Starting phenix.real_space_refine on Wed Jun 4 17:31:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mel_48217/06_2025/9mel_48217.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mel_48217/06_2025/9mel_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_48217/06_2025/9mel_48217.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mel_48217/06_2025/9mel_48217.map" model { file = "/net/cci-nas-00/data/ceres_data/9mel_48217/06_2025/9mel_48217.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mel_48217/06_2025/9mel_48217.cif" } resolution = 3.17 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 6, '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: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 6, '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: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 6, '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: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 6, '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, 3 Unusual residues: {' K': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: 5.07, per 1000 atoms: 1.41 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: 0.92 Conformation dependent library (CDL) restraints added in 783.4 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: 0.27 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: 0.90 Time building geometry restraints manager: 1.07 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 2.850 nonbonded pdb=" O GLY B 108 " pdb=" K K A 401 " model vdw 2.218 2.850 nonbonded pdb=" O GLY B 216 " pdb=" K K A 401 " model vdw 2.362 2.850 nonbonded pdb=" O GLY A 216 " pdb=" K K A 401 " model vdw 2.378 2.850 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: 3.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.660 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 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:2.890 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 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 : 4.44 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.40 (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 TRP 0.008 0.001 TRP A 171 HIS 0.003 0.001 HIS A 32 PHE 0.013 0.002 PHE A 122 TYR 0.010 0.002 TYR B 206 ARG 0.001 0.000 ARG A 144 Details of bonding type rmsd hydrogen bonds : bond 0.10239 ( 280) hydrogen bonds : angle 4.74274 ( 838) SS BOND : bond 0.00106 ( 1) SS BOND : angle 0.02827 ( 2) covalent geometry : bond 0.00446 ( 3676) covalent geometry : angle 0.73350 ( 5046) *********************** 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 : 0.342 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: 0.7613 (mt-10) REVERT: A 144 ARG cc_start: 0.6391 (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: 0.2874 time to fit residues: 17.6154 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 : 0.362 ------------------------------------------------------------------------------- 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 38 optimal weight: 0.1980 chunk 34 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 21 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 41 optimal weight: 0.0470 overall best weight: 0.4078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.176754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.133878 restraints weight = 8002.689| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 3.15 r_work: 0.3144 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3126 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3126 r_free = 0.3126 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3126 r_free = 0.3126 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3126 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.0526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3677 Z= 0.137 Angle : 0.623 9.837 5048 Z= 0.286 Chirality : 0.037 0.191 636 Planarity : 0.003 0.024 600 Dihedral : 19.628 131.236 570 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.83 (0.41), residues: 466 helix: 3.21 (0.25), residues: 376 sheet: None (None), residues: 0 loop : -0.70 (0.86), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 171 HIS 0.002 0.001 HIS A 32 PHE 0.012 0.002 PHE A 122 TYR 0.010 0.002 TYR B 206 ARG 0.001 0.000 ARG B 27 Details of bonding type rmsd hydrogen bonds : bond 0.03034 ( 280) hydrogen bonds : angle 3.66070 ( 838) SS BOND : bond 0.00115 ( 1) SS BOND : angle 0.20913 ( 2) covalent geometry : bond 0.00327 ( 3676) covalent geometry : angle 0.62330 ( 5046) *********************** 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 54 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.318 Fit side-chains REVERT: A 20 LEU cc_start: 0.8164 (tp) cc_final: 