Starting phenix.real_space_refine on Wed Jul 1 23:38:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jh1_61469/07_2026/9jh1_61469.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jh1_61469/07_2026/9jh1_61469.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jh1_61469/07_2026/9jh1_61469.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jh1_61469/07_2026/9jh1_61469.map" model { file = "/net/cci-nas-00/data/ceres_data/9jh1_61469/07_2026/9jh1_61469.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jh1_61469/07_2026/9jh1_61469.cif" } resolution = 3.07 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= 0.000 sd= 0.042 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians K 2 8.98 5 S 32 5.16 5 C 2799 2.51 5 N 705 2.21 5 O 717 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s 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: 4255 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2095 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 5, 'TRANS': 256} Chain breaks: 1 Chain: "B" Number of atoms: 2102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2102 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 6, 'TRANS': 256} Chain breaks: 1 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 28 Ad-hoc single atom residues: {' K': 1} Unusual residues: {'EIC': 1, 'POV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-1': 1, 'POV:plan-2': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 28 Ad-hoc single atom residues: {' K': 1} Unusual residues: {'EIC': 1, 'POV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-1': 1, 'POV:plan-2': 1} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 1.22, per 1000 atoms: 0.29 Number of scatterers: 4255 At special positions: 0 Unit cell: (68.036, 88.54, 95.064, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) K 2 19.00 S 32 16.00 O 717 8.00 N 705 7.00 C 2799 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: 0.38 Conformation dependent library (CDL) restraints added in 147.1 milliseconds 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 970 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 0 sheets defined 81.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'A' and resid 20 through 22 No H-bonds generated for 'chain 'A' and resid 20 through 22' Processing helix chain 'A' and resid 23 through 63 removed outlier: 3.582A pdb=" N GLU A 42 " --> pdb=" O PHE A 38 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N ALA A 44 " --> pdb=" O ALA A 40 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N HIS A 45 " --> pdb=" O LEU A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 84 Processing helix chain 'A' and resid 96 through 109 Processing helix chain 'A' and resid 120 through 167 Proline residue: A 136 - end of helix 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 'B' and resid 20 through 22 No H-bonds generated for 'chain 'B' and resid 20 through 22' Processing helix chain 'B' and resid 23 through 63 removed outlier: 3.582A pdb=" N GLU B 42 " --> pdb=" O PHE B 38 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N ALA B 44 " --> pdb=" O ALA B 40 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N HIS B 45 " --> pdb=" O LEU B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 84 Processing helix chain 'B' and resid 96 through 109 Processing helix chain 'B' and resid 120 through 167 Proline residue: B 136 - end of helix 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 298 346 hydrogen bonds defined for protein. 1038 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: 0.52 Time building geometry restraints manager: 0.