Starting phenix.real_space_refine on Wed Jul 1 22:38:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mel_48217/07_2026/9mel_48217.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mel_48217/07_2026/9mel_48217.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9mel_48217/07_2026/9mel_48217.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mel_48217/07_2026/9mel_48217.map" model { file = "/net/cci-nas-00/data/ceres_data/9mel_48217/07_2026/9mel_48217.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mel_48217/07_2026/9mel_48217.cif" } resolution = 3.17 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= -0.001 sd= 0.049 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 3 8.98 5 S 14 5.16 5 C 2410 2.51 5 N 562 2.21 5 O 596 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 3589 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1759 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 238, 1754 Classifications: {'peptide': 238} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 9, 'TRANS': 228} Chain breaks: 2 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 47 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 6, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 53 Conformer: "B" Number of residues, atoms: 238, 1754 Classifications: {'peptide': 238} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 9, 'TRANS': 228} Chain breaks: 2 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 47 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 6, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 53 bond proxies already assigned to first conformer: 1788 Chain: "B" Number of atoms: 1759 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 238, 1754 Classifications: {'peptide': 238} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 9, 'TRANS': 228} Chain breaks: 2 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 47 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 6, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 53 Conformer: "B" Number of residues, atoms: 238, 1754 Classifications: {'peptide': 238} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 9, 'TRANS': 228} Chain breaks: 2 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 47 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 6, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 53 bond proxies already assigned to first conformer: 1788 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 0 Ad-hoc single atom residues: {' K': 3} Chain breaks: 3 Chain: "B" Number of atoms: 68 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1, 34 Unusual residues: {'1II': 1} Classifications: {'undetermined': 1} Conformer: "B" Number of residues, atoms: 1, 34 Unusual residues: {'1II': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" C07A1II B 401 " occ=0.50 ... (66 atoms not shown) pdb=" O03B1II B 401 " occ=0.50 Time building chain proxies: 1.57, per 1000 atoms: 0.44 Number of scatterers: 3589 At special positions: 0 Unit cell: (71.775, 61.625, 88.45, 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 3 19.00 S 14 16.00 F 4 9.00 O 596 8.00 N 562 7.00 C 2410 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 53 " - pdb=" SG CYS B 53 " distance=2.03 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: 0.34 Conformation dependent library (CDL) restraints added in 248.2 milliseconds 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 892 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 0 sheets defined 77.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.08 Creating SS restraints... Processing helix chain 'A' and resid 7 through 51 Proline residue: A 31 - end of helix Processing helix chain 'A' and resid 55 through 69 Processing helix chain 'A' and resid 72 through 78 removed outlier: 4.171A pdb=" N VAL A 76 " --> pdb=" O LEU A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 105 Processing helix chain 'A' and resid 116 through 150 Proline residue: A 132 - end of helix Processing helix chain 'A' and resid 167 through 195 removed outlier: 3.604A pdb=" N TRP A 171 " --> pdb=" O ARG A 167 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N LEU A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N VAL A 187 " --> pdb=" O VAL A 183 " (cutoff:3.500A) Proline residue: A 188 - end of helix Processing helix chain 'A' and resid 200 through 213 Processing helix chain 'A' and resid 230 through 263 Processing helix chain 'A' and resid 266 through 271 Processing helix chain 'B' and resid 8 through 51 Proline residue: B 31 - end of helix Processing helix chain 'B' and resid 55 through 69 Processing helix chain 'B' and resid 72 through 78 removed outlier: 4.171A pdb=" N VAL B 76 " --> pdb=" O LEU B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 105 Processing helix chain 'B' and resid 116 through 150 Proline residue: B 132 - end of helix Processing helix chain 'B' and resid 200 through 213 Processing helix chain 'B' and resid 230 through 263 Processing helix chain 'B' and resid 266 through 271 280 hydrogen bonds defined for protein. 