Starting phenix.real_space_refine on Fri Oct 23 03:11:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/45im_83302/10_2026/45im_83302.cif Found real_map, /net/cci-nas-00/data/ceres_data/45im_83302/10_2026/45im_83302.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/45im_83302/10_2026/45im_83302.cif" } default_model = "/net/cci-nas-00/data/ceres_data/45im_83302/10_2026/45im_83302.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/45im_83302/10_2026/45im_83302.map" default_real_map = "/net/cci-nas-00/data/ceres_data/45im_83302/10_2026/45im_83302.map" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians K 4 8.98 5 P 2 5.49 5 S 50 5.16 5 C 5367 2.51 5 N 1234 2.21 5 O 1326 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7983 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3854 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 482, 3843 Classifications: {'peptide': 482} Link IDs: {'PTRANS': 17, 'TRANS': 464} Chain breaks: 4 Conformer: "B" Number of residues, atoms: 482, 3843 Classifications: {'peptide': 482} Link IDs: {'PTRANS': 17, 'TRANS': 464} Chain breaks: 4 bond proxies already assigned to first conformer: 3931 Chain: "B" Number of atoms: 3854 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 482, 3843 Classifications: {'peptide': 482} Link IDs: {'PTRANS': 17, 'TRANS': 464} Chain breaks: 4 Conformer: "B" Number of residues, atoms: 482, 3843 Classifications: {'peptide': 482} Link IDs: {'PTRANS': 17, 'TRANS': 464} Chain breaks: 4 bond proxies already assigned to first conformer: 3931 Chain: "A" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 106 Unusual residues: {' K': 4, 'LBN': 1, 'Y01': 3} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'Y01:plan-1': 2, 'Y01:plan-2': 2, 'LBN:plan-1': 1, 'LBN:plan-2': 1, 'LBN:plan-3': 1} Unresolved non-hydrogen planarities: 25 Chain: "B" Number of atoms: 169 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4, 130 Unusual residues: {'LBN': 1, 'Y01': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'Y01:plan-1': 2, 'Y01:plan-2': 2} Unresolved non-hydrogen planarities: 14 Conformer: "B" Number of residues, atoms: 4, 130 Unusual residues: {'LBN': 1, 'Y01': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'Y01:plan-1': 2, 'Y01:plan-2': 2} Unresolved non-hydrogen planarities: 14 bond proxies already assigned to first conformer: 100 Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N APHE A 320 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE A 320 " occ=0.50 residue: pdb=" N APHE B 320 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE B 320 " occ=0.50 residue: pdb=" C1 ALBN B 804 " occ=0.50 ... (76 atoms not shown) pdb=" P1 BLBN B 804 " occ=0.50 Time building chain proxies: 3.29, per 1000 atoms: 0.41 Number of scatterers: 7983 At special positions: 0 Unit cell: (96.96, 84.84, 106.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 4 19.00 S 50 16.00 P 2 15.00 O 1326 8.00 N 1234 7.00 C 5367 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.88 Conformation dependent library (CDL) restraints added in 588.0 milliseconds 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1804 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 0 sheets defined 83.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 46 through 53 Processing helix chain 'A' and resid 56 through 61 Processing helix chain 'A' and resid 70 through 81 Processing helix chain 'A' and resid 81 through 109 Proline residue: A 91 - end of helix Processing helix chain 'A' and resid 136 through 161 Processing helix chain 'A' and resid 165 through 194 Processing helix chain 'A' and resid 203 through 232 removed outlier: 3.624A pdb=" N TRP A 207 " --> pdb=" O THR A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 270 removed outlier: 3.731A pdb=" N GLY A 268 " --> pdb=" O GLY A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 286 Processing helix chain 'A' and resid 297 through 354 removed outlier: 4.007A pdb=" N SER A 329 " --> pdb=" O ILE A 325 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N GLY A 331 " --> pdb=" O GLN A 327 " (cutoff:3.500A) Proline residue: A 332 - end of helix Processing helix chain 'A' and resid 358 through 405 removed outlier: 3.702A pdb=" N TRP A 379 " --> pdb=" O ARG A 375 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N SER A 381 " --> pdb=" O GLN A 377 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N LEU A 382 " --> pdb=" O HIS