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1303 1.34 - 1.46: 1024 1.46 - 1.58: 1985 1.58 - 1.69: 0 1.69 - 1.81: 44 Bond restraints: 4356 Sorted by residual: bond pdb=" C10 EIC A 402 " pdb=" C9 EIC A 402 " ideal model delta sigma weight residual 1.332 1.528 -0.196 2.00e-02 2.50e+03 9.57e+01 bond pdb=" C12 EIC A 402 " pdb=" C13 EIC A 402 " ideal model delta sigma weight residual 1.332 1.527 -0.195 2.00e-02 2.50e+03 9.55e+01 bond pdb=" C12 EIC B 402 " pdb=" C13 EIC B 402 " ideal model delta sigma weight residual 1.332 1.527 -0.195 2.00e-02 2.50e+03 9.53e+01 bond pdb=" C10 EIC B 402 " pdb=" C9 EIC B 402 " ideal model delta sigma weight residual 1.332 1.527 -0.195 2.00e-02 2.50e+03 9.46e+01 bond pdb=" C31 POV A 401 " pdb=" O31 POV A 401 " ideal model delta sigma weight residual 1.327 1.261 0.066 2.00e-02 2.50e+03 1.08e+01 ... (remaining 4351 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.18: 5748 3.18 - 6.35: 100 6.35 - 9.53: 11 9.53 - 12.70: 7 12.70 - 15.88: 8 Bond angle restraints: 5874 Sorted by residual: angle pdb=" C12 EIC A 402 " pdb=" C13 EIC A 402 " pdb=" C14 EIC A 402 " ideal model delta sigma weight residual 128.16 112.28 15.88 3.00e+00 1.11e-01 2.80e+01 angle pdb=" C12 EIC B 402 " pdb=" C13 EIC B 402 " pdb=" C14 EIC B 402 " ideal model delta sigma weight residual 128.16 112.28 15.88 3.00e+00 1.11e-01 2.80e+01 angle pdb=" C10 EIC A 402 " pdb=" C9 EIC A 402 " pdb=" C8 EIC A 402 " ideal model delta sigma weight residual 127.75 112.16 15.59 3.00e+00 1.11e-01 2.70e+01 angle pdb=" C10 EIC B 402 " pdb=" C9 EIC B 402 " pdb=" C8 EIC B 402 " ideal model delta sigma weight residual 127.75 112.23 15.52 3.00e+00 1.11e-01 2.68e+01 angle pdb=" C11 EIC B 402 " pdb=" C12 EIC B 402 " pdb=" C13 EIC B 402 " ideal model delta sigma weight residual 127.66 112.40 15.26 3.00e+00 1.11e-01 2.59e+01 ... (remaining 5869 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.80: 2134 19.80 - 39.60: 306 39.60 - 59.40: 54 59.40 - 79.20: 10 79.20 - 98.99: 8 Dihedral angle restraints: 2512 sinusoidal: 995 harmonic: 1517 Sorted by residual: dihedral pdb=" CA ARG B 87 " pdb=" C ARG B 87 " pdb=" N VAL B 88 " pdb=" CA VAL B 88 " ideal model delta harmonic sigma weight residual -180.00 -156.83 -23.17 0 5.00e+00 4.00e-02 2.15e+01 dihedral pdb=" CA ARG A 87 " pdb=" C ARG A 87 " pdb=" N VAL A 88 " pdb=" CA VAL A 88 " ideal model delta harmonic sigma weight residual -180.00 -156.86 -23.14 0 5.00e+00 4.00e-02 2.14e+01 dihedral pdb=" CA ARG B 92 " pdb=" C ARG B 92 " pdb=" N PRO B 93 " pdb=" CA PRO B 93 " ideal model delta harmonic sigma weight residual 180.00 160.83 19.17 0 5.00e+00 4.00e-02 1.47e+01 ... (remaining 2509 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 487 0.043 - 0.087: 122 0.087 - 0.130: 26 0.130 - 0.174: 6 0.174 - 0.217: 4 Chirality restraints: 645 Sorted by residual: chirality pdb=" CA GLU B 42 " pdb=" N GLU B 42 " pdb=" C GLU B 42 " pdb=" CB GLU B 42 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CA GLU A 42 " pdb=" N GLU A 42 " pdb=" C GLU A 42 " pdb=" CB GLU A 42 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CB ILE B 283 " pdb=" CA ILE B 283 " pdb=" CG1 ILE B 283 " pdb=" CG2 ILE B 283 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.55e-01 ... (remaining 642 not shown) Planarity restraints: 728 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C11 EIC A 402 " -0.355 2.00e-02 2.50e+03 3.43e-01 1.18e+03 pdb=" C12 EIC A 402 " 0.383 2.00e-02 2.50e+03 pdb=" C13 EIC A 402 " 0.300 2.00e-02 2.50e+03 pdb=" C14 EIC A 402 " -0.328 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C11 EIC B 402 " 0.352 2.00e-02 2.50e+03 3.43e-01 1.17e+03 pdb=" C12 EIC B 402 " -0.373 2.00e-02 2.50e+03 pdb=" C13 EIC B 402 " -0.311 2.00e-02 2.50e+03 pdb=" C14 EIC B 402 " 0.332 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 EIC A 402 " 0.439 2.00e-02 2.50e+03 3.29e-01 1.08e+03 pdb=" C11 EIC A 402 " -0.158 2.00e-02 2.50e+03 pdb=" C8 EIC A 402 " 0.156 2.00e-02 2.50e+03 pdb=" C9 EIC A 402 " -0.437 2.00e-02 2.50e+03 ... (remaining 725 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.71: 189 2.71 - 3.32: 5444 3.32 - 3.93: 8454 3.93 - 4.53: 10968 4.53 - 5.14: 16369 Nonbonded interactions: 41424 Sorted by model distance: nonbonded pdb=" OE2 GLU A 220 " pdb=" OH TYR A 257 " model vdw 2.104 3.040 nonbonded pdb=" OE2 GLU B 220 " pdb=" OH TYR B 257 " model vdw 2.104 3.040 nonbonded pdb=" CG2 THR A 237 " pdb=" K K A 403 " model vdw 2.220 4.010 nonbonded pdb=" CG2 THR B 237 " pdb=" K K A 403 " model vdw 2.236 4.010 nonbonded pdb=" OD1 ASP A 89 " pdb=" NH2 ARG B 72 " model vdw 2.250 3.120 ... (remaining 41419 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 