838 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: 0.50 Time building geometry restraints manager: 0.42 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: 1066 1.34 - 1.46: 840 1.46 - 1.58: 1750 1.58 - 1.69: 0 1.69 - 1.81: 20 Bond restraints: 3676 Sorted by residual: bond pdb=" C31B1II B 401 " pdb=" C33B1II B 401 " ideal model delta sigma weight residual 1.378 1.350 0.028 2.00e-02 2.50e+03 1.99e+00 bond pdb=" C31A1II B 401 " pdb=" C33A1II B 401 " ideal model delta sigma weight residual 1.378 1.351 0.027 2.00e-02 2.50e+03 1.88e+00 bond pdb=" C07A1II B 401 " pdb=" C09A1II B 401 " ideal model delta sigma weight residual 1.546 1.521 0.025 2.00e-02 2.50e+03 1.58e+00 bond pdb=" C07B1II B 401 " pdb=" C09B1II B 401 " ideal model delta sigma weight residual 1.546 1.521 0.025 2.00e-02 2.50e+03 1.50e+00 bond pdb=" C30A1II B 401 " pdb=" C34A1II B 401 " ideal model delta sigma weight residual 1.383 1.360 0.023 2.00e-02 2.50e+03 1.31e+00 ... (remaining 3671 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 4891 1.73 - 3.46: 110 3.46 - 5.19: 33 5.19 - 6.92: 7 6.92 - 8.64: 5 Bond angle restraints: 5046 Sorted by residual: angle pdb=" C20B1II B 401 " pdb=" C17B1II B 401 " pdb=" C21B1II B 401 " ideal model delta sigma weight residual 110.45 119.09 -8.64 3.00e+00 1.11e-01 8.30e+00 angle pdb=" C20A1II B 401 " pdb=" C17A1II B 401 " pdb=" C21A1II B 401 " ideal model delta sigma weight residual 110.45 118.50 -8.05 3.00e+00 1.11e-01 7.20e+00 angle pdb=" C LEU B 265 " pdb=" N THR B 266 " pdb=" CA THR B 266 " ideal model delta sigma weight residual 121.54 126.54 -5.00 1.91e+00 2.74e-01 6.85e+00 angle pdb=" C LEU A 265 " pdb=" N THR A 266 " pdb=" CA THR A 266 " ideal model delta sigma weight residual 121.54 126.52 -4.98 1.91e+00 2.74e-01 6.78e+00 angle pdb=" C THR B 105 " pdb=" N THR B 106 " pdb=" CA THR B 106 " ideal model delta sigma weight residual 122.08 125.67 -3.59 1.47e+00 4.63e-01 5.96e+00 ... (remaining 5041 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.02: 2015 31.02 - 62.04: 87 62.04 - 93.06: 11 93.06 - 124.08: 4 124.08 - 155.10: 6 Dihedral angle restraints: 2123 sinusoidal: 739 harmonic: 1384 Sorted by residual: dihedral pdb=" C15A1II B 401 " pdb=" C12A1II B 401 " pdb=" C13A1II B 401 " pdb=" N04A1II B 401 " ideal model delta sinusoidal sigma weight residual 187.89 32.79 155.10 1 3.00e+01 1.11e-03 2.03e+01 dihedral pdb=" C11B1II B 401 " pdb=" C12B1II B 401 " pdb=" N04B1II B 401 " pdb=" C13B1II B 401 " ideal model delta sinusoidal sigma weight residual -58.54 88.01 -146.55 1 3.00e+01 1.11e-03 1.96e+01 dihedral pdb=" C11A1II B 401 " pdb=" C12A1II B 401 " pdb=" N04A1II B 401 " pdb=" C13A1II B 401 " ideal model delta sinusoidal sigma weight residual -58.54 82.41 -140.95 1 3.00e+01 1.11e-03 1.90e+01 ... (remaining 2120 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.109: 626 0.109 - 0.218: 8 0.218 - 0.327: 0 0.327 - 0.436: 0 0.436 - 0.545: 2 Chirality restraints: 636 Sorted by residual: chirality pdb=" C07B1II B 401 " pdb=" C08B1II B 401 " pdb=" C09B1II B 401 " pdb=" N05B1II B 401 " both_signs ideal model delta sigma weight residual False -2.31 -1.77 -0.55 2.00e-01 2.50e+01 7.44e+00 chirality pdb=" C07A1II B 401 " pdb=" C08A1II B 401 " pdb=" C09A1II B 401 " pdb=" N05A1II B 401 " both_signs ideal model delta sigma weight residual False -2.31 -1.82 -0.49 2.00e-01 2.50e+01 6.03e+00 chirality pdb=" CA THR A 214 " pdb=" N THR A 214 " pdb=" C THR A 214 " pdb=" CB THR A 214 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.14 2.00e-01 2.50e+01 4.76e-01 ... (remaining 633 not shown) Planarity restraints: 600 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 266 " -0.010 2.00e-02 2.50e+03 2.05e-02 4.19e+00 pdb=" C THR A 266 " 0.035 2.00e-02 2.50e+03 pdb=" O THR A 266 " -0.013 2.00e-02 2.50e+03 pdb=" N GLU A 267 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 266 " 0.010 2.00e-02 2.50e+03 2.04e-02 4.18e+00 pdb=" C THR B 266 " -0.035 2.00e-02 2.50e+03 pdb=" O THR B 266 " 0.013 2.00e-02 2.50e+03 pdb=" N GLU B 267 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 181 " -0.005 2.00e-02 2.50e+03 1.02e-02 1.03e+00 pdb=" C VAL B 181 " 0.018 2.00e-02 2.50e+03 pdb=" O VAL B 181 " -0.007 2.00e-02 2.50e+03 pdb=" N THR B 182 " -0.006 2.00e-02 2.50e+03 ... (remaining 597 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.79: 857 2.79 - 3.38: 4311 3.38 - 3.97: 6823 3.97 - 4.55: 9414 4.55 - 5.14: 13336 Nonbonded interactions: 34741 Sorted by model distance: nonbonded pdb=" O GLY A 108 " pdb=" K K A 401 " model vdw 2.206 3.590 nonbonded pdb=" O GLY B 108 " pdb=" K K A 401 " model vdw 2.218 3.590 nonbonded pdb=" O GLY B 216 " pdb=" K K A 401 " model vdw 2.362 3.590 nonbonded pdb=" O GLY A 216 " pdb=" K K A 401 " model vdw 2.378 3.590 nonbonded pdb=" O SER B 213 " pdb=" OG1 THR B 214 " model vdw 2.566 3.040 ... (remaining 34736 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' and (resid 7 through 134 or resid 136 through 271)) selection = (chain 'B' and (resid 7 through 134 or resid 136 through 271)) } 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=0.47 max=1.00 mean=0.99 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: 4.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 5.950 Find NCS groups from input model: 0.160 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:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 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 : 0.004 0.030 3677 Z= 0.192 Angle : 0.733 8.644 5048 Z= 0.337 Chirality : 0.047 0.545 636 Planarity : 0.003 0.024 600 Dihedral : 20.720 155.097 1228 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.72 % Allowed : 17.82 % Favored : 80.46 % 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: 3.40 (0.40), residues: 466 helix: 2.98 (0.25), residues: 374 sheet: None (None), residues: 0 loop : -1.07 (0.80), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 144 TYR 0.010 0.002 TYR B 206 PHE 0.013 0.002 PHE A 122 TRP 0.008 0.001 TRP A 171 HIS 0.003 0.001 HIS A 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.19 ( 3676) covalent geometry : angle 0.73350 / 0.34 ( 5046) SS BOND : bond 0.00106 / 0.06 ( 1) SS BOND : angle 0.02827 / 0.02 ( 2) hydrogen bonds : bond 0.10239 / 7.32 ( 280) hydrogen bonds : angle 4.74274 / 3.38 ( 838) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 0.120 Fit side-chains REVERT: A 20 LEU cc_start: 0.8165 (tp) cc_final: 0.7552 (mt) REVERT: A 64 GLU cc_start: 0.8263 (tp30) cc_final: 0.7612 (mt-10) REVERT: A 144 ARG cc_start: 0.6392 (mtt180) cc_final: 0.5868 (mmm160) REVERT: A 237 LEU cc_start: 0.8110 (mm) cc_final: 0.7705 (mm) REVERT: A 257 ARG cc_start: 0.7644 (ttp80) cc_final: 0.6559 (tpp-160) REVERT: B 20 LEU cc_start: 0.8154 (tp) cc_final: 0.7540 (mt) REVERT: B 64 GLU cc_start: 0.8261 (tp30) cc_final: 0.7607 (mt-10) REVERT: B 144 ARG cc_start: 0.6345 (mtt180) cc_final: 0.5842 (mmm160) REVERT: B 237 LEU cc_start: 0.8103 (mm) cc_final: 0.7697 (mm) REVERT: B 257 ARG cc_start: 0.7643 (ttp80) cc_final: 0.6558 (tpp-160) outliers start: 6 outliers final: 6 residues processed: 54 average time/residue: 0.1308 time to fit residues: 7.9874 Evaluate side-chains 56 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 236 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 24 optimal weight: 0.1980 chunk 26 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 30 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 37 optimal weight: 0.1980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 = 0.3932 r_free = 0.3932 target = 0.176518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.132192 restraints weight = 11127.215| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 3.88 r_work: 0.3093 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3072 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3072 r_free = 0.3072 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3072 r_free = 0.3072 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3072 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.0561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3677 Z= 0.149 Angle : 0.638 10.105 5048 Z= 0.293 Chirality : 0.038 0.205 636 Planarity : 0.004 0.024 600 Dihedral : 20.002 131.284 570 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.01 % Allowed : 18.68 % Favored : 79.31 % 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: 3.80 (0.40), residues: 466 helix: 3.19 (0.25), residues: 376 sheet: None (None), residues: 0 loop : -0.73 (0.84), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 27 TYR 0.009 0.002 TYR B 234 PHE 0.013 0.002 PHE A 122 TRP 0.007 0.001 TRP A 171 HIS 0.003 0.001 HIS B 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 ( 3676) covalent geometry : angle 0.63769 / 0.29 ( 5046) SS BOND : bond 0.00134 / 0.07 ( 1) SS BOND : angle 0.21714 / 0.12 ( 2) hydrogen bonds : bond 0.03113 / 2.20 ( 280) hydrogen bonds : angle 3.73072 / 2.64 ( 838) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 48 time to evaluate : 0.127 Fit side-chains REVERT: A 20 LEU cc_start: 0.8177 (tp) cc_final: 