A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 420 Processing helix chain 'A' and resid 431 through 464 Proline residue: A 447 - end of helix Processing helix chain 'A' and resid 582 through 602 Processing helix chain 'A' and resid 608 through 623 Processing helix chain 'A' and resid 641 through 645 removed outlier: 4.152A pdb=" N LYS A 644 " --> pdb=" O THR A 641 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N PHE A 645 " --> pdb=" O PRO A 642 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 641 through 645' Processing helix chain 'A' and resid 648 through 669 Processing helix chain 'B' and resid 46 through 53 Processing helix chain 'B' and resid 56 through 61 Processing helix chain 'B' and resid 70 through 81 Processing helix chain 'B' and resid 81 through 109 Proline residue: B 91 - end of helix Processing helix chain 'B' and resid 136 through 161 Processing helix chain 'B' and resid 165 through 194 Processing helix chain 'B' and resid 203 through 232 removed outlier: 3.624A pdb=" N TRP B 207 " --> pdb=" O THR B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 270 removed outlier: 3.731A pdb=" N GLY B 268 " --> pdb=" O GLY B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 286 Processing helix chain 'B' and resid 297 through 354 removed outlier: 4.007A pdb=" N SER B 329 " --> pdb=" O ILE B 325 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N GLY B 331 " --> pdb=" O GLN B 327 " (cutoff:3.500A) Proline residue: B 332 - end of helix Processing helix chain 'B' and resid 358 through 405 removed outlier: 3.702A pdb=" N TRP B 379 " --> pdb=" O ARG B 375 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N SER B 381 " --> pdb=" O GLN B 377 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N LEU B 382 " --> pdb=" O HIS B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 420 Processing helix chain 'B' and resid 431 through 464 Proline residue: B 447 - end of helix Processing helix chain 'B' and resid 582 through 602 Processing helix chain 'B' and resid 608 through 623 Processing helix chain 'B' and resid 641 through 645 removed outlier: 4.152A pdb=" N LYS B 644 " --> pdb=" O THR B 641 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N PHE B 645 " --> pdb=" O PRO B 642 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 641 through 645' Processing helix chain 'B' and resid 648 through 669 638 hydrogen bonds defined for protein. 1916 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: 1.24 Time building geometry restraints manager: 1.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1202 1.32 - 1.44: 2248 1.44 - 1.57: 4670 1.57 - 1.69: 4 1.69 - 1.81: 76 Bond restraints: 8200 Sorted by residual: bond pdb=" O2 ALBN B 804 " pdb=" P1 ALBN B 804 " ideal model delta sigma weight residual 1.650 1.595 0.055 2.00e-02 2.50e+03 7.64e+00 bond pdb=" O2 BLBN B 804 " pdb=" P1 BLBN B 804 " ideal model delta sigma weight residual 1.650 1.596 0.054 2.00e-02 2.50e+03 7.36e+00 bond pdb=" C9 ALBN B 804 " pdb=" O2 ALBN B 804 " ideal model delta sigma weight residual 1.409 1.449 -0.040 2.00e-02 2.50e+03 3.96e+00 bond pdb=" C9 BLBN B 804 " pdb=" O2 BLBN B 804 " ideal model delta sigma weight residual 1.409 1.447 -0.038 2.00e-02 2.50e+03 3.67e+00 bond pdb=" O1 BLBN B 804 " pdb=" P1 BLBN B 804 " ideal model delta sigma weight residual 1.632 1.595 0.037 2.00e-02 2.50e+03 3.48e+00 ... (remaining 8195 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.07: 10610 1.07 - 2.14: 406 2.14 - 3.21: 73 3.21 - 4.28: 32 4.28 - 5.36: 16 Bond angle restraints: 11137 Sorted by residual: angle pdb=" N TYR A 235 " pdb=" CA TYR A 235 " pdb=" C TYR A 235 " ideal model delta sigma weight residual 108.22 110.88 -2.66 9.00e-01 1.23e+00 8.72e+00 angle pdb=" N TYR B 235 " pdb=" CA TYR B 235 " pdb=" C TYR B 235 " ideal model delta sigma weight residual 108.22 110.88 -2.66 9.00e-01 1.23e+00 8.72e+00 angle pdb=" CA TRP B 441 " pdb=" CB TRP B 441 " pdb=" CG TRP B 441 " ideal model delta sigma weight residual 113.60 118.36 -4.76 1.90e+00 2.77e-01 6.27e+00 angle pdb=" CA TRP A 441 " pdb=" CB TRP A 441 " pdb=" CG TRP A 441 " ideal model delta sigma weight residual 113.60 118.36 -4.76 1.90e+00 2.77e-01 6.27e+00 angle pdb=" CA TRP B 393 " pdb=" CB TRP B 393 " pdb=" CG TRP B 393 " ideal model delta sigma weight residual 113.60 118.27 -4.67 1.90e+00 2.77e-01 6.04e+00 ... (remaining 11132 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.54: 4926 29.54 - 59.08: 115 59.08 - 