Starting phenix.real_space_refine on Wed Mar 12 06:02:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gi9_40063/03_2025/8gi9_40063.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gi9_40063/03_2025/8gi9_40063.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gi9_40063/03_2025/8gi9_40063.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gi9_40063/03_2025/8gi9_40063.map" model { file = "/net/cci-nas-00/data/ceres_data/8gi9_40063/03_2025/8gi9_40063.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gi9_40063/03_2025/8gi9_40063.cif" } resolution = 2.84 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= -0.000 sd= 0.222 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 P 6 5.49 5 S 39 5.16 5 Na 9 4.78 5 C 4842 2.51 5 N 894 2.21 5 O 1062 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 6852 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1948 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 12, 'TRANS': 227} Chain: "A" Number of atoms: 336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 336 Unusual residues: {' NA': 3, 'CLR': 7, 'PEE': 2, 'RET': 1} Classifications: {'undetermined': 13, 'water': 15} Link IDs: {None: 27} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "C" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Restraints were copied for chains: C, B Time building chain proxies: 4.65, per 1000 atoms: 0.68 Number of scatterers: 6852 At special positions: 0 Unit cell: (79.31, 78.28, 76.22, 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) S 39 16.00 P 6 15.00 Na 9 11.00 O 1062 8.00 N 894 7.00 C 4842 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.90 Conformation dependent library (CDL) restraints added in 874.0 milliseconds 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1326 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 0 sheets defined 79.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 21 through 48 removed outlier: 3.562A pdb=" N ASP A 48 " --> pdb=" O LEU A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 67 removed outlier: 3.523A pdb=" N ASN A 67 " --> pdb=" O PRO A 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 64 through 67' Processing helix chain 'A' and resid 68 through 90 removed outlier: 3.570A pdb=" N CYS A 74 " --> pdb=" O SER A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.576A pdb=" N VAL A 107 " --> pdb=" O TYR A 103 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N PHE A 108 " --> pdb=" O LEU A 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 103 through 108' Processing helix chain 'A' and resid 109 through 122 Processing helix chain 'A' and resid 125 through 146 Processing helix chain 'A' and resid 150 through 177 Proline residue: A 164 - end of helix Processing helix chain 'A' and resid 181 through 199 removed outlier: 3.904A pdb=" N LEU A 187 " --> pdb=" O LYS A 183 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TRP A 190 " --> pdb=" O LYS A 186 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N TRP A 199 " --> pdb=" O PHE A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 209 removed outlier: 3.755A pdb=" N ILE A 204 " --> pdb=" O PRO A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 233 Processing helix chain 'A' and resid 233 through 252 Processing helix chain 'B' and resid 21 through 48 removed outlier: 3.562A pdb=" N ASP B 48 " --> pdb=" O LEU B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 67 removed outlier: 3.523A pdb=" N ASN B 67 " --> pdb=" O PRO B 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 64 through 67' Processing helix chain 'B' and resid 68 through 90 removed outlier: 3.570A pdb=" N CYS B 74 " --> pdb=" O SER B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 108 removed outlier: 3.576A pdb=" N VAL B 107 " --> pdb=" O TYR B 103 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N PHE B 108 " --> pdb=" O LEU B 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 103 through 108' Processing helix chain 'B' and resid 109 