0.7556 (mt) REVERT: A 144 ARG cc_start: 0.6387 (mtt180) cc_final: 0.5934 (mmm160) REVERT: A 237 LEU cc_start: 0.8187 (mm) cc_final: 0.7779 (mm) REVERT: A 257 ARG cc_start: 0.7675 (ttp80) cc_final: 0.6578 (tpp-160) REVERT: B 20 LEU cc_start: 0.8169 (tp) cc_final: 0.7543 (mt) REVERT: B 144 ARG cc_start: 0.6384 (mtt180) cc_final: 0.5941 (mmm160) REVERT: B 237 LEU cc_start: 0.8173 (mm) cc_final: 0.7769 (mm) REVERT: B 257 ARG cc_start: 0.7674 (ttp80) cc_final: 0.6577 (tpp-160) outliers start: 7 outliers final: 3 residues processed: 55 average time/residue: 0.1292 time to fit residues: 8.0587 Evaluate side-chains 51 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 48 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 123 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 33 optimal weight: 0.9990 chunk 43 optimal weight: 0.5980 chunk 13 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 15 optimal weight: 0.0470 chunk 29 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 overall best weight: 0.5678 ------------------------------------------------------------------------------- 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 = 0.3950 r_free = 0.3950 target = 0.177739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.133800 restraints weight = 8539.110| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 3.27 r_work: 0.3101 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3085 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3085 r_free = 0.3085 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3085 r_free = 0.3085 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3085 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.0795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3677 Z= 0.163 Angle : 0.640 10.401 5048 Z= 0.294 Chirality : 0.038 0.200 636 Planarity : 0.003 0.025 600 Dihedral : 19.770 135.110 562 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.01 % Allowed : 17.82 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 3.84 (0.40), residues: 466 helix: 3.24 (0.25), residues: 376 sheet: None (None), residues: 0 loop : -0.81 (0.82), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 65 TYR 0.012 0.002 TYR B 234 PHE 0.013 0.002 PHE A 122 TRP 0.008 0.001 TRP A 171 HIS 0.002 0.001 HIS B 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.16 ( 3676) covalent geometry : angle 0.64001 / 0.29 ( 5046) SS BOND : bond 0.00100 / 0.05 ( 1) SS BOND : angle 0.18504 / 0.10 ( 2) hydrogen bonds : bond 0.03068 / 2.16 ( 280) hydrogen bonds : angle 3.52678 / 2.52 ( 838) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 54 time to evaluate : 0.118 Fit side-chains REVERT: A 20 LEU cc_start: 0.8192 (tp) cc_final: 0.7564 (mt) REVERT: A 144 ARG cc_start: 0.6387 (mtt180) cc_final: 0.5924 (mmm160) REVERT: A 237 LEU cc_start: 0.8191 (mm) cc_final: 0.7774 (mm) REVERT: A 257 ARG cc_start: 0.7681 (ttp80) cc_final: 0.6581 (tpp-160) REVERT: B 20 LEU cc_start: 0.8173 (tp) cc_final: 0.7546 (mt) REVERT: B 144 ARG cc_start: 0.6396 (mtt180) cc_final: 0.5949 (mmm160) REVERT: B 237 LEU cc_start: 0.8180 (mm) cc_final: 0.7766 (mm) REVERT: B 257 ARG cc_start: 0.7691 (ttp80) cc_final: 0.6581 (tpp-160) outliers start: 7 outliers final: 4 residues processed: 61 average time/residue: 0.1187 time to fit residues: 8.2798 Evaluate side-chains 57 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 53 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 123 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 0 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 chunk 38 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3840 r_free = 0.3840 target = 0.169891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.124126 restraints weight = 8578.267| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 3.29 r_work: 0.3073 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3058 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3058 r_free = 0.3058 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3058 r_free = 0.3058 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3058 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.0981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 3677 Z= 0.195 Angle : 0.678 11.007 5048 Z= 0.312 Chirality : 0.039 0.200 636 Planarity : 0.004 0.024 600 Dihedral : 20.051 138.748 562 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.01 % Allowed : 17.53 % Favored : 80.46 % 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: 3.62 (0.40), residues: 466 helix: 3.09 (0.25), residues: 376 sheet: None (None), residues: 0 loop : -0.89 (0.82), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 144 TYR 0.018 0.002 TYR B 234 PHE 0.015 0.002 PHE A 122 TRP 