18 through 299 or resid 401 through 403)) } 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: 0.890 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: 0.010 Set scattering table: 0.010 Process input model: 5.700 Find NCS groups from input model: 0.080 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: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 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 : 0.008 0.196 4356 Z= 0.383 Angle : 1.141 15.879 5874 Z= 0.526 Chirality : 0.043 0.217 645 Planarity : 0.027 0.343 728 Dihedral : 18.632 98.995 1542 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 17.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 1.81 % Allowed : 34.76 % Favored : 63.43 % 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: -0.19 (0.36), residues: 517 helix: 0.52 (0.24), residues: 414 sheet: None (None), residues: 0 loop : -2.57 (0.58), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.033 0.002 ARG B 56 TYR 0.013 0.002 TYR B 155 PHE 0.008 0.001 PHE B 38 TRP 0.061 0.006 TRP A 95 HIS 0.004 0.001 HIS B 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00780 / 0.38 ( 4356) covalent geometry : angle 1.14055 / 0.53 ( 5874) hydrogen bonds : bond 0.08409 / 6.11 ( 346) hydrogen bonds : angle 5.33111 / 3.93 ( 1038) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 162 time to evaluate : 0.162 Fit side-chains revert: symmetry clash REVERT: A 21 LEU cc_start: 0.8281 (mt) cc_final: 0.7699 (mm) REVERT: A 70 GLU cc_start: 0.8292 (mm-30) cc_final: 0.7977 (mm-30) REVERT: A 273 TYR cc_start: 0.8557 (t80) cc_final: 0.8163 (t80) REVERT: B 21 LEU cc_start: 0.8227 (mt) cc_final: 0.7548 (mt) REVERT: B 48 GLN cc_start: 0.8144 (tm-30) cc_final: 0.7907 (tm-30) REVERT: B 70 GLU cc_start: 0.8284 (mm-30) cc_final: 0.7967 (mm-30) REVERT: B 213 SER cc_start: 0.9059 (m) cc_final: 0.8751 (p) REVERT: B 289 TRP cc_start: 0.5463 (t60) cc_final: 0.4904 (t60) outliers start: 8 outliers final: 2 residues processed: 167 average time/residue: 0.0639 time to fit residues: 13.5490 Evaluate side-chains 154 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 152 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain B residue 80 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 0.5980 chunk 48 optimal weight: 0.8980 chunk 26 optimal weight: 0.0000 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 chunk 50 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 overall best weight: 0.5184 ------------------------------------------------------------------------------- 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 = 0.3948 r_free = 0.3948 target = 0.138761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.117443 restraints weight = 8417.681| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 3.70 r_work: 0.3473 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 4356 Z= 0.164 Angle : 0.690 9.335 5874 Z= 0.349 Chirality : 0.038 0.171 645 Planarity : 0.004 0.037 728 Dihedral : 8.630 72.701 625 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 4.29 % Allowed : 27.99 % Favored : 67.72 % 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: 1.36 (0.38), residues: 517 helix: 1.57 (0.25), residues: 414 sheet: None (None), residues: 0 loop : -1.88 (0.62), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 56 TYR 0.030 0.002 TYR B 30 PHE 0.007 0.001 PHE B 225 TRP 0.017 0.002 TRP A 95 HIS 0.010 0.002 HIS A 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.16 ( 4356) covalent geometry : angle 0.69006 / 0.35 ( 5874) hydrogen bonds : bond 0.04150 / 2.78 ( 346) hydrogen bonds : angle 4.37849 / 3.29 ( 1038) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 155 time to evaluate : 0.