through 122 Processing helix chain 'B' and resid 125 through 146 Processing helix chain 'B' and resid 150 through 177 Proline residue: B 164 - end of helix Processing helix chain 'B' and resid 181 through 199 removed outlier: 3.904A pdb=" N LEU B 187 " --> pdb=" O LYS B 183 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TRP B 190 " --> pdb=" O LYS B 186 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N TRP B 199 " --> pdb=" O PHE B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 209 removed outlier: 3.755A pdb=" N ILE B 204 " --> pdb=" O PRO B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 233 Processing helix chain 'B' and resid 233 through 252 Processing helix chain 'C' and resid 21 through 48 removed outlier: 3.562A pdb=" N ASP C 48 " --> pdb=" O LEU C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 67 removed outlier: 3.522A pdb=" N ASN C 67 " --> pdb=" O PRO C 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 64 through 67' Processing helix chain 'C' and resid 68 through 90 removed outlier: 3.570A pdb=" N CYS C 74 " --> pdb=" O SER C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 108 removed outlier: 3.576A pdb=" N VAL C 107 " --> pdb=" O TYR C 103 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N PHE C 108 " --> pdb=" O LEU C 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 103 through 108' Processing helix chain 'C' and resid 109 through 122 Processing helix chain 'C' and resid 125 through 146 Processing helix chain 'C' and resid 150 through 177 Proline residue: C 164 - end of helix Processing helix chain 'C' and resid 181 through 199 removed outlier: 3.904A pdb=" N LEU C 187 " --> pdb=" O LYS C 183 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TRP C 190 " --> pdb=" O LYS C 186 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N TRP C 199 " --> pdb=" O PHE C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 209 removed outlier: 3.755A pdb=" N ILE C 204 " --> pdb=" O PRO C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 233 Processing helix chain 'C' and resid 233 through 252 408 hydrogen bonds defined for protein. 1224 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: 1.52 Time building geometry restraints manager: 2.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1518 1.33 - 1.45: 1521 1.45 - 1.57: 3876 1.57 - 1.69: 114 1.69 - 1.81: 57 Bond restraints: 7086 Sorted by residual: bond pdb=" O4P PEE A 312 " pdb=" P PEE A 312 " ideal model delta sigma weight residual 1.653 1.786 -0.133 2.00e-02 2.50e+03 4.41e+01 bond pdb=" O4P PEE B 312 " pdb=" P PEE B 312 " ideal model delta sigma weight residual 1.653 1.786 -0.133 2.00e-02 2.50e+03 4.39e+01 bond pdb=" O4P PEE C 312 " pdb=" P PEE C 312 " ideal model delta sigma weight residual 1.653 1.785 -0.132 2.00e-02 2.50e+03 4.39e+01 bond pdb=" O4P PEE B 313 " pdb=" P PEE B 313 " ideal model delta sigma weight residual 1.653 1.778 -0.125 2.00e-02 2.50e+03 3.91e+01 bond pdb=" O4P PEE A 313 " pdb=" P PEE A 313 " ideal model delta sigma weight residual 1.653 1.778 -0.125 2.00e-02 2.50e+03 3.90e+01 ... (remaining 7081 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.72: 9300 2.72 - 5.44: 318 5.44 - 8.15: 78 8.15 - 10.87: 3 10.87 - 13.59: 6 Bond angle restraints: 9705 Sorted by residual: angle pdb=" O1P PEE B 312 " pdb=" P PEE B 312 " pdb=" O2P PEE B 312 " ideal model delta sigma weight residual 119.43 133.02 -13.59 3.00e+00 1.11e-01 2.05e+01 angle pdb=" O1P PEE A 312 " pdb=" P PEE A 312 " pdb=" O2P PEE A 312 " ideal model delta sigma weight residual 119.43 133.01 -13.58 3.00e+00 1.11e-01 2.05e+01 angle pdb=" O1P PEE C 312 " pdb=" P PEE C 312 " pdb=" O2P PEE C 312 " ideal model delta sigma weight residual 119.43 133.01 -13.58 3.00e+00 1.11e-01 2.05e+01 angle pdb=" O1P PEE B 313 " pdb=" P PEE B 313 " pdb=" O2P PEE B 313 " ideal model delta sigma weight residual 119.43 133.01 -13.58 3.00e+00 1.11e-01 2.05e+01 angle pdb=" O1P PEE A 313 " pdb=" P PEE A 313 " pdb=" O2P PEE A 313 " ideal model