88.61: 10 88.61 - 118.15: 3 118.15 - 147.69: 4 Dihedral angle restraints: 5058 sinusoidal: 2264 harmonic: 2794 Sorted by residual: dihedral pdb=" C1 BLBN B 804 " pdb=" O1 BLBN B 804 " pdb=" P1 BLBN B 804 " pdb=" O3 BLBN B 804 " ideal model delta sinusoidal sigma weight residual -84.60 63.09 -147.69 1 3.00e+01 1.11e-03 1.97e+01 dihedral pdb=" C1 ALBN B 804 " pdb=" O1 ALBN B 804 " pdb=" P1 ALBN B 804 " pdb=" O3 ALBN B 804 " ideal model delta sinusoidal sigma weight residual -84.60 62.36 -146.96 1 3.00e+01 1.11e-03 1.96e+01 dihedral pdb=" O5 BLBN B 804 " pdb=" C2 BLBN B 804 " pdb=" C3 BLBN B 804 " pdb=" O7 BLBN B 804 " ideal model delta sinusoidal sigma weight residual 62.67 -154.22 -143.11 1 3.00e+01 1.11e-03 1.92e+01 ... (remaining 5055 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 930 0.034 - 0.068: 266 0.068 - 0.102: 76 0.102 - 0.136: 14 0.136 - 0.170: 2 Chirality restraints: 1288 Sorted by residual: chirality pdb=" C2 BLBN B 804 " pdb=" C1 BLBN B 804 " pdb=" C3 BLBN B 804 " pdb=" O7 BLBN B 804 " both_signs ideal model delta sigma weight residual False -2.36 -2.53 0.17 2.00e-01 2.50e+01 7.20e-01 chirality pdb=" C2 ALBN B 804 " pdb=" C1 ALBN B 804 " pdb=" C3 ALBN B 804 " pdb=" O7 ALBN B 804 " both_signs ideal model delta sigma weight residual False -2.36 -2.53 0.16 2.00e-01 2.50e+01 6.74e-01 chirality pdb=" CA ILE A 293 " pdb=" N ILE A 293 " pdb=" C ILE A 293 " pdb=" CB ILE A 293 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.96e-01 ... (remaining 1285 not shown) Planarity restraints: 1298 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 294 " 0.021 5.00e-02 4.00e+02 3.17e-02 1.61e+00 pdb=" N PRO A 295 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO A 295 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 295 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 294 " -0.021 5.00e-02 4.00e+02 3.17e-02 1.61e+00 pdb=" N PRO B 295 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO B 295 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 295 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 72 " -0.006 2.00e-02 2.50e+03 1.10e-02 1.21e+00 pdb=" C PHE B 72 " 0.019 2.00e-02 2.50e+03 pdb=" O PHE B 72 " -0.007 2.00e-02 2.50e+03 pdb=" N VAL B 73 " -0.006 2.00e-02 2.50e+03 ... (remaining 1295 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.84: 2593 2.84 - 3.42: 9398 3.42 - 3.99: 14975 3.99 - 4.57: 23020 4.57 - 5.14: 31368 Nonbonded interactions: 81354 Sorted by model distance: nonbonded pdb=" OE1 GLN A 327 " pdb=" OG SER A 454 " model vdw 2.269 3.040 nonbonded pdb=" OE1 GLN B 327 " pdb=" OG SER B 454 " model vdw 2.269 3.040 nonbonded pdb=" NH1 ARG A 343 " pdb=" O ILE A 637 " model vdw 2.441 3.120 nonbonded pdb=" NH1 ARG B 343 " pdb=" O ILE B 637 " model vdw 2.441 3.120 nonbonded pdb=" O ILE B 174 " pdb=" OG1 THR B 178 " model vdw 2.446 3.040 ... (remaining 81349 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 44 through 319 or resid 321 through 803)) selection = (chain 'B' and (resid 44 through 319 or resid 321 through 803)) } 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=0.42 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: 1.360 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: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.880 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 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:6.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6782 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 : 0.003 0.055 8200 Z= 0.160 Angle : 0.549 5.355 11137 Z= 0.308 Chirality : 0.036 0.170 1288 Planarity : 0.004 0.032 1298 Dihedral : 14.173 147.689 3254 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Rotamer: Outliers : 0.71 % Allowed : 5.91 % Favored : 93.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.31 (0.27), residues: 950 helix: 2.70 (0.18), residues: 768 sheet: None (None), residues: 0 loop : -0.15 (0.45), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 246 TYR 0.014 0.001 TYR B 413 PHE 0.010 0.001 PHE A 437 TRP 0.015 0.001 TRP A 441 HIS 0.006 0.001 HIS A 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.16 ( 8200) covalent geometry : angle 0.54910 / 0.31 (11137) hydrogen bonds : bond 0.11665 / 7.66 ( 638) hydrogen bonds : angle 5.09006 / 3.67 ( 1916) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 272 time to evaluate : 0.