0.009 0.001 TRP A 171 HIS 0.003 0.001 HIS A 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.19 ( 3676) covalent geometry : angle 0.67819 / 0.31 ( 5046) SS BOND : bond 0.00123 / 0.06 ( 1) SS BOND : angle 0.10017 / 0.06 ( 2) hydrogen bonds : bond 0.03211 / 2.25 ( 280) hydrogen bonds : angle 3.52669 / 2.54 ( 838) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 54 time to evaluate : 0.100 Fit side-chains REVERT: A 144 ARG cc_start: 0.6387 (mtt180) cc_final: 0.5915 (mmm160) REVERT: A 237 LEU cc_start: 0.8182 (mm) cc_final: 0.7775 (mm) REVERT: A 257 ARG cc_start: 0.7624 (ttp80) cc_final: 0.6504 (tpp-160) REVERT: B 20 LEU cc_start: 0.8194 (tp) cc_final: 0.7552 (mt) REVERT: B 144 ARG cc_start: 0.6373 (mtt180) cc_final: 0.5913 (mmm160) REVERT: B 237 LEU cc_start: 0.8169 (mm) cc_final: 0.7746 (mm) REVERT: B 257 ARG cc_start: 0.7634 (ttp80) cc_final: 0.6516 (tpp-160) outliers start: 7 outliers final: 7 residues processed: 58 average time/residue: 0.0933 time to fit residues: 6.2247 Evaluate side-chains 59 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 129 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 15 optimal weight: 0.2980 chunk 4 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 chunk 24 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 42 optimal weight: 0.0050 chunk 11 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 chunk 45 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 overall best weight: 0.4394 ------------------------------------------------------------------------------- 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 = 0.3886 r_free = 0.3886 target = 0.173846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.130206 restraints weight = 13619.911| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 4.85 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3292 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3292 r_free = 0.3292 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3292 r_free = 0.3292 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3292 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.1043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3677 Z= 0.140 Angle : 0.640 10.167 5048 Z= 0.290 Chirality : 0.037 0.188 636 Planarity : 0.003 0.025 600 Dihedral : 19.174 129.107 562 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.59 % Allowed : 16.67 % Favored : 80.75 % 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: 3.87 (0.40), residues: 466 helix: 3.29 (0.25), residues: 376 sheet: None (None), residues: 0 loop : -0.90 (0.82), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 27 TYR 0.010 0.002 TYR B 234 PHE 0.012 0.002 PHE B 122 TRP 0.008 0.001 TRP A 171 HIS 0.002 0.001 HIS B 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.14 ( 3676) covalent geometry : angle 0.64012 / 0.29 ( 5046) SS BOND : bond 0.00119 / 0.06 ( 1) SS BOND : angle 0.22691 / 0.13 ( 2) hydrogen bonds : bond 0.02882 / 2.02 ( 280) hydrogen bonds : angle 3.38433 / 2.44 ( 838) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.116 Fit side-chains REVERT: A 20 LEU cc_start: 0.8074 (tp) cc_final: 0.7443 (mt) REVERT: A 144 ARG cc_start: 0.6147 (mtt180) cc_final: 0.5830 (mmm160) REVERT: A 237 LEU cc_start: 0.8143 (mm) cc_final: 0.7705 (mm) REVERT: A 257 ARG cc_start: 0.7256 (ttp80) cc_final: 0.6321 (tpp-160) REVERT: B 20 LEU cc_start: 0.8095 (tp) cc_final: 0.7461 (mt) REVERT: B 144 ARG cc_start: 0.6182 (mtt180) cc_final: 0.5868 (mmm160) REVERT: B 237 LEU cc_start: 0.8130 (mm) cc_final: 0.7696 (mm) REVERT: B 257 ARG cc_start: 0.7300 (ttp80) cc_final: 0.6361 (tpp-160) outliers start: 9 outliers final: 8 residues processed: 60 average time/residue: 0.0955 time to fit residues: 6.5790 Evaluate side-chains 61 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 183 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 34 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 32 optimal weight: 0.0970 chunk 24 optimal weight: 0.0970 chunk 9 optimal weight: 0.0570 chunk 30 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.3494 ------------------------------------------------------------------------------- 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 = 0.3980 r_free = 0.3980 target = 0.180959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.136614 restraints weight = 12152.218| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 4.57 r_work: 0.3103 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3082 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3082 r_free = 0.3082 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3082 r_free = 0.3082 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3082 