delta sigma weight residual 119.43 133.00 -13.57 3.00e+00 1.11e-01 2.05e+01 ... (remaining 9700 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.20: 4794 29.20 - 58.39: 168 58.39 - 87.59: 21 87.59 - 116.78: 12 116.78 - 145.98: 9 Dihedral angle restraints: 5004 sinusoidal: 2922 harmonic: 2082 Sorted by residual: dihedral pdb=" C32 PEE A 312 " pdb=" C30 PEE A 312 " pdb=" C31 PEE A 312 " pdb=" O3 PEE A 312 " ideal model delta sinusoidal sigma weight residual 161.16 -52.86 -145.98 1 3.00e+01 1.11e-03 1.95e+01 dihedral pdb=" C32 PEE C 312 " pdb=" C30 PEE C 312 " pdb=" C31 PEE C 312 " pdb=" O3 PEE C 312 " ideal model delta sinusoidal sigma weight residual 161.16 -52.87 -145.97 1 3.00e+01 1.11e-03 1.95e+01 dihedral pdb=" C32 PEE B 312 " pdb=" C30 PEE B 312 " pdb=" C31 PEE B 312 " pdb=" O3 PEE B 312 " ideal model delta sinusoidal sigma weight residual 161.16 -52.89 -145.95 1 3.00e+01 1.11e-03 1.95e+01 ... (remaining 5001 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 892 0.078 - 0.157: 74 0.157 - 0.235: 3 0.235 - 0.313: 54 0.313 - 0.391: 33 Chirality restraints: 1056 Sorted by residual: chirality pdb=" C2 PEE A 312 " pdb=" C1 PEE A 312 " pdb=" C3 PEE A 312 " pdb=" O2 PEE A 312 " both_signs ideal model delta sigma weight residual False -2.33 -2.72 0.39 2.00e-01 2.50e+01 3.83e+00 chirality pdb=" C2 PEE C 312 " pdb=" C1 PEE C 312 " pdb=" C3 PEE C 312 " pdb=" O2 PEE C 312 " both_signs ideal model delta sigma weight residual False -2.33 -2.72 0.39 2.00e-01 2.50e+01 3.80e+00 chirality pdb=" C17 CLR A 305 " pdb=" C13 CLR A 305 " pdb=" C16 CLR A 305 " pdb=" C20 CLR A 305 " both_signs ideal model delta sigma weight residual False 2.55 2.94 -0.39 2.00e-01 2.50e+01 3.79e+00 ... (remaining 1053 not shown) Planarity restraints: 1035 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 94 " 0.015 5.00e-02 4.00e+02 2.27e-02 8.24e-01 pdb=" N PRO A 95 " -0.039 5.00e-02 4.00e+02 pdb=" CA PRO A 95 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO A 95 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 94 " 0.015 5.00e-02 4.00e+02 2.26e-02 8.18e-01 pdb=" N PRO C 95 " -0.039 5.00e-02 4.00e+02 pdb=" CA PRO C 95 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO C 95 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 94 " 0.015 5.00e-02 4.00e+02 2.25e-02 8.12e-01 pdb=" N PRO B 95 " -0.039 5.00e-02 4.00e+02 pdb=" CA PRO B 95 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO B 95 " 0.013 5.00e-02 4.00e+02 ... (remaining 1032 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.48: 39 2.48 - 3.09: 4814 3.09 - 3.69: 9987 3.69 - 4.30: 16770 4.30 - 4.90: 27808 Nonbonded interactions: 59418 Sorted by model distance: nonbonded pdb=" OH TYR B 62 " pdb=" OE1 GLN C 175 " model vdw 1.878 3.040 nonbonded pdb=" OH TYR A 62 " pdb=" OE1 GLN B 175 " model vdw 1.878 3.040 nonbonded pdb=" OE1 GLN A 175 " pdb=" OH TYR C 62 " model vdw 1.878 3.040 nonbonded pdb=" O ALA A 132 " pdb=" OG1 THR A 136 " model vdw 2.243 3.040 nonbonded pdb=" O ALA B 132 " pdb=" OG1 THR B 136 " model vdw 2.243 3.040 ... (remaining 59413 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 18.240 Find NCS groups from input model: 0.120 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:12.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 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 : 0.009 0.133 7086 Z= 0.572 Angle : 1.113 13.589 9705 Z= 0.394 Chirality : 0.100 0.391 1056 Planarity : 0.003 0.023 1035 Dihedral : 15.912 145.981 3678 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % 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: 1.20 (0.33), residues: 714 helix: 1.73 (0.24), residues: 504 sheet: None (None), residues: 0 loop : -1.58 (0.42), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 190 HIS 0.002 0.001 HIS A 225 PHE 0.005 0.001 PHE B 221 TYR 0.006 0.001 TYR C 177 ARG 0.001 0.000 ARG B 176 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.729 Fit side-chains revert: symmetry clash REVERT: A 116 ASP cc_start: 