0.7547 (mt) REVERT: A 144 ARG cc_start: 0.6360 (mtt180) cc_final: 0.5921 (mmm160) REVERT: A 237 LEU cc_start: 0.8135 (mm) cc_final: 0.7739 (mm) REVERT: A 257 ARG cc_start: 0.7624 (ttp80) cc_final: 0.6556 (tpp-160) REVERT: B 20 LEU cc_start: 0.8144 (tp) cc_final: 0.7522 (mt) REVERT: B 144 ARG cc_start: 0.6369 (mtt180) cc_final: 0.5943 (mmm160) REVERT: B 237 LEU cc_start: 0.8114 (mm) cc_final: 0.7721 (mm) REVERT: B 257 ARG cc_start: 0.7619 (ttp80) cc_final: 0.6558 (tpp-160) outliers start: 6 outliers final: 2 residues processed: 54 average time/residue: 0.2873 time to fit residues: 17.5490 Evaluate side-chains 49 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 47 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 SER 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 35 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 37 optimal weight: 0.4980 chunk 14 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.174609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.129308 restraints weight = 11205.733| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 4.03 r_work: 0.3091 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3053 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3053 r_free = 0.3053 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3053 r_free = 0.3053 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3053 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.0704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3677 Z= 0.177 Angle : 0.646 10.738 5048 Z= 0.299 Chirality : 0.038 0.183 636 Planarity : 0.003 0.025 600 Dihedral : 19.846 138.081 562 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.30 % Allowed : 16.95 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.76 (0.41), residues: 466 helix: 3.15 (0.25), residues: 376 sheet: None (None), residues: 0 loop : -0.64 (0.87), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 171 HIS 0.003 0.001 HIS A 32 PHE 0.014 0.002 PHE A 122 TYR 0.014 0.002 TYR B 234 ARG 0.001 0.000 ARG B 65 Details of bonding type rmsd hydrogen bonds : bond 0.03203 ( 280) hydrogen bonds : angle 3.54036 ( 838) SS BOND : bond 0.00120 ( 1) SS BOND : angle 0.17543 ( 2) covalent geometry : bond 0.00437 ( 3676) covalent geometry : angle 0.64564 ( 5046) *********************** 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: 8 poor density : 53 time to evaluate : 0.326 Fit side-chains REVERT: A 20 LEU cc_start: 0.8195 (tp) cc_final: 0.7564 (mt) REVERT: A 144 ARG cc_start: 0.6402 (mtt180) cc_final: 0.5912 (mmm160) REVERT: A 237 LEU cc_start: 0.8165 (mm) cc_final: 0.7760 (mm) REVERT: A 257 ARG cc_start: 0.7641 (ttp80) cc_final: 0.6523 (tpp-160) REVERT: B 20 LEU cc_start: 0.8191 (tp) cc_final: 0.7552 (mt) REVERT: B 144 ARG cc_start: 0.6385 (mtt180) cc_final: 0.5915 (mmm160) REVERT: B 237 LEU cc_start: 0.8162 (mm) cc_final: 0.7763 (mm) REVERT: B 257 ARG cc_start: 0.7642 (ttp80) cc_final: 0.6526 (tpp-160) outliers start: 8 outliers final: 5 residues processed: 60 average time/residue: 0.2682 time to fit residues: 18.3056 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 : 0.326 ------------------------------------------------------------------------------- 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 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 25 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 44 optimal weight: 0.4980 chunk 34 optimal weight: 0.6980 chunk 41 optimal weight: 0.0470 chunk 20 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 40 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 chunk 31 optimal weight: 0.5980 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.179728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.134465 restraints weight = 9848.821| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 3.70 r_work: 0.3106 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3085 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3085 r_free = 0.3085 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3085 r_free = 0.3085 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3085 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.0897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3677 Z= 0.141 Angle : 0.628 10.328 5048 Z= 0.285 Chirality : 0.036 0.146 636 Planarity : 0.003 0.025 600 Dihedral : 19.011 129.940 562 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.44 % Allowed : 18.10 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.89 (0.41), residues: 466 helix: 3.26 (0.25), residues: 376 sheet: None (None), residues: 0 loop : -0.69 (0.86), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 171 HIS 0.002 0.001 HIS B 32 PHE 0.012 0.001 PHE A 122 TYR 0.010 0.002 