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 LEU cc_start: 0.7737 (mt) cc_final: 0.7490 (mt) REVERT: A 129 PHE cc_start: 0.8628 (m-80) cc_final: 0.8322 (m-80) REVERT: B 80 GLU cc_start: 0.8737 (tm-30) cc_final: 0.8504 (tm-30) REVERT: B 95 TRP cc_start: 0.4303 (t60) cc_final: 0.3989 (t60) REVERT: B 129 PHE cc_start: 0.8659 (m-80) cc_final: 0.8357 (m-80) outliers start: 19 outliers final: 11 residues processed: 169 average time/residue: 0.0616 time to fit residues: 13.3834 Evaluate side-chains 154 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 143 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 279 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 22 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 0 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.3884 r_free = 0.3884 target = 0.134296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.112167 restraints weight = 8286.610| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 3.63 r_work: 0.3382 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 4356 Z= 0.172 Angle : 0.675 9.781 5874 Z= 0.340 Chirality : 0.038 0.187 645 Planarity : 0.004 0.034 728 Dihedral : 6.165 39.480 619 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 2.26 % Allowed : 31.38 % Favored : 66.37 % 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: 2.02 (0.38), residues: 517 helix: 2.02 (0.26), residues: 414 sheet: None (None), residues: 0 loop : -1.58 (0.62), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 56 TYR 0.020 0.002 TYR A 30 PHE 0.009 0.001 PHE B 225 TRP 0.011 0.002 TRP A 95 HIS 0.003 0.001 HIS B 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.17 ( 4356) covalent geometry : angle 0.67516 / 0.34 ( 5874) hydrogen bonds : bond 0.03967 / 2.64 ( 346) hydrogen bonds : angle 4.16864 / 3.14 ( 1038) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 143 time to evaluate : 0.170 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 GLU cc_start: 0.8508 (mm-30) cc_final: 0.8280 (mm-30) REVERT: A 95 TRP cc_start: 0.4670 (t60) cc_final: 0.4264 (t60) REVERT: A 129 PHE cc_start: 0.8666 (m-80) cc_final: 0.8456 (m-80) REVERT: A 162 GLN cc_start: 0.8974 (tp-100) cc_final: 0.8689 (tp-100) REVERT: A 220 GLU cc_start: 0.8384 (mp0) cc_final: 0.8114 (mp0) REVERT: B 80 GLU cc_start: 0.8748 (tm-30) cc_final: 0.8466 (tm-30) REVERT: B 95 TRP cc_start: 0.5038 (t60) cc_final: 0.4834 (t60) REVERT: B 129 PHE cc_start: 0.8695 (m-80) cc_final: 0.8494 (m-80) REVERT: B 220 GLU cc_start: 0.8397 (mp0) cc_final: 0.8133 (mp0) outliers start: 10 outliers final: 9 residues processed: 150 average time/residue: 0.0484 time to fit residues: 10.1193 Evaluate side-chains 147 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 138 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 279 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 9 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 chunk 47 optimal weight: 4.9990 chunk 15 optimal weight: 7.9990 chunk 6 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 4 optimal weight: 0.0170 chunk 41 optimal weight: 6.9990 overall best weight: 0.7018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 64 HIS B 64 HIS B 254 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.134348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.112271 restraints weight = 8407.428| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 3.61 r_work: 0.3375 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 4356 Z= 0.150 Angle : 0.656 9.813 5874 Z= 0.330 Chirality : 0.038 0.174 645 Planarity : 0.004 0.035 728 Dihedral : 5.635 34.748 619 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 4.51 % Allowed : 31.15 % Favored : 64.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.36 (0.38), residues: 517 helix: 2.19 (0.26), residues: 413 sheet: None (None), residues: 0 loop : -1.09 (0.65), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 72 TYR 0.020 0.001 TYR B 30 PHE 0.008 0.001 PHE A 225 TRP 0.007 0.001 TRP B 95 HIS 0.004 0.001 HIS B 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 ( 4356) covalent geometry : angle 0.65585 / 0.33 ( 5874) hydrogen bonds : bond 0.03812 / 2.54 ( 346) hydrogen bonds : angle 4.08466 / 3.08 ( 1038) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 152 time to evaluate : 0.