0.8221 (t0) cc_final: 0.7866 (t0) REVERT: A 186 LYS cc_start: 0.7719 (mptt) cc_final: 0.7415 (ttmm) REVERT: B 144 PHE cc_start: 0.7667 (t80) cc_final: 0.7043 (t80) REVERT: B 186 LYS cc_start: 0.7894 (mptt) cc_final: 0.7558 (ttmm) REVERT: C 186 LYS cc_start: 0.7595 (mptt) cc_final: 0.7142 (ttmm) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 1.2496 time to fit residues: 100.8128 Evaluate side-chains 68 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 60 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 56 optimal weight: 9.9990 chunk 21 optimal weight: 0.9990 chunk 34 optimal weight: 0.0470 chunk 42 optimal weight: 4.9990 chunk 65 optimal weight: 0.0870 overall best weight: 0.4256 ------------------------------------------------------------------------------- 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 = 0.3788 r_free = 0.3788 target = 0.154359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.127929 restraints weight = 6760.368| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 1.40 r_work: 0.3285 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.0977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 7086 Z= 0.387 Angle : 1.072 17.992 9705 Z= 0.532 Chirality : 0.059 0.495 1056 Planarity : 0.016 0.325 1035 Dihedral : 16.544 162.502 2445 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.62 % Favored : 95.24 % Rotamer: Outliers : 1.80 % Allowed : 4.90 % Favored : 93.30 % 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: -0.74 (0.30), residues: 714 helix: 0.30 (0.22), residues: 507 sheet: None (None), residues: 0 loop : -2.40 (0.40), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.123 0.010 TRP B 210 HIS 0.031 0.003 HIS C 125 PHE 0.170 0.006 PHE C 144 TYR 0.089 0.006 TYR B 81 ARG 0.107 0.006 ARG B 128 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 71 time to evaluate : 0.610 Fit side-chains REVERT: A 116 ASP cc_start: 0.8299 (t0) cc_final: 0.8026 (t0) REVERT: A 174 LYS cc_start: 0.7578 (OUTLIER) cc_final: 0.7339 (mtmm) REVERT: A 186 LYS cc_start: 0.7815 (mptt) cc_final: 0.7554 (ttmm) REVERT: B 144 PHE cc_start: 0.7716 (t80) cc_final: 0.7098 (t80) REVERT: B 186 LYS cc_start: 0.8038 (mptt) cc_final: 0.7699 (ttmm) REVERT: C 186 LYS cc_start: 0.7840 (mptt) cc_final: 0.7432 (ttmm) REVERT: C 240 MET cc_start: 0.8623 (mmp) cc_final: 0.8396 (tpt) outliers start: 11 outliers final: 1 residues processed: 72 average time/residue: 1.2120 time to fit residues: 92.2359 Evaluate side-chains 69 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 67 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain B residue 109 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 66 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 42 optimal weight: 0.1980 chunk 0 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3787 r_free = 0.3787 target = 0.154264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.127524 restraints weight = 6820.358| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 1.40 r_work: 0.3274 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7086 Z= 0.222 Angle : 0.574 6.307 9705 Z= 0.269 Chirality : 0.041 0.248 1056 Planarity : 0.006 0.076 1035 Dihedral : 15.100 179.860 2445 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.14 % Allowed : 5.72 % Favored : 93.14 % 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: 0.96 (0.31), residues: 714 helix: 1.61 (0.22), residues: 522 sheet: None (None), residues: 0 loop : -2.16 (0.41), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 161 HIS 0.006 0.001 HIS B 125 PHE 0.018 0.001 PHE A 144 TYR 0.015 0.001 TYR C 154 ARG 0.004 0.001 ARG A 244 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 76 time to evaluate : 0.694 Fit side-chains REVERT: A 116 ASP cc_start: 0.8470 (t0) cc_final: 0.8227 (t0) REVERT: A 176 ARG cc_start: 0.7431 (mtp85) cc_final: 0.7097 (ttt90) REVERT: A 186 LYS cc_start: 0.7880 (mptt) cc_final: 0.7668 (ttmm) REVERT: B 144 PHE cc_start: 0.7839 (t80) cc_final: 0.7318 (t80) REVERT: B 186 LYS cc_start: 0.8069 (mptt) cc_final: 0.7740 (ttmm) REVERT: C 183 LYS cc_start: 0.8341 (tppp) cc_final: 0.8127 (ttmt) REVERT: C 186 LYS cc_start: 0.7933 (mptt) cc_final: 0.7572 (ttmm) outliers start: 7 outliers final: 2 residues processed: 79 average time/residue: 1.6058 time to fit residues: 133.9412 Evaluate side-chains 70 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 68 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain C residue 247 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 22 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 7 optimal weight: 0.4980 chunk 51 optimal weight: 5.9990 chunk 58 optimal weight: 0.2980 chunk 11 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 35 optimal weight: 0.5980 chunk 42 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 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 = 0.3797 r_free = 0.3797 target = 0.154963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.128244 restraints weight = 6875.906| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 1.41 r_work: 0.3249 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7086 Z= 0.185 Angle : 0.522 6.042 9705 Z= 0.243 Chirality : 0.039 0.218 1056 Planarity : 0.005 0.053 1035 Dihedral : 14.058 159.714 2445 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.98 % Allowed : 8.66 % Favored : 90.36 % 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: 1.56 (0.31), residues: 714 helix: 2.09 (0.22), residues: 522 sheet: None (None), residues: 0 loop : -2.10 (0.41), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 161 HIS 0.003 0.001 HIS C 125 PHE 0.019 0.001 PHE A 144 TYR 0.011 0.001 TYR A 177 ARG 0.005 0.001 ARG A 244 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 89 time to evaluate : 0.715 Fit side-chains REVERT: A 106 TYR cc_start: 0.8868 (m-10) cc_final: 0.8550 (m-80) REVERT: A 186 LYS cc_start: 0.7890 (mptt) cc_final: 0.7645 (ttmm) REVERT: B 144 PHE cc_start: 0.7693 (t80) cc_final: 0.7158 (t80) REVERT: B 186 LYS cc_start: 0.8033 (mptt) cc_final: 0.7763 (ttmm) REVERT: C 103 TYR cc_start: 0.8770 (m-80) cc_final: 0.8558 (m-80) REVERT: C 186 LYS cc_start: 0.7954 (mptt) cc_final: 0.7611 (ttmm) outliers start: 6 outliers final: 2 residues processed: 91 average time/residue: 1.2105 time to fit residues: 116.2946 Evaluate side-chains 76 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 74 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain C residue 109 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 22 optimal weight: 0.9990 chunk 64 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 61 optimal weight: 0.6980 chunk 68 optimal weight: 2.9990 chunk 21 optimal weight: 0.0770 chunk 12 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 HIS B 172 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.154193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.127648 restraints weight = 6826.396| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 1.40 r_work: 0.3279 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7086 Z= 0.197 Angle : 0.522 5.817 9705 Z= 0.243 Chirality : 0.039 0.204 1056 Planarity : 0.005 0.054 1035 Dihedral : 13.640 142.068 2445 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.63 % Allowed : 10.46 % Favored : 87.91 % 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: 1.66 (0.31), residues: 714 helix: 2.16 (0.22), residues: 522 sheet: None (None), residues: 0 loop : -2.04 (0.41), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 161 HIS 0.003 0.001 HIS C 125 PHE 0.016 0.001 PHE A 144 TYR 0.013 0.001 TYR B 177 ARG 0.005 0.000 ARG B 176 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 0.632 Fit side-chains revert: symmetry clash REVERT: A 106 TYR cc_start: 0.8867 (m-10) cc_final: 0.8592 (m-80) REVERT: A 186 LYS cc_start: 0.7952 (mptt) cc_final: 0.7683 (ttmm) REVERT: B 186 LYS cc_start: 0.8017 (mptt) cc_final: 0.7717 (ttmm) REVERT: C 170 LEU cc_start: 0.8513 (tp) cc_final: 0.8152 (tp) REVERT: C 