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 275 average time/residue: 0.3377 time to fit residues: 101.3952 Evaluate side-chains 158 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 156 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 PHE Chi-restraints excluded: chain B residue 426 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: [49, 53, 5, 33, 65, 62, 51, 38, 61, 45, 74] chunk 49 optimal weight: 0.4980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 94 ASN A 619 HIS B 377 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.108118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.079094 restraints weight = 47759.616| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 4.36 r_work: 0.2965 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2954 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2954 r_free = 0.2954 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2952 r_free = 0.2952 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (12 function evaluations) r_final: 0.2952 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.3942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 8200 Z= 0.181 Angle : 0.734 12.023 11137 Z= 0.361 Chirality : 0.045 0.214 1288 Planarity : 0.005 0.077 1298 Dihedral : 10.663 131.194 1502 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 3.43 % Allowed : 19.86 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.47 (0.26), residues: 950 helix: 2.81 (0.17), residues: 768 sheet: None (None), residues: 0 loop : -0.03 (0.49), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 583 TYR 0.017 0.002 TYR B 424 PHE 0.025 0.002 PHE A 635 TRP 0.032 0.002 TRP A 261 HIS 0.007 0.002 HIS A 651 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.18 ( 8200) covalent geometry : angle 0.73421 / 0.36 (11137) hydrogen bonds : bond 0.04508 / 2.97 ( 638) hydrogen bonds : angle 4.10774 / 3.01 ( 1916) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 159 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 377 GLN cc_start: 0.9183 (tt0) cc_final: 0.8683 (pp30) REVERT: A 381 SER cc_start: 0.8344 (OUTLIER) cc_final: 0.7930 (p) REVERT: A 382 LEU cc_start: 0.8345 (tp) cc_final: 0.7985 (tt) REVERT: A 635 PHE cc_start: 0.6786 (t80) cc_final: 0.6584 (t80) REVERT: A 655 MET cc_start: 0.7736 (mtp) cc_final: 0.7457 (mtt) REVERT: B 221 ILE cc_start: 0.8873 (OUTLIER) cc_final: 0.8653 (mt) REVERT: B 437 PHE cc_start: 0.8620 (t80) cc_final: 0.8327 (t80) REVERT: B 655 MET cc_start: 0.8201 (mmm) cc_final: 0.7892 (mmm) outliers start: 27 outliers final: 3 residues processed: 176 average time/residue: 0.3481 time to fit residues: 66.8944 Evaluate side-chains 129 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 124 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ASN Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain B residue 221 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: [45, 44, 41, 21, 53, 24, 50, 6, 3, 34, 77] chunk 45 optimal weight: 0.7980 chunk 44 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 50 optimal weight: 4.9990 chunk 6 optimal weight: 7.9990 chunk 3 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 chunk 77 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 371 GLN A 616 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.106391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.077142 restraints weight = 37918.404| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 3.89 r_work: 0.2955 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2954 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2954 r_free = 0.2954 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2954 r_free = 0.2954 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2954 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.6165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 8200 Z= 0.178 Angle : 0.709 11.603 11137 Z= 0.354 Chirality : 0.045 0.190 1288 Planarity : 0.005 0.044 1298 Dihedral : 9.124 125.619 1498 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 3.19 % Allowed : 21.51 % Favored : 75.