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 TRP cc_start: 0.5063 (t60) cc_final: 0.4610 (t60) REVERT: A 129 PHE cc_start: 0.8594 (m-80) cc_final: 0.8326 (m-80) REVERT: A 158 LYS cc_start: 0.9178 (OUTLIER) cc_final: 0.8956 (mmtt) REVERT: A 220 GLU cc_start: 0.8356 (mp0) cc_final: 0.8137 (mp0) REVERT: B 70 GLU cc_start: 0.8436 (mm-30) cc_final: 0.8171 (mm-30) REVERT: B 129 PHE cc_start: 0.8675 (m-80) cc_final: 0.8413 (m-80) REVERT: B 158 LYS cc_start: 0.9195 (OUTLIER) cc_final: 0.8962 (mmtt) REVERT: B 162 GLN cc_start: 0.9051 (tp-100) cc_final: 0.8732 (tp-100) REVERT: B 220 GLU cc_start: 0.8383 (mp0) cc_final: 0.8161 (mp0) outliers start: 20 outliers final: 12 residues processed: 166 average time/residue: 0.0519 time to fit residues: 11.5508 Evaluate side-chains 161 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 147 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 158 LYS Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 158 LYS Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 279 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 49 optimal weight: 0.5980 chunk 14 optimal weight: 6.9990 chunk 4 optimal weight: 0.0050 chunk 17 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 48 optimal weight: 0.6980 chunk 42 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 21 optimal weight: 4.9990 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3861 r_free = 0.3861 target = 0.132918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.111379 restraints weight = 8445.631| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 3.61 r_work: 0.3377 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.2938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 4356 Z= 0.144 Angle : 0.733 17.048 5874 Z= 0.344 Chirality : 0.039 0.165 645 Planarity : 0.003 0.032 728 Dihedral : 5.379 32.170 619 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 4.74 % Allowed : 32.05 % Favored : 63.21 % 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: 2.56 (0.39), residues: 517 helix: 2.28 (0.26), residues: 413 sheet: None (None), residues: 0 loop : -0.76 (0.68), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 56 TYR 0.020 0.001 TYR B 30 PHE 0.008 0.001 PHE A 225 TRP 0.021 0.002 TRP B 95 HIS 0.004 0.001 HIS A 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 ( 4356) covalent geometry : angle 0.73349 / 0.34 ( 5874) hydrogen bonds : bond 0.03687 / 2.47 ( 346) hydrogen bonds : angle 4.05911 / 3.04 ( 1038) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 152 time to evaluate : 0.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 GLN cc_start: 0.8763 (tt0) cc_final: 0.8289 (tp40) REVERT: A 129 PHE cc_start: 0.8557 (m-80) cc_final: 0.8300 (m-80) REVERT: A 162 GLN cc_start: 0.8979 (tp-100) cc_final: 0.8537 (tp-100) REVERT: B 70 GLU cc_start: 0.8461 (mm-30) cc_final: 0.8222 (mm-30) REVERT: B 129 PHE cc_start: 0.8595 (m-80) cc_final: 0.8334 (m-80) REVERT: B 158 LYS cc_start: 0.9214 (OUTLIER) cc_final: 0.8979 (mmtt) outliers start: 21 outliers final: 13 residues processed: 167 average time/residue: 0.0507 time to fit residues: 11.4307 Evaluate side-chains 156 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 142 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 158 LYS Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 279 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 38 optimal weight: 0.7980 chunk 49 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 chunk 48 optimal weight: 0.7980 chunk 14 optimal weight: 10.0000 chunk 22 optimal weight: 0.6980 chunk 30 optimal weight: 0.7980 chunk 35 optimal weight: 0.4980 chunk 28 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3850 r_free = 0.3850 target = 0.131667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.110476 restraints weight = 8595.776| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 3.65 r_work: 0.3357 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.3208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4356 Z= 0.140 Angle : 0.731 15.447 5874 Z= 0.348 Chirality : 0.039 0.181 645 Planarity : 0.004 0.030 728 Dihedral : 5.241 30.416 619 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 3.61 % Allowed : 32.51 % Favored : 63.88 % 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: 2.73 (0.39), residues: 517 helix: 2.37 (0.26), residues: 413 sheet: None (None), residues: 0 loop : -0.53 (0.71), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 56 TYR 0.019 0.001 TYR B 30 PHE 0.009 0.001 PHE B 103 TRP 0.039 0.002 TRP A 95 HIS 0.004 0.001 HIS A 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 ( 4356) covalent geometry : angle 0.73058 / 0.35 ( 5874) hydrogen bonds : bond 0.03628 / 2.42 ( 346) hydrogen bonds : angle 4.00243 / 2.99 ( 1038) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 147 time to evaluate : 0.