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3677 Z= 0.126 Angle : 0.626 9.819 5048 Z= 0.283 Chirality : 0.036 0.175 636 Planarity : 0.003 0.026 600 Dihedral : 18.631 124.956 562 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.72 % Allowed : 18.39 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.08 (0.40), residues: 466 helix: 3.44 (0.25), residues: 376 sheet: None (None), residues: 0 loop : -0.87 (0.82), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 44 TYR 0.009 0.001 TYR A 206 PHE 0.010 0.001 PHE A 122 TRP 0.007 0.001 TRP A 171 HIS 0.002 0.001 HIS B 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 ( 3676) covalent geometry : angle 0.62626 / 0.28 ( 5046) SS BOND : bond 0.00086 / 0.05 ( 1) SS BOND : angle 0.22083 / 0.12 ( 2) hydrogen bonds : bond 0.02755 / 1.92 ( 280) hydrogen bonds : angle 3.20057 / 2.33 ( 838) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.122 Fit side-chains REVERT: A 20 LEU cc_start: 0.8158 (tp) cc_final: 0.7543 (mt) REVERT: A 144 ARG cc_start: 0.6427 (mtt180) cc_final: 0.5948 (mmm160) REVERT: A 237 LEU cc_start: 0.8196 (mm) cc_final: 0.7804 (mm) REVERT: A 257 ARG cc_start: 0.7663 (ttp80) cc_final: 0.6515 (tpp-160) REVERT: B 20 LEU cc_start: 0.8157 (tp) cc_final: 0.7543 (mt) REVERT: B 144 ARG cc_start: 0.6458 (mtt180) cc_final: 0.6012 (mmm160) REVERT: B 237 LEU cc_start: 0.8139 (mm) cc_final: 0.7742 (mm) REVERT: B 257 ARG cc_start: 0.7669 (ttp80) cc_final: 0.6559 (tpp-160) outliers start: 6 outliers final: 6 residues processed: 58 average time/residue: 0.0972 time to fit residues: 6.3941 Evaluate side-chains 57 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 183 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 15 optimal weight: 0.3980 chunk 28 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 chunk 5 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 32 optimal weight: 0.0970 chunk 18 optimal weight: 0.8980 chunk 29 optimal weight: 0.3980 overall best weight: 0.4378 ------------------------------------------------------------------------------- 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 = 0.3980 r_free = 0.3980 target = 0.180415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.135987 restraints weight = 11241.406| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 4.00 r_work: 0.3133 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3112 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3112 r_free = 0.3112 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3112 r_free = 0.3112 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3112 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3677 Z= 0.142 Angle : 0.632 10.052 5048 Z= 0.288 Chirality : 0.037 0.176 636 Planarity : 0.003 0.025 600 Dihedral : 18.715 125.845 562 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.72 % Allowed : 19.25 % Favored : 79.02 % 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: 4.04 (0.40), residues: 466 helix: 3.40 (0.25), residues: 376 sheet: None (None), residues: 0 loop : -0.82 (0.82), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 44 TYR 0.011 0.002 TYR B 234 PHE 0.012 0.002 PHE A 122 TRP 0.007 0.001 TRP A 171 HIS 0.002 0.001 HIS B 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.14 ( 3676) covalent geometry : angle 0.63243 / 0.29 ( 5046) SS BOND : bond 0.00092 / 0.05 ( 1) SS BOND : angle 0.26087 / 0.15 ( 2) hydrogen bonds : bond 0.02807 / 1.96 ( 280) hydrogen bonds : angle 3.21888 / 2.34 ( 838) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.084 Fit side-chains REVERT: A 20 LEU cc_start: 0.8182 (tp) cc_final: 0.7572 (mt) REVERT: A 144 ARG cc_start: 0.6457 (mtt180) cc_final: 0.5985 (mmm160) REVERT: A 237 LEU cc_start: 0.8201 (mm) cc_final: 0.7803 (mm) REVERT: A 257 ARG cc_start: 0.7693 (ttp80) cc_final: 0.6596 (tpp-160) REVERT: B 20 LEU cc_start: 0.8185 (tp) cc_final: 0.7573 (mt) REVERT: B 144 ARG cc_start: 0.6444 (mtt180) cc_final: 0.6039 (mmm160) REVERT: B 237 LEU cc_start: 0.8200 (mm) cc_final: 0.7805 (mm) REVERT: B 257 ARG cc_start: 0.7694 (ttp80) cc_final: 0.6621 (tpp-160) outliers start: 6 outliers final: 5 residues processed: 58 average time/residue: 0.0924 time to fit residues: 6.1145 Evaluate side-chains 58 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 53 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 183 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 37 optimal weight: 0.3980 chunk 25 optimal weight: 0.6980 chunk 18 optimal weight: 0.4980 chunk 43 optimal weight: 0.8980 chunk 20 optimal weight: 0.5980 chunk 40 optimal weight: 0.5980 chunk 8 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 15 optimal weight: 0.1980 chunk 33 optimal weight: 1.