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.47 (0.26), residues: 950 helix: 2.76 (0.17), residues: 772 sheet: None (None), residues: 0 loop : 0.16 (0.50), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 583 TYR 0.021 0.002 TYR B 605 PHE 0.021 0.002 PHE A 437 TRP 0.024 0.002 TRP A 612 HIS 0.016 0.002 HIS B 596 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.18 ( 8200) covalent geometry : angle 0.70898 / 0.35 (11137) hydrogen bonds : bond 0.04459 / 2.89 ( 638) hydrogen bonds : angle 3.93405 / 2.87 ( 1916) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 119 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 ASP cc_start: 0.8890 (t0) cc_final: 0.8599 (t0) REVERT: A 285 LEU cc_start: 0.9451 (OUTLIER) cc_final: 0.9235 (mp) REVERT: A 351 MET cc_start: 0.8193 (tpp) cc_final: 0.7880 (mmp) REVERT: A 377 GLN cc_start: 0.9318 (tt0) cc_final: 0.8918 (pp30) REVERT: A 590 LYS cc_start: 0.8306 (OUTLIER) cc_final: 0.8101 (ptpt) REVERT: B 217 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8704 (mt) REVERT: B 655 MET cc_start: 0.8562 (mmm) cc_final: 0.8355 (mmp) outliers start: 25 outliers final: 5 residues processed: 134 average time/residue: 0.3498 time to fit residues: 51.0901 Evaluate side-chains 105 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 97 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 590 LYS Chi-restraints excluded: chain B residue 150 PHE Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 452 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: [32, 73, 93, 60, 34, 11, 9, 23, 25, 82, 42] chunk 32 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 82 optimal weight: 0.0870 chunk 42 optimal weight: 5.9990 overall best weight: 1.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 244 ASN A 371 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.101693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.072202 restraints weight = 27402.754| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 3.37 r_work: 0.2892 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2904 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2904 r_free = 0.2904 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2904 r_free = 0.2904 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2904 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.7858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 8200 Z= 0.204 Angle : 0.711 11.332 11137 Z= 0.352 Chirality : 0.045 0.266 1288 Planarity : 0.005 0.040 1298 Dihedral : 9.027 110.336 1498 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 3.90 % Allowed : 21.63 % Favored : 74.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.46 (0.27), residues: 950 helix: 2.77 (0.18), residues: 772 sheet: None (None), residues: 0 loop : 0.05 (0.50), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 430 TYR 0.023 0.002 TYR A 413 PHE 0.030 0.002 PHE A 461 TRP 0.025 0.002 TRP A 261 HIS 0.019 0.002 HIS B 596 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.20 ( 8200) covalent geometry : angle 0.71055 / 0.35 (11137) hydrogen bonds : bond 0.04513 / 2.89 ( 638) hydrogen bonds : angle 4.00037 / 2.94 ( 1916) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 92 time to evaluate : 0.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 MET cc_start: 0.9350 (mmm) cc_final: 0.8851 (mtp) REVERT: A 187 ASP cc_start: 0.8896 (t0) cc_final: 0.8511 (t0) REVERT: A 327 GLN cc_start: 0.9143 (tp40) cc_final: 0.8830 (mm110) REVERT: A 377 GLN cc_start: 0.9363 (tt0) cc_final: 0.9133 (pp30) REVERT: A 392 PHE cc_start: 0.9284 (OUTLIER) cc_final: 0.9028 (t80) REVERT: A 635 PHE cc_start: 0.7363 (t80) cc_final: 0.6829 (t80) REVERT: B 150 PHE cc_start: 0.8892 (OUTLIER) cc_final: 0.8505 (m-80) outliers start: 31 outliers final: 6 residues processed: 115 average time/residue: 0.3928 time to fit residues: 49.1526 Evaluate side-chains 84 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain B residue 150 PHE Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 452 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: [71, 15, 17, 43, 27, 58, 78, 75, 81, 85, 60] chunk 71 optimal weight: 0.6980 chunk 15 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 27 optimal weight: 9.9990 chunk 58 optimal weight: 0.6980 chunk 78 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 81 optimal weight: 0.7980 chunk 85 optimal weight: 0.0070 chunk 60 optimal weight: 3.9990 overall best weight: 1.2400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 170 GLN A 371 GLN B 170 GLN B 586 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.101340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.071258 restraints weight = 45870.067| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 4.23 r_work: 0.2845 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2839 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2839 r_free = 0.2839 