186 LYS cc_start: 0.7957 (mptt) cc_final: 0.7661 (ttmm) outliers start: 10 outliers final: 3 residues processed: 86 average time/residue: 1.2041 time to fit residues: 109.1700 Evaluate side-chains 81 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 78 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain C residue 109 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 56 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 58 optimal weight: 0.0170 chunk 60 optimal weight: 0.5980 chunk 15 optimal weight: 0.7980 chunk 68 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 55 optimal weight: 0.0970 overall best weight: 0.5016 ------------------------------------------------------------------------------- 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 = 0.3798 r_free = 0.3798 target = 0.154881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.128488 restraints weight = 6868.710| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 1.41 r_work: 0.3287 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7086 Z= 0.178 Angle : 0.507 5.652 9705 Z= 0.235 Chirality : 0.038 0.190 1056 Planarity : 0.005 0.054 1035 Dihedral : 13.266 133.005 2445 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 1.47 % Allowed : 10.95 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.77 (0.31), residues: 714 helix: 2.25 (0.22), residues: 522 sheet: None (None), residues: 0 loop : -2.05 (0.40), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 102 HIS 0.003 0.001 HIS C 125 PHE 0.018 0.001 PHE A 144 TYR 0.010 0.001 TYR B 177 ARG 0.002 0.000 ARG B 176 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 79 time to evaluate : 0.632 Fit side-chains revert: symmetry clash REVERT: A 106 TYR cc_start: 0.8865 (m-10) cc_final: 0.8554 (m-80) REVERT: A 186 LYS cc_start: 0.7934 (mptt) cc_final: 0.7690 (ttmm) REVERT: B 144 PHE cc_start: 0.7783 (t80) cc_final: 0.7558 (t80) REVERT: B 186 LYS cc_start: 0.7903 (mptt) cc_final: 0.7696 (ttmm) REVERT: C 170 LEU cc_start: 0.8528 (tp) cc_final: 0.8171 (tp) REVERT: C 186 LYS cc_start: 0.7922 (mptt) cc_final: 0.7628 (ttmm) outliers start: 9 outliers final: 3 residues processed: 83 average time/residue: 1.2495 time to fit residues: 109.2334 Evaluate side-chains 85 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 82 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain C residue 109 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 63 optimal weight: 0.8980 chunk 54 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 69 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3777 r_free = 0.3777 target = 0.153220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.126852 restraints weight = 6852.322| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 1.40 r_work: 0.3261 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7086 Z= 0.221 Angle : 0.537 5.656 9705 Z= 0.251 Chirality : 0.039 0.184 1056 Planarity : 0.005 0.047 1035 Dihedral : 13.167 129.284 2445 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.14 % Allowed : 11.11 % Favored : 87.75 % 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: 1.67 (0.31), residues: 714 helix: 2.16 (0.22), residues: 522 sheet: None (None), residues: 0 loop : -2.02 (0.40), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 161 HIS 0.003 0.001 HIS C 125 PHE 0.019 0.001 PHE A 144 TYR 0.013 0.001 TYR C 177 ARG 0.002 0.000 ARG C 176 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 0.623 Fit side-chains revert: symmetry clash REVERT: A 21 ASP cc_start: 0.7706 (OUTLIER) cc_final: 0.7032 (t0) REVERT: A 186 LYS cc_start: 0.7976 (mptt) cc_final: 0.7711 (ttmm) REVERT: B 144 PHE cc_start: 0.7848 (t80) cc_final: 0.7564 (t80) REVERT: B 186 LYS cc_start: 0.8009 (mptt) cc_final: 0.7718 (ttmm) REVERT: C 170 LEU cc_start: 0.8527 (tp) cc_final: 0.8169 (tp) REVERT: C 186 LYS cc_start: 0.7956 (mptt) cc_final: 0.7662 (ttmm) outliers start: 7 outliers final: 3 residues processed: 74 average time/residue: 1.4216 time to fit residues: 