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 = 0.3970 r_free = 0.3970 target = 0.179385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.135382 restraints weight = 10106.713| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 3.51 r_work: 0.3121 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3106 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3106 r_free = 0.3106 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3106 r_free = 0.3106 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3106 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.1273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3677 Z= 0.145 Angle : 0.636 10.229 5048 Z= 0.289 Chirality : 0.037 0.180 636 Planarity : 0.003 0.025 600 Dihedral : 18.641 125.317 562 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.30 % Allowed : 18.39 % Favored : 79.31 % 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: 3.89 (0.40), residues: 466 helix: 3.18 (0.25), residues: 386 sheet: None (None), residues: 0 loop : -0.77 (0.86), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG B 144 TYR 0.011 0.002 TYR B 234 PHE 0.012 0.002 PHE A 122 TRP 0.007 0.001 TRP A 171 HIS 0.002 0.001 HIS B 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.14 ( 3676) covalent geometry : angle 0.63566 / 0.29 ( 5046) SS BOND : bond 0.00077 / 0.04 ( 1) SS BOND : angle 0.23767 / 0.13 ( 2) hydrogen bonds : bond 0.02826 / 1.97 ( 280) hydrogen bonds : angle 3.22121 / 2.35 ( 838) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.126 Fit side-chains REVERT: A 20 LEU cc_start: 0.8128 (tp) cc_final: 0.7523 (mt) REVERT: A 144 ARG cc_start: 0.6398 (mtt180) cc_final: 0.5917 (mmm160) REVERT: A 237 LEU cc_start: 0.8121 (mm) cc_final: 0.7717 (mm) REVERT: A 257 ARG cc_start: 0.7598 (ttp80) cc_final: 0.6538 (tpp-160) REVERT: B 20 LEU cc_start: 0.8139 (tp) cc_final: 0.7529 (mt) REVERT: B 144 ARG cc_start: 0.6384 (mtt180) cc_final: 0.5978 (mmm160) REVERT: B 237 LEU cc_start: 0.8121 (mm) cc_final: 0.7720 (mm) REVERT: B 257 ARG cc_start: 0.7605 (ttp80) cc_final: 0.6544 (tpp-160) outliers start: 8 outliers final: 8 residues processed: 57 average time/residue: 0.1173 time to fit residues: 7.5711 Evaluate side-chains 59 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 51 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 270 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 30 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 32 optimal weight: 0.2980 chunk 13 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 chunk 34 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3970 r_free = 0.3970 target = 0.179034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.136930 restraints weight = 7970.554| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 3.09 r_work: 0.3144 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3119 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3119 r_free = 0.3119 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3119 r_free = 0.3119 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3119 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.1269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3677 Z= 0.158 Angle : 0.646 10.507 5048 Z= 0.295 Chirality : 0.037 0.178 636 Planarity : 0.003 0.025 600 Dihedral : 18.818 127.641 562 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.30 % Allowed : 19.25 % Favored : 78.45 % 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: 3.82 (0.40), residues: 466 helix: 3.13 (0.25), residues: 386 sheet: None (None), residues: 0 loop : -0.79 (0.85), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 144 TYR 0.013 0.002 TYR B 234 PHE 0.013 0.002 PHE B 122 TRP 0.007 0.001 TRP A 171 HIS 0.003 0.001 HIS A 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.16 ( 3676) covalent geometry : angle 0.64648 / 0.30 ( 5046) SS BOND : bond 0.00074 / 0.04 ( 1) SS BOND : angle 0.20817 / 0.12 ( 2) hydrogen bonds : bond 0.02895 / 2.02 ( 280) hydrogen bonds : angle 3.26628 / 2.38 ( 838) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 51 time to evaluate : 0.116 Fit side-chains REVERT: A 20 LEU cc_start: 0.8183 (tp) cc_final: 0.7579 (mt) REVERT: A 144 ARG cc_start: 0.6456 (mtt180) cc_final: 0.6007 (mmm160) REVERT: A 237 LEU cc_start: 0.8195 (mm) cc_final: 0.7808 (mm) REVERT: A 257 ARG cc_start: 0.7629 (ttp80) cc_final: 0.6551 (tpp-160) REVERT: B 20 LEU cc_start: 0.8206 (tp) cc_final: 0.7592 (mt) REVERT: B 144 ARG cc_start: 0.6436 (mtt180) cc_final: 0.6067 (mmm160) REVERT: B 237 LEU cc_start: 0.8206 (mm) cc_final: 0.7803 (mm) REVERT: B 257 ARG cc_start: 0.7598 (ttp80) cc_final: 0.6572 (tpp-160) outliers start: 8 outliers final: 8 residues processed: 56 average time/residue: 0.1150 time to fit residues: 7.3428 