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 ASP cc_start: 0.7528 (p0) cc_final: 0.6883 (p0) REVERT: A 129 PHE cc_start: 0.8548 (m-80) cc_final: 0.8292 (m-80) REVERT: A 162 GLN cc_start: 0.8978 (tp-100) cc_final: 0.8703 (tp-100) REVERT: A 220 GLU cc_start: 0.8395 (mp0) cc_final: 0.8180 (mp0) REVERT: B 70 GLU cc_start: 0.8473 (mm-30) cc_final: 0.8240 (mm-30) REVERT: B 129 PHE cc_start: 0.8576 (m-80) cc_final: 0.8306 (m-80) REVERT: B 158 LYS cc_start: 0.9233 (OUTLIER) cc_final: 0.9019 (mmtt) REVERT: B 220 GLU cc_start: 0.8407 (mp0) cc_final: 0.8200 (mp0) outliers start: 16 outliers final: 14 residues processed: 155 average time/residue: 0.0466 time to fit residues: 9.7431 Evaluate side-chains 159 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 144 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 158 LYS Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 279 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 46 optimal weight: 0.4980 chunk 33 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 3 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 chunk 18 optimal weight: 0.0030 chunk 45 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 40 optimal weight: 8.9990 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3848 r_free = 0.3848 target = 0.131583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.110063 restraints weight = 8570.380| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 3.68 r_work: 0.3360 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.3237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4356 Z= 0.134 Angle : 0.726 16.760 5874 Z= 0.341 Chirality : 0.039 0.169 645 Planarity : 0.003 0.030 728 Dihedral : 5.093 28.896 619 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 3.39 % Allowed : 32.05 % Favored : 64.56 % 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: 2.80 (0.39), residues: 517 helix: 2.41 (0.26), residues: 413 sheet: None (None), residues: 0 loop : -0.49 (0.70), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 56 TYR 0.020 0.001 TYR A 30 PHE 0.009 0.001 PHE B 103 TRP 0.032 0.003 TRP A 95 HIS 0.004 0.001 HIS A 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 ( 4356) covalent geometry : angle 0.72635 / 0.34 ( 5874) hydrogen bonds : bond 0.03638 / 2.43 ( 346) hydrogen bonds : angle 3.98762 / 2.97 ( 1038) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 147 time to evaluate : 0.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 PHE cc_start: 0.8517 (m-80) cc_final: 0.8256 (m-80) REVERT: A 162 GLN cc_start: 0.8969 (tp-100) cc_final: 0.8686 (tp-100) REVERT: A 229 TYR cc_start: 0.9133 (t80) cc_final: 0.8208 (t80) REVERT: A 242 ASP cc_start: 0.8602 (p0) cc_final: 0.8014 (p0) REVERT: B 70 GLU cc_start: 0.8479 (mm-30) cc_final: 0.8268 (mm-30) REVERT: B 129 PHE cc_start: 0.8485 (m-80) cc_final: 0.8174 (m-80) REVERT: B 158 LYS cc_start: 0.9225 (OUTLIER) cc_final: 0.8987 (mmtt) REVERT: B 215 MET cc_start: 0.9449 (ttp) cc_final: 0.8953 (ttp) outliers start: 15 outliers final: 14 residues processed: 155 average time/residue: 0.0508 time to fit residues: 10.6885 Evaluate side-chains 156 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 141 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 158 LYS Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 279 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 2 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 36 optimal weight: 0.2980 chunk 4 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 254 GLN ** B 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 254 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.130306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.108716 