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2839 r_free = 0.2839 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2839 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.8599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8200 Z= 0.169 Angle : 0.646 11.001 11137 Z= 0.323 Chirality : 0.043 0.199 1288 Planarity : 0.004 0.048 1298 Dihedral : 8.438 110.109 1498 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 3.31 % Allowed : 21.75 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.72 (0.27), residues: 950 helix: 2.96 (0.17), residues: 774 sheet: None (None), residues: 0 loop : 0.05 (0.51), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 597 TYR 0.020 0.001 TYR B 605 PHE 0.019 0.002 PHE A 437 TRP 0.016 0.002 TRP A 261 HIS 0.012 0.001 HIS B 596 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.17 ( 8200) covalent geometry : angle 0.64606 / 0.32 (11137) hydrogen bonds : bond 0.04360 / 2.82 ( 638) hydrogen bonds : angle 3.89522 / 2.87 ( 1916) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 85 time to evaluate : 0.323 Fit side-chains revert: symmetry clash REVERT: A 183 MET cc_start: 0.9348 (mmm) cc_final: 0.9031 (mtp) REVERT: A 187 ASP cc_start: 0.8992 (t0) cc_final: 0.8723 (t0) REVERT: A 655 MET cc_start: 0.8465 (mpp) cc_final: 0.7007 (mpt) REVERT: B 50 LYS cc_start: 0.8540 (pttp) cc_final: 0.8165 (ptpp) REVERT: B 150 PHE cc_start: 0.8882 (OUTLIER) cc_final: 0.8560 (m-80) REVERT: B 245 GLU cc_start: 0.9287 (OUTLIER) cc_final: 0.8776 (mp0) outliers start: 26 outliers final: 3 residues processed: 103 average time/residue: 0.4359 time to fit residues: 48.4218 Evaluate side-chains 75 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 70 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 378 HIS Chi-restraints excluded: chain B residue 150 PHE Chi-restraints excluded: chain B residue 245 GLU Chi-restraints excluded: chain B residue 394 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: [30, 81, 69, 82, 86, 53, 76, 85, 4, 12, 27] chunk 30 optimal weight: 5.9990 chunk 81 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 chunk 86 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 76 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 170 GLN A 377 GLN B 170 GLN B 356 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.098785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.068634 restraints weight = 45561.623| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 4.21 r_work: 0.2814 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2797 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2797 r_free = 0.2797 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2797 r_free = 0.2797 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2797 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.9099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 8200 Z= 0.195 Angle : 0.643 9.603 11137 Z= 0.327 Chirality : 0.044 0.249 1288 Planarity : 0.005 0.063 1298 Dihedral : 8.497 107.151 1498 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 3.07 % Allowed : 22.22 % Favored : 74.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.71 (0.27), residues: 950 helix: 2.99 (0.17), residues: 774 sheet: None (None), residues: 0 loop : -0.18 (0.49), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 621 TYR 0.021 0.002 TYR A 413 PHE 0.030 0.002 PHE A 461 TRP 0.016 0.002 TRP A 261 HIS 0.013 0.001 HIS B 596 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.20 ( 8200) covalent geometry : angle 0.64322 / 0.33 (11137) hydrogen bonds : bond 0.04557 / 2.93 ( 638) hydrogen bonds : angle 3.94886 / 2.93 ( 1916) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 72 time to evaluate : 0.307 Fit side-chains revert: symmetry clash REVERT: A 106 ARG cc_start: 0.8647 (mmt-90) cc_final: 0.7627 (mmt90) REVERT: A 183 MET cc_start: 0.9411 (mmm) cc_final: 0.9012 (mtp) REVERT: A 187 ASP cc_start: 0.8979 (t0) cc_final: 0.8740 (t0) REVERT: A 327 GLN cc_start: 0.9217 (tp40) cc_final: 0.8964 (mm110) REVERT: A 377 GLN cc_start: 0.9257 (OUTLIER) cc_final: 0.8955 (pp30) REVERT: A 392 PHE cc_start: 0.9343 (OUTLIER) cc_final: 0.9141 (t80) REVERT: B 150 PHE cc_start: 0.8874 (OUTLIER) cc_final: 0.8579 (m-80) REVERT: B 245 GLU cc_start: 0.9259 (OUTLIER) cc_final: 0.8591 (mp0) REVERT: B 655 MET cc_start: 0.8806 (mmm) cc_final: 0.8553 (mmm) outliers start: 24 outliers final: 2 residues processed: 89 average time/residue: 0.4412 time to fit