Evaluate side-chains 59 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 51 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 270 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 36 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 1 optimal weight: 0.5980 chunk 35 optimal weight: 0.6980 chunk 4 optimal weight: 0.6980 chunk 45 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3964 r_free = 0.3964 target = 0.179093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.136933 restraints weight = 11561.217| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 3.69 r_work: 0.3081 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3066 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3066 r_free = 0.3066 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3066 r_free = 0.3066 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3066 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 3677 Z= 0.184 Angle : 0.665 11.050 5048 Z= 0.305 Chirality : 0.038 0.180 636 Planarity : 0.004 0.025 600 Dihedral : 19.252 132.933 562 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.16 % Allowed : 18.39 % Favored : 78.45 % 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: 3.68 (0.40), residues: 466 helix: 3.02 (0.25), residues: 386 sheet: None (None), residues: 0 loop : -0.79 (0.85), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 144 TYR 0.017 0.002 TYR B 234 PHE 0.014 0.002 PHE A 122 TRP 0.008 0.001 TRP A 171 HIS 0.003 0.001 HIS B 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.18 ( 3676) covalent geometry : angle 0.66469 / 0.31 ( 5046) SS BOND : bond 0.00094 / 0.05 ( 1) SS BOND : angle 0.17582 / 0.10 ( 2) hydrogen bonds : bond 0.03054 / 2.13 ( 280) hydrogen bonds : angle 3.36653 / 2.45 ( 838) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 932 Ramachandran restraints generated. 466 Oldfield, 0 Emsley, 466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 49 time to evaluate : 0.077 Fit side-chains REVERT: A 20 LEU cc_start: 0.8266 (tp) cc_final: 0.7640 (mt) REVERT: A 144 ARG cc_start: 0.6576 (mtt180) cc_final: 0.6108 (mmm160) REVERT: A 237 LEU cc_start: 0.8291 (mm) cc_final: 0.7888 (mm) REVERT: A 257 ARG cc_start: 0.7691 (ttp80) cc_final: 0.6601 (tpp-160) REVERT: B 20 LEU cc_start: 0.8264 (tp) cc_final: 0.7631 (mt) REVERT: B 144 ARG cc_start: 0.6509 (mtt180) cc_final: 0.6091 (mmm160) REVERT: B 237 LEU cc_start: 0.8279 (mm) cc_final: 0.7880 (mm) REVERT: B 257 ARG cc_start: 0.7689 (ttp80) cc_final: 0.6625 (tpp-160) outliers start: 11 outliers final: 9 residues processed: 56 average time/residue: 0.1014 time to fit residues: 6.4498 Evaluate side-chains 58 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 49 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 270 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 23 optimal weight: 0.0370 chunk 4 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 41 optimal weight: 0.3980 chunk 9 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 overall best weight: 0.4858 ------------------------------------------------------------------------------- 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 = 0.3982 r_free = 0.3982 target = 0.180756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.139272 restraints weight = 11245.338| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 3.59 r_work: 0.3100 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3084 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3084 r_free = 0.3084 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3084 r_free = 0.3084 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3084 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.1326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3677 Z= 0.149 Angle : 0.647 10.410 5048 Z= 0.295 Chirality : 0.037 0.180 636 Planarity : 0.003 0.025 600 Dihedral : 18.762 127.602 562 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.59 % Allowed : 18.39 % Favored : 79.02 % 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: 3.82 (0.40), residues: 466 helix: 3.12 (0.25), residues: 386 sheet: None (None), residues: 0 loop : -0.73 (0.86), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 144 TYR 0.012 0.002 TYR B 234 PHE 0.013 0.002 PHE A 122 TRP 0.008 0.001 TRP A 171 HIS 0.002 0.001 HIS A 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.15 ( 3676) covalent geometry : angle 0.64718 / 0.29 ( 5046) SS BOND : bond 0.00075 / 0.04 ( 1) SS BOND : angle 0.21829 / 0.12 ( 2) hydrogen bonds : bond 0.02874 / 2.01 ( 280) hydrogen bonds : angle 3.30048 / 2.40 ( 838) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1122.33 seconds wall clock time: 19 minutes 51.36 seconds (1191.36 seconds total)