restraints weight = 8426.671| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 3.60 r_work: 0.3338 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.3422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4356 Z= 0.147 Angle : 0.761 17.512 5874 Z= 0.358 Chirality : 0.039 0.180 645 Planarity : 0.004 0.029 728 Dihedral : 5.134 28.240 619 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 4.06 % Allowed : 32.51 % Favored : 63.43 % 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: 2.86 (0.39), residues: 517 helix: 2.44 (0.25), residues: 413 sheet: None (None), residues: 0 loop : -0.40 (0.71), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 56 TYR 0.020 0.001 TYR A 30 PHE 0.009 0.001 PHE B 103 TRP 0.039 0.003 TRP B 53 HIS 0.004 0.001 HIS A 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.15 ( 4356) covalent geometry : angle 0.76106 / 0.36 ( 5874) hydrogen bonds : bond 0.03661 / 2.46 ( 346) hydrogen bonds : angle 3.99878 / 2.98 ( 1038) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 143 time to evaluate : 0.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 PHE cc_start: 0.8531 (m-80) cc_final: 0.8283 (m-80) REVERT: A 162 GLN cc_start: 0.8972 (tp-100) cc_final: 0.8675 (tp-100) REVERT: B 70 GLU cc_start: 0.8476 (mm-30) cc_final: 0.8225 (mm-30) REVERT: B 129 PHE cc_start: 0.8471 (m-80) cc_final: 0.8231 (m-80) outliers start: 18 outliers final: 15 residues processed: 154 average time/residue: 0.0477 time to fit residues: 10.0432 Evaluate side-chains 156 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 141 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 95 TRP Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain B residue 20 PHE Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 95 TRP Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 279 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 19 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 2 optimal weight: 0.1980 chunk 18 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 14 optimal weight: 7.9990 chunk 38 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3830 r_free = 0.3830 target = 0.130148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.108581 restraints weight = 8512.378| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 3.61 r_work: 0.3330 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.3434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4356 Z= 0.144 Angle : 0.752 16.647 5874 Z= 0.356 Chirality : 0.039 0.180 645 Planarity : 0.003 0.027 728 Dihedral : 5.102 27.715 619 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 3.39 % Allowed : 33.86 % Favored : 62.75 % 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: 2.91 (0.38), residues: 517 helix: 2.45 (0.25), residues: 412 sheet: None (None), residues: 0 loop : -0.25 (0.72), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 56 TYR 0.019 0.001 TYR A 30 PHE 0.009 0.001 PHE B 103 TRP 0.029 0.003 TRP B 53 HIS 0.004 0.001 HIS A 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 ( 4356) covalent geometry : angle 0.75247 / 0.36 ( 5874) hydrogen bonds : bond 0.03664 / 2.46 ( 346) hydrogen bonds : angle 4.04972 / 3.01 ( 1038) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 139 time to evaluate : 0.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 PHE cc_start: 0.8533 (m-80) cc_final: 0.8260 (m-80) REVERT: A 162 GLN cc_start: 0.8939 (tp-100) cc_final: 0.8650 (tp-100) REVERT: B 70 GLU cc_start: 0.8493 (mm-30) cc_final: 0.8270 (mm-30) REVERT: B 129 PHE cc_start: 0.8480 (m-80) cc_final: 0.8225 (m-80) outliers start: 15 outliers final: 15 residues processed: 148 average time/residue: 0.0480 time to fit residues: 9.7707 Evaluate side-chains 153 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 138 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 95 TRP Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain B residue 20 PHE Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 95 TRP Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 279 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 18 