 292 ARG cc_start: 0.8777 (ttm-80) cc_final: 0.8469 (ttp-110) outliers start: 14 outliers final: 11 residues processed: 91 average time/residue: 0.5295 time to fit residues: 49.8188 Evaluate side-chains 93 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 223 SER 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 66 LEU Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 223 SER 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: 1.9990 chunk 10 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 8 optimal weight: 0.0770 chunk 21 optimal weight: 0.9990 overall best weight: 0.7538 ------------------------------------------------------------------------------- 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 = 0.3509 r_free = 0.3509 target = 0.120836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.081714 restraints weight = 7005.251| |-----------------------------------------------------------------------------| r_work (start): 0.2862 rms_B_bonded: 2.35 r_work: 0.2706 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4992 Z= 0.148 Angle : 0.543 7.683 6648 Z= 0.282 Chirality : 0.036 0.143 700 Planarity : 0.004 0.043 826 Dihedral : 12.753 131.495 886 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.90 % Allowed : 27.18 % Favored : 69.92 % 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: 3.39 (0.22), residues: 434 sheet: None (None), residues: 0 loop : 0.05 (0.58), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 292 TYR 0.014 0.001 TYR A 78 PHE 0.010 0.001 PHE A 232 TRP 0.005 0.001 TRP B 190 HIS 0.002 0.000 HIS B 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 ( 4992) covalent geometry : angle 0.54313 / 0.28 ( 6648) hydrogen bonds : bond 0.04502 / 3.14 ( 376) hydrogen bonds : angle 3.61187 / 2.69 ( 1128) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1506.77 seconds wall clock time: 26 minutes 22.86 seconds (1582.86 seconds total)