TYR B 206 ARG 0.001 0.000 ARG B 144 Details of bonding type rmsd hydrogen bonds : bond 0.02926 ( 280) hydrogen bonds : angle 3.36125 ( 838) SS BOND : bond 0.00094 ( 1) SS BOND : angle 0.16771 ( 2) covalent geometry : bond 0.00343 ( 3676) covalent geometry : angle 0.62772 ( 5046) *********************** 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 58 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 53 time to evaluate : 0.328 Fit side-chains REVERT: A 20 LEU cc_start: 0.8134 (tp) cc_final: 0.7524 (mt) REVERT: A 144 ARG cc_start: 0.6386 (mtt180) cc_final: 0.5934 (mmm160) REVERT: A 237 LEU cc_start: 0.8133 (mm) cc_final: 0.7722 (mm) REVERT: A 257 ARG cc_start: 0.7652 (ttp80) cc_final: 0.6525 (tpp-160) REVERT: B 20 LEU cc_start: 0.8126 (tp) cc_final: 0.7516 (mt) REVERT: B 144 ARG cc_start: 0.6362 (mtt180) cc_final: 0.5923 (mmm160) REVERT: B 237 LEU cc_start: 0.8115 (mm) cc_final: 0.7707 (mm) REVERT: B 257 ARG cc_start: 0.7660 (ttp80) cc_final: 0.6529 (tpp-160) outliers start: 5 outliers final: 5 residues processed: 56 average time/residue: 0.2915 time to fit residues: 18.5583 Evaluate side-chains 57 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 52 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 39 optimal weight: 0.0370 chunk 4 optimal weight: 0.0670 chunk 44 optimal weight: 0.3980 chunk 24 optimal weight: 0.0980 chunk 0 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 1 optimal weight: 0.4980 chunk 37 optimal weight: 0.8980 overall best weight: 0.2196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.181756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.138501 restraints weight = 9653.059| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 3.59 r_work: 0.3162 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3143 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3143 r_free = 0.3143 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3143 r_free = 0.3143 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3143 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.1146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3677 Z= 0.109 Angle : 0.621 9.910 5048 Z= 0.275 Chirality : 0.034 0.118 636 Planarity : 0.003 0.026 600 Dihedral : 17.706 119.610 562 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.01 % Allowed : 17.24 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.12 (0.41), residues: 466 helix: 3.44 (0.25), residues: 376 sheet: None (None), residues: 0 loop : -0.70 (0.85), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 171 HIS 0.002 0.001 HIS B 32 PHE 0.008 0.001 PHE A 122 TYR 0.009 0.001 TYR B 17 ARG 0.001 0.000 ARG B 37 Details of bonding type rmsd hydrogen bonds : bond 0.02649 ( 280) hydrogen bonds : angle 3.17390 ( 838) SS BOND : bond 0.00077 ( 1) SS BOND : angle 0.21861 ( 2) covalent geometry : bond 0.00246 ( 3676) covalent geometry : angle 0.62078 ( 5046) *********************** 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 60 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 0.346 Fit side-chains REVERT: A 20 LEU cc_start: 0.8164 (tp) cc_final: 0.7564 (mt) REVERT: A 144 ARG cc_start: 0.6457 (mtt180) cc_final: 0.6021 (mmm160) REVERT: A 237 LEU cc_start: 0.8170 (mm) cc_final: 0.7801 (mm) REVERT: A 257 ARG cc_start: 0.7672 (ttp80) cc_final: 0.6608 (tpp-160) REVERT: B 20 LEU cc_start: 0.8155 (tp) cc_final: 0.7555 (mt) REVERT: B 144 ARG cc_start: 0.6497 (mtt180) cc_final: 0.6075 (mmm160) REVERT: B 237 LEU cc_start: 0.8149 (mm) cc_final: 0.7786 (mm) REVERT: B 257 ARG cc_start: 0.7660 (ttp80) cc_final: 0.6606 (tpp-160) outliers start: 7 outliers final: 6 residues processed: 56 average time/residue: 0.2789 time to fit residues: 17.7614 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 : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 4 optimal weight: 0.9990 chunk 37 optimal weight: 0.0870 chunk 1 optimal weight: 0.9980 chunk 25 optimal weight: 0.0980 chunk 15 optimal weight: 0.2980 chunk 19 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 9 optimal weight: 0.0040 chunk 0 optimal weight: 0.9980 overall best weight: 0.2570 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.182298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.138326 restraints weight = 7915.878| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 3.10 r_work: 0.3182 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3173 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3173 r_free = 0.3173 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3173 r_free = 0.3173 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3173 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.1231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3677 