110.3721 Evaluate side-chains 81 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 77 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ASP Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain C residue 109 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 69 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 66 optimal weight: 0.5980 chunk 59 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 16 optimal weight: 0.1980 chunk 36 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.153922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.127468 restraints weight = 6946.064| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 1.41 r_work: 0.3262 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7086 Z= 0.197 Angle : 0.519 5.536 9705 Z= 0.243 Chirality : 0.039 0.184 1056 Planarity : 0.005 0.048 1035 Dihedral : 12.867 122.054 2445 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.80 % Allowed : 10.46 % Favored : 87.75 % 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: 1.74 (0.31), residues: 714 helix: 2.21 (0.22), residues: 522 sheet: None (None), residues: 0 loop : -2.01 (0.40), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 161 HIS 0.003 0.001 HIS C 125 PHE 0.021 0.001 PHE A 144 TYR 0.012 0.001 TYR B 177 ARG 0.002 0.000 ARG C 244 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 82 time to evaluate : 0.643 Fit side-chains revert: symmetry clash REVERT: A 21 ASP cc_start: 0.7632 (OUTLIER) cc_final: 0.6944 (t0) REVERT: A 106 TYR cc_start: 0.8868 (m-10) cc_final: 0.8576 (m-80) REVERT: B 65 GLU cc_start: 0.6773 (tp30) cc_final: 0.6559 (tp30) REVERT: B 144 PHE cc_start: 0.7918 (t80) cc_final: 0.7571 (t80) REVERT: B 186 LYS cc_start: 0.7996 (mptt) cc_final: 0.7698 (ttmm) REVERT: C 21 ASP cc_start: 0.7379 (OUTLIER) cc_final: 0.6611 (t0) REVERT: C 170 LEU cc_start: 0.8512 (tp) cc_final: 0.8155 (tp) REVERT: C 186 LYS cc_start: 0.7921 (mptt) cc_final: 0.7616 (ttmm) outliers start: 11 outliers final: 4 residues processed: 88 average time/residue: 1.2731 time to fit residues: 117.9677 Evaluate side-chains 87 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 81 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ASP Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain C residue 21 ASP Chi-restraints excluded: chain C residue 109 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 23 optimal weight: 0.3980 chunk 60 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 65 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 64 optimal weight: 0.9990 chunk 46 optimal weight: 0.5980 chunk 18 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3789 r_free = 0.3789 target = 0.154351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.127790 restraints weight = 6972.411| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 1.42 r_work: 0.3266 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7086 Z= 0.194 Angle : 0.522 5.486 9705 Z= 0.244 Chirality : 0.039 0.187 1056 Planarity : 0.005 0.043 1035 Dihedral : 12.653 114.240 2445 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 1.31 % Allowed : 11.27 % Favored : 87.42 % 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: 1.75 (0.31), residues: 714 helix: 2.21 (0.22), residues: 522 sheet: None (None), residues: 0 loop : -1.96 (0.41), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 161 HIS 0.002 0.001 HIS C 125 PHE 0.021 0.001 PHE A 144 TYR 0.012 0.001 TYR B 177 ARG 0.002 0.000 ARG A 244 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 79 time to evaluate : 0.696 Fit side-chains revert: symmetry clash REVERT: A 21 ASP cc_start: 0.7624 (OUTLIER) cc_final: 0.6934 (t0) REVERT: A 106 TYR cc_start: 0.8866 (m-10) cc_final: 0.8586 (m-80) REVERT: B 144 PHE cc_start: 0.7921 (t80) cc_final: 0.7592 (t80) REVERT: B 186 LYS cc_start: 0.7991 (mptt) cc_final: 0.7690 (ttmm) REVERT: C 21 ASP cc_start: 0.7469 (OUTLIER) cc_final: 0.6754 (t0) REVERT: C 170 LEU cc_start: 0.8489 (tp) cc_final: 0.8146 (tp) REVERT: C 178 GLN