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 42 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 48 optimal weight: 0.5980 chunk 28 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 254 GLN ** B 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 48 GLN B 254 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.129634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.108126 restraints weight = 8490.930| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 3.59 r_work: 0.3332 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.3536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4356 Z= 0.152 Angle : 0.779 17.401 5874 Z= 0.372 Chirality : 0.040 0.181 645 Planarity : 0.003 0.027 728 Dihedral : 5.113 27.564 619 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 4.29 % Allowed : 32.73 % Favored : 62.98 % 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: 2.90 (0.39), residues: 517 helix: 2.44 (0.25), residues: 412 sheet: None (None), residues: 0 loop : -0.21 (0.73), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 72 TYR 0.019 0.001 TYR B 30 PHE 0.010 0.001 PHE B 103 TRP 0.027 0.002 TRP A 95 HIS 0.005 0.001 HIS A 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 ( 4356) covalent geometry : angle 0.77860 / 0.37 ( 5874) hydrogen bonds : bond 0.03701 / 2.48 ( 346) hydrogen bonds : angle 4.10251 / 3.05 ( 1038) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1034 Ramachandran restraints generated. 517 Oldfield, 0 Emsley, 517 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 139 time to evaluate : 0.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 PHE cc_start: 0.8520 (m-80) cc_final: 0.8259 (m-80) REVERT: A 162 GLN cc_start: 0.8915 (tp-100) cc_final: 0.8573 (tp-100) REVERT: B 48 GLN cc_start: 0.8749 (OUTLIER) cc_final: 0.8377 (pp30) REVERT: B 70 GLU cc_start: 0.8509 (mm-30) cc_final: 0.8295 (mm-30) REVERT: B 129 PHE cc_start: 0.8464 (m-80) cc_final: 0.8215 (m-80) outliers start: 19 outliers final: 16 residues processed: 150 average time/residue: 0.0478 time to fit residues: 9.7894 Evaluate side-chains 153 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 136 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 95 TRP Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain B residue 20 PHE Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 48 GLN Chi-restraints excluded: chain B residue 95 TRP Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 279 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 29 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 19 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 chunk 43 optimal weight: 0.6980 chunk 2 optimal weight: 0.0370 chunk 41 optimal weight: 0.0570 chunk 23 optimal weight: 0.9980 overall best weight: 0.4576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 254 GLN ** B 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 48 GLN B 254 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.130544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.108917 restraints weight = 8482.833| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 3.62 r_work: 0.3350 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.3536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 4356 Z= 0.139 Angle : 0.773 17.277 5874 Z= 0.367 Chirality : 0.039 0.176 645 Planarity : 0.003 0.027 728 Dihedral : 5.071 27.058 619 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 3.61 % Allowed : 33.41 % Favored : 62.98 % 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: 2.88 (0.39), residues: 517 helix: 2.43 (0.25), residues: 412 sheet: None (None), residues: 0 loop : -0.21 (0.73), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 72 TYR 0.018 0.001 TYR B 30 PHE 0.010 0.001 PHE A 103 TRP 0.025 0.002 TRP B 53 HIS 0.005 0.001 HIS B 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.14 ( 4356) covalent geometry : angle 0.77257 / 0.37 ( 5874) hydrogen bonds : bond 0.03682 / 2.46 ( 346) hydrogen bonds : angle 4.12510 / 3.06 ( 1038) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1108.66 seconds wall clock time: 19 minutes 45.09 seconds (1185.09 seconds total)