Z= 0.113 Angle : 0.629 10.539 5048 Z= 0.278 Chirality : 0.034 0.119 636 Planarity : 0.003 0.026 600 Dihedral : 17.296 117.122 562 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.72 % Allowed : 18.10 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.20 (0.41), residues: 466 helix: 3.50 (0.25), residues: 376 sheet: None (None), residues: 0 loop : -0.70 (0.85), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 171 HIS 0.002 0.001 HIS A 32 PHE 0.010 0.001 PHE A 122 TYR 0.008 0.001 TYR B 206 ARG 0.001 0.000 ARG A 44 Details of bonding type rmsd hydrogen bonds : bond 0.02661 ( 280) hydrogen bonds : angle 3.07720 ( 838) SS BOND : bond 0.00072 ( 1) SS BOND : angle 0.23444 ( 2) covalent geometry : bond 0.00263 ( 3676) covalent geometry : angle 0.62898 ( 5046) *********************** 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 61 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 55 time to evaluate : 0.328 Fit side-chains REVERT: A 20 LEU cc_start: 0.8163 (tp) cc_final: 0.7555 (mt) REVERT: A 144 ARG cc_start: 0.6461 (mtt180) cc_final: 0.6039 (mmm160) REVERT: A 237 LEU cc_start: 0.8185 (mm) cc_final: 0.7814 (mm) REVERT: A 257 ARG cc_start: 0.7668 (ttp80) cc_final: 0.6610 (tpp-160) REVERT: B 20 LEU cc_start: 0.8146 (tp) cc_final: 0.7543 (mt) REVERT: B 144 ARG cc_start: 0.6460 (mtt180) cc_final: 0.6070 (mmm160) REVERT: B 237 LEU cc_start: 0.8166 (mm) cc_final: 0.7795 (mm) REVERT: B 257 ARG cc_start: 0.7651 (ttp80) cc_final: 0.6604 (tpp-160) outliers start: 6 outliers final: 6 residues processed: 58 average time/residue: 0.2754 time to fit residues: 18.1863 Evaluate side-chains 59 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 53 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 129 LEU 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 21 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 41 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 44 optimal weight: 0.4980 chunk 32 optimal weight: 0.1980 chunk 39 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.173529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.127964 restraints weight = 11932.588| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 4.27 r_work: 0.3064 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3045 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3045 r_free = 0.3045 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3045 r_free = 0.3045 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3045 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.1113 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= 0.157 Angle : 0.662 12.003 5048 Z= 0.297 Chirality : 0.036 0.139 636 Planarity : 0.003 0.025 600 Dihedral : 17.506 119.280 562 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.00 (0.40), residues: 466 helix: 3.36 (0.25), residues: 376 sheet: None (None), residues: 0 loop : -0.75 (0.84), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 171 HIS 0.003 0.001 HIS B 32 PHE 0.014 0.002 PHE A 122 TYR 0.012 0.002 TYR B 234 ARG 0.001 0.000 ARG A 37 Details of bonding type rmsd hydrogen bonds : bond 0.02920 ( 280) hydrogen bonds : angle 3.21104 ( 838) SS BOND : bond 0.00068 ( 1) SS BOND : angle 0.13719 ( 2) covalent geometry : bond 0.00385 ( 3676) covalent geometry : angle 0.66204 ( 5046) *********************** 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 57 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 0.327 Fit side-chains REVERT: A 20 LEU cc_start: 0.8205 (tp) cc_final: 0.7582 (mt) REVERT: A 144 ARG cc_start: 0.6474 (mtt180) cc_final: 0.5988 (mmm160) REVERT: A 237 LEU cc_start: 0.8191 (mm) cc_final: 0.7810 (mm) REVERT: A 257 ARG cc_start: 0.7703 (ttp80) cc_final: 0.6581 (tpp-160) REVERT: B 20 LEU cc_start: 0.8188 (tp) cc_final: 0.7569 (mt) REVERT: B 144 ARG cc_start: 0.6483 (mtt180) cc_final: 0.6042 (mmm160) REVERT: B 237 LEU cc_start: 0.8192 (mm) cc_final: 0.7797 (mm) REVERT: B 257 ARG cc_start: 0.7679 (ttp80) cc_final: 0.6593 (tpp-160) outliers start: 6 outliers final: 6 residues processed: 55 average time/residue: 0.2785 time to fit residues: 17.3969 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 : 0.351 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 46 random chunks: chunk 8 optimal weight: 0.5980 chunk 32 optimal weight: 0.7980 chunk 4 optimal weight: 0.0020 chunk 5 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 40 optimal weight: 0.0670 chunk 19 optimal weight: 0.8980 chunk 31 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 overall best weight: 0.