cc_start: 0.8251 (mt0) cc_final: 0.7784 (mp10) REVERT: C 186 LYS cc_start: 0.7918 (mptt) cc_final: 0.7601 (ttmm) outliers start: 8 outliers final: 3 residues processed: 82 average time/residue: 1.2539 time to fit residues: 108.4715 Evaluate side-chains 83 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 78 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ASP Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain C residue 21 ASP Chi-restraints excluded: chain C residue 109 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 23 optimal weight: 5.9990 chunk 32 optimal weight: 0.4980 chunk 64 optimal weight: 0.0070 chunk 6 optimal weight: 2.9990 chunk 42 optimal weight: 0.4980 chunk 54 optimal weight: 0.7980 chunk 58 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 61 optimal weight: 0.6980 overall best weight: 0.4998 ------------------------------------------------------------------------------- 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 = 0.3799 r_free = 0.3799 target = 0.155256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.129509 restraints weight = 7029.403| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 1.36 r_work: 0.3293 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7086 Z= 0.178 Angle : 0.512 5.619 9705 Z= 0.239 Chirality : 0.038 0.195 1056 Planarity : 0.005 0.044 1035 Dihedral : 12.368 107.267 2445 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 0.98 % Allowed : 11.60 % Favored : 87.42 % 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: 1.81 (0.31), residues: 714 helix: 2.25 (0.22), residues: 522 sheet: None (None), residues: 0 loop : -1.93 (0.41), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 161 HIS 0.002 0.000 HIS C 125 PHE 0.020 0.001 PHE A 144 TYR 0.010 0.001 TYR B 177 ARG 0.002 0.000 ARG A 244 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 82 time to evaluate : 0.676 Fit side-chains revert: symmetry clash REVERT: A 21 ASP cc_start: 0.7523 (OUTLIER) cc_final: 0.6896 (t0) REVERT: A 106 TYR cc_start: 0.8850 (m-10) cc_final: 0.8583 (m-80) REVERT: B 144 PHE cc_start: 0.7891 (t80) cc_final: 0.7573 (t80) REVERT: B 186 LYS cc_start: 0.7980 (mptt) cc_final: 0.7675 (ttmm) REVERT: C 21 ASP cc_start: 0.7537 (OUTLIER) cc_final: 0.6987 (t0) REVERT: C 170 LEU cc_start: 0.8425 (tp) cc_final: 0.8106 (tp) REVERT: C 178 GLN cc_start: 0.8224 (mt0) cc_final: 0.7781 (mp10) outliers start: 6 outliers final: 3 residues processed: 85 average time/residue: 1.2209 time to fit residues: 109.5348 Evaluate side-chains 86 residues out of total 612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 81 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ASP Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain C residue 21 ASP Chi-restraints excluded: chain C residue 109 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 47 optimal weight: 0.0770 chunk 13 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 46 optimal weight: 0.6980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 172 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.154645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.128092 restraints weight = 6966.075| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 1.42 r_work: 0.3293 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7086 Z= 0.192 Angle : 0.521 5.708 9705 Z= 0.244 Chirality : 0.039 0.202 1056 Planarity : 0.005 0.044 1035 Dihedral : 12.235 103.997 2445 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.31 % Allowed : 11.44 % Favored : 87.25 % 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: 1.76 (0.31), residues: 714 helix: 2.21 (0.22), residues: 522 sheet: None (None), residues: 0 loop : -1.95 (0.41), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 161 HIS 0.002 0.000 HIS C 125 PHE 0.021 0.001 PHE A 144 TYR 0.011 0.001 TYR B 177 ARG 0.002 0.000 ARG B 176 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4109.24 seconds wall clock time: 71 minutes 12.68 seconds (4272.68 seconds total)