residues: 42.2860 Evaluate side-chains 70 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 64 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 377 GLN Chi-restraints excluded: chain A residue 378 HIS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain B residue 150 PHE Chi-restraints excluded: chain B residue 245 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: [84, 59, 17, 12, 28, 85, 11, 26, 75, 33, 10] chunk 84 optimal weight: 0.5980 chunk 59 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 28 optimal weight: 0.3980 chunk 85 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 75 optimal weight: 5.9990 chunk 33 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 153 ASN A 170 GLN B 170 GLN ** B 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.100526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.071006 restraints weight = 34675.045| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 3.75 r_work: 0.2855 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2847 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2847 r_free = 0.2847 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2847 r_free = 0.2847 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2847 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.9171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8200 Z= 0.132 Angle : 0.606 8.287 11137 Z= 0.305 Chirality : 0.041 0.286 1288 Planarity : 0.004 0.039 1298 Dihedral : 8.277 106.120 1498 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 2.25 % Allowed : 22.22 % Favored : 75.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.92 (0.27), residues: 950 helix: 3.12 (0.17), residues: 774 sheet: None (None), residues: 0 loop : -0.03 (0.50), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 621 TYR 0.019 0.001 TYR B 605 PHE 0.018 0.001 PHE A 437 TRP 0.016 0.001 TRP B 441 HIS 0.009 0.001 HIS B 596 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 ( 8200) covalent geometry : angle 0.60605 / 0.31 (11137) hydrogen bonds : bond 0.04187 / 2.70 ( 638) hydrogen bonds : angle 3.81817 / 2.84 ( 1916) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 70 time to evaluate : 0.303 Fit side-chains revert: symmetry clash REVERT: A 105 TRP cc_start: 0.8274 (t60) cc_final: 0.7855 (t-100) REVERT: A 106 ARG cc_start: 0.8624 (mmt-90) cc_final: 0.7612 (mmt90) REVERT: A 183 MET cc_start: 0.9364 (mmm) cc_final: 0.9015 (mtp) REVERT: A 187 ASP cc_start: 0.8972 (t0) cc_final: 0.8715 (t0) REVERT: A 327 GLN cc_start: 0.9207 (tp40) cc_final: 0.8901 (mm110) REVERT: A 377 GLN cc_start: 0.9361 (tm-30) cc_final: 0.8953 (pp30) REVERT: A 655 MET cc_start: 0.8544 (mpp) cc_final: 0.7798 (mpt) REVERT: A 663 GLU cc_start: 0.8819 (mm-30) cc_final: 0.8459 (mp0) REVERT: B 50 LYS cc_start: 0.8704 (pttp) cc_final: 0.8418 (ptpp) REVERT: B 150 PHE cc_start: 0.8838 (OUTLIER) cc_final: 0.8568 (m-80) REVERT: B 245 GLU cc_start: 0.9219 (OUTLIER) cc_final: 0.8716 (mp0) REVERT: B 315 MET cc_start: 0.7856 (OUTLIER) cc_final: 0.7644 (tmt) REVERT: B 327 GLN cc_start: 0.9194 (OUTLIER) cc_final: 0.8936 (tp40) REVERT: B 655 MET cc_start: 0.8762 (mmm) cc_final: 0.8523 (mmm) REVERT: B 656 MET cc_start: 0.9119 (tpp) cc_final: 0.8313 (mpp) outliers start: 17 outliers final: 2 residues processed: 80 average time/residue: 0.4914 time to fit residues: 42.1067 Evaluate side-chains 73 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 HIS Chi-restraints excluded: chain B residue 150 PHE Chi-restraints excluded: chain B residue 245 GLU Chi-restraints excluded: chain B residue 315 MET Chi-restraints excluded: chain B residue 327 GLN Chi-restraints excluded: chain B residue 394 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: [1, 29, 68, 17, 56, 50, 45, 83, 13, 78, 10] chunk 1 optimal weight: 0.0980 chunk 29 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 83 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 170 GLN A 377 GLN B 170 GLN B 586 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.100924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.071133 restraints weight = 42530.996| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 4.10 r_work: 0.2847 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2840 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2840 r_free = 0.2840 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2840 r_free = 0.2840 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2840 