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.181950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.136265 restraints weight = 10999.738| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 3.93 r_work: 0.3137 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3111 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3111 r_free = 0.3111 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 = 0.3111 r_free = 0.3111 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3111 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.1266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3677 Z= 0.129 Angle : 0.607 8.581 5048 Z= 0.275 Chirality : 0.036 0.134 636 Planarity : 0.003 0.025 600 Dihedral : 14.904 100.086 562 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.30 % Allowed : 17.53 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.98 (0.40), residues: 466 helix: 3.21 (0.25), residues: 386 sheet: None (None), residues: 0 loop : -0.59 (0.91), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 171 HIS 0.002 0.001 HIS B 32 PHE 0.011 0.001 PHE A 122 TYR 0.009 0.001 TYR B 17 ARG 0.001 0.000 ARG A 37 Details of bonding type rmsd hydrogen bonds : bond 0.02728 ( 280) hydrogen bonds : angle 3.14225 ( 838) SS BOND : bond 0.00039 ( 1) SS BOND : angle 0.19756 ( 2) covalent geometry : bond 0.00308 ( 3676) covalent geometry : angle 0.60746 ( 5046) *********************** 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 59 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 51 time to evaluate : 0.355 Fit side-chains REVERT: A 20 LEU cc_start: 0.8151 (tp) cc_final: 0.7546 (mt) REVERT: A 144 ARG cc_start: 0.6436 (mtt180) cc_final: 0.5953 (mmm160) REVERT: A 237 LEU cc_start: 0.8123 (mm) cc_final: 0.7739 (mm) REVERT: A 257 ARG cc_start: 0.7590 (ttp80) cc_final: 0.6526 (tpp-160) REVERT: B 20 LEU cc_start: 0.8137 (tp) cc_final: 0.7535 (mt) REVERT: B 144 ARG cc_start: 0.6407 (mtt180) cc_final: 0.6005 (mmm160) REVERT: B 237 LEU cc_start: 0.8069 (mm) cc_final: 0.7685 (mm) REVERT: B 257 ARG cc_start: 0.7575 (ttp80) cc_final: 0.6536 (tpp-160) outliers start: 8 outliers final: 7 residues processed: 54 average time/residue: 0.2902 time to fit residues: 17.8193 Evaluate side-chains 58 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 51 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 123 SER Chi-restraints excluded: chain B residue 129 LEU 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 21 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 34 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 5 optimal weight: 0.3980 chunk 13 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 chunk 41 optimal weight: 0.0070 overall best weight: 0.4398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.180637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.138016 restraints weight = 12824.571| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 4.48 r_work: 0.3057 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3043 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3043 r_free = 0.3043 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3043 r_free = 0.3043 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3043 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.1277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3677 Z= 0.142 Angle : 0.585 8.870 5048 Z= 0.276 Chirality : 0.035 0.133 636 Planarity : 0.003 0.025 600 Dihedral : 11.031 90.277 562 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.94 (0.40), residues: 466 helix: 3.19 (0.25), residues: 386 sheet: None (None), residues: 0 loop : -0.62 (0.90), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 171 HIS 0.002 0.001 HIS B 32 PHE 0.013 0.002 PHE A 122 TYR 0.011 0.002 TYR B 234 ARG 0.001 0.000 ARG A 37 Details of bonding type rmsd hydrogen bonds : bond 0.02799 ( 280) hydrogen bonds : angle 3.16392 ( 838) SS BOND : bond 0.00055 ( 1) SS BOND : angle 0.17390 ( 2) covalent geometry : bond 0.00345 ( 3676) covalent geometry : angle 0.58473 ( 5046) *********************** 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 60 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.336 Fit side-chains REVERT: A 20 LEU cc_start: 0.8237 (tp) cc_final: 0.7627 (mt) REVERT: A 144 ARG cc_start: 0.6540 (mtt180) cc_final: 0.6042 (mmm160) REVERT: A 237 LEU cc_start: 0.8249 (mm) cc_final: 0.7861 (mm) REVERT: A 257 ARG cc_start: 0.7671 (ttp80) cc_final: 0.6605 (tpp-160) REVERT: B 20 LEU cc_start: 0.8228 (tp) cc_final: 0.7613 (mt) REVERT: B 144 ARG cc_start: 0.6552 (mtt180) cc_final: 0.6108 (mmm160) REVERT: B 237 LEU cc_start: 0.8245 (mm) cc_final: 0.7859 (mm) REVERT: B 257 ARG cc_start: 0.7642 (ttp80) cc_final: 0.6593 (tpp-160) outliers start: 8 outliers final: 8 residues processed: 56 average time/residue: 0.2780 time to fit residues: 17.7124 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 : 0.325 ------------------------------------------------------------------------------- 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 129 LEU 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 5 optimal weight: 0.0980 chunk 11 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 1 optimal weight: 0.4980 chunk 24 optimal weight: 0.0980 chunk 31 optimal weight: 0.5980 chunk 44 optimal weight: 0.7980 chunk 15 optimal weight: 0.1980 chunk 22 optimal weight: 0.8980 chunk 16 optimal weight: 0.0770 chunk 17 optimal weight: 0.7980 overall best weight: 0.1938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.181098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.135335 restraints weight = 9755.235| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 3.63 r_work: 0.3159 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3141 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3141 r_free = 0.3141 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3141 r_free = 0.3141 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3141 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.1406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3677 Z= 0.107 Angle : 0.522 5.438 5048 Z= 0.252 Chirality : 0.034 0.122 636 Planarity : 0.003 0.026 600 Dihedral : 9.038 79.186 562 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.01 % Allowed : 18.97 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.12 (0.41), residues: 466 helix: 3.32 (0.25), residues: 386 sheet: None (None), residues: 0 loop : -0.59 (0.90), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 171 HIS 0.002 0.001 HIS B 32 PHE 0.010 0.001 PHE B 126 TYR 0.008 0.001 TYR B 17 ARG 0.001 0.000 ARG A 37 Details of bonding type rmsd hydrogen bonds : bond 0.02602 ( 280) hydrogen bonds : angle 3.06096 ( 838) SS BOND : bond 0.00030 ( 1) SS BOND : angle 0.22896 ( 2) covalent geometry : bond 0.00242 ( 3676) covalent geometry : angle 0.52237 ( 5046) ********************** 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 57 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.361 Fit side-chains REVERT: A 20 LEU cc_start: 0.8149 (tp) cc_final: 0.7554 (mt) REVERT: A 144 ARG cc_start: 0.6423 (mtt180) cc_final: 0.5981 (mmm160) REVERT: A 237 LEU cc_start: 0.8115 (mm) cc_final: 0.7741 (mm) REVERT: A 257 ARG cc_start: 0.7574 (ttp80) cc_final: 0.6535 (tpp-160) REVERT: B 20 LEU cc_start: 0.8135 (tp) cc_final: 0.7536 (mt) REVERT: B 144 ARG cc_start: 0.6437 (mtt180) cc_final: 0.6029 (mmm160) REVERT: B 237 LEU cc_start: 0.8091 (mm) cc_final: 0.7723 (mm) REVERT: B 257 ARG cc_start: 0.7567 (ttp80) cc_final: 0.6407 (mmt-90) outliers start: 7 outliers final: 7 residues processed: 54 average time/residue: 0.2988 time to fit residues: 18.3629 Evaluate side-chains 57 residues out of total 368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 129 LEU 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 41 optimal weight: 0.2980 chunk 1 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 chunk 42 optimal weight: 0.0060 chunk 40 optimal weight: 0.7980 chunk 34 optimal weight: 0.0370 chunk 26 optimal weight: 0.9990 chunk 39 optimal weight: 0.0030 chunk 44 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 overall best weight: 0.1884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.185091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.142718 restraints weight = 9928.057| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 3.57 r_work: 0.3205 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3181 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3181 r_free = 0.3181 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3181 r_free = 0.3181 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3181 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3677 Z= 0.106 Angle : 0.516 5.473 5048 Z= 0.250 Chirality : 0.034 0.121 636 Planarity : 0.003 0.027 600 Dihedral : 7.905 69.473 562 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.01 % Allowed : 18.97 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.24 (0.40), residues: 466 helix: 3.41 (0.25), residues: 386 sheet: None (None), residues: 0 loop : -0.65 (0.88), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 171 HIS 0.002 0.001 HIS B 263 PHE 0.009 0.001 PHE B 126 TYR 0.008 0.001 TYR B 17 ARG 0.002 0.000 ARG B 37 Details of bonding type rmsd hydrogen bonds : bond 0.02505 ( 280) hydrogen bonds : angle 2.94942 ( 838) SS BOND : bond 0.00022 ( 1) SS BOND : angle 0.28900 ( 2) covalent geometry : bond 0.00242 ( 3676) covalent geometry : angle 0.51582 ( 5046) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2742.18 seconds wall clock time: 47 minutes 25.06 seconds (2845.06 seconds total)