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.9376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8200 Z= 0.133 Angle : 0.602 10.138 11137 Z= 0.300 Chirality : 0.041 0.292 1288 Planarity : 0.004 0.039 1298 Dihedral : 8.059 105.724 1498 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.77 % Allowed : 22.81 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.06 (0.27), residues: 950 helix: 3.23 (0.17), residues: 774 sheet: None (None), residues: 0 loop : -0.00 (0.50), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 621 TYR 0.018 0.001 TYR B 605 PHE 0.032 0.002 PHE A 461 TRP 0.016 0.001 TRP B 441 HIS 0.009 0.001 HIS A 651 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 ( 8200) covalent geometry : angle 0.60219 / 0.30 (11137) hydrogen bonds : bond 0.04006 / 2.59 ( 638) hydrogen bonds : angle 3.72180 / 2.77 ( 1916) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.209 Fit side-chains revert: symmetry clash REVERT: A 105 TRP cc_start: 0.8268 (t60) cc_final: 0.7861 (t-100) REVERT: A 106 ARG cc_start: 0.8622 (mmt-90) cc_final: 0.7589 (mmt90) REVERT: A 183 MET cc_start: 0.9330 (mmm) cc_final: 0.9082 (mtp) REVERT: A 187 ASP cc_start: 0.8985 (t0) cc_final: 0.8702 (t0) REVERT: A 303 MET cc_start: 0.8342 (mmt) cc_final: 0.7836 (mmt) REVERT: A 327 GLN cc_start: 0.9217 (tp40) cc_final: 0.8925 (mm110) REVERT: A 377 GLN cc_start: 0.9362 (OUTLIER) cc_final: 0.9036 (pp30) REVERT: A 449 MET cc_start: 0.7065 (mtt) cc_final: 0.6669 (mmp) REVERT: A 655 MET cc_start: 0.8198 (mpp) cc_final: 0.7092 (mpt) REVERT: B 106 ARG cc_start: 0.8575 (mmt-90) cc_final: 0.7545 (mmt90) REVERT: B 150 PHE cc_start: 0.8795 (OUTLIER) cc_final: 0.8554 (m-80) REVERT: B 245 GLU cc_start: 0.9187 (OUTLIER) cc_final: 0.8690 (mp0) REVERT: B 315 MET cc_start: 0.7847 (OUTLIER) cc_final: 0.7601 (tmt) REVERT: B 655 MET cc_start: 0.8788 (mmm) cc_final: 0.8494 (mmm) REVERT: B 656 MET cc_start: 0.9155 (tpp) cc_final: 0.8276 (mpp) outliers start: 13 outliers final: 4 residues processed: 81 average time/residue: 0.5000 time to fit residues: 43.1134 Evaluate side-chains 75 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 377 GLN Chi-restraints excluded: chain A residue 378 HIS Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain B residue 150 PHE Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 245 GLU Chi-restraints excluded: chain B residue 315 MET Chi-restraints excluded: chain B residue 394 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: [55, 54, 21, 52, 39, 10, 66, 91, 45, 7, 30] chunk 55 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 chunk 45 optimal weight: 0.2980 chunk 7 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 170 GLN B 170 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.100593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.071092 restraints weight = 36191.303| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 3.81 r_work: 0.2855 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2860 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2860 r_free = 0.2860 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2860 r_free = 0.2860 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2860 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.9414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8200 Z= 0.140 Angle : 0.608 9.002 11137 Z= 0.306 Chirality : 0.042 0.290 1288 Planarity : 0.004 0.039 1298 Dihedral : 8.024 105.804 1498 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 1.54 % Allowed : 23.17 % Favored : 75.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.07 (0.27), residues: 950 helix: 3.23 (0.17), residues: 774 sheet: None (None), residues: 0 loop : 0.02 (0.50), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 621 TYR 0.018 0.001 TYR B 605 PHE 0.017 0.001 PHE A 437 TRP 0.016 0.001 TRP B 441 HIS 0.009 0.001 HIS B 596 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 ( 8200) covalent geometry : angle 0.60816 / 0.31 (11137) hydrogen bonds : bond 0.04054 / 2.62 ( 638) hydrogen bonds : angle 3.69948 / 2.76 ( 1916) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 0.233 Fit side-chains revert: symmetry clash REVERT: A 105 TRP cc_start: 0.8278 (t60) cc_final: 0.7859 (t-100) REVERT: A 106 ARG cc_start: 0.8627 (mmt-90) cc_final: 0.7584 (mmt90) REVERT: A 183 MET cc_start: 0.9332 (mmm) cc_final: 0.9099 (mtp) REVERT: A 187 ASP cc_start: 0.8968 (t0) cc_final: 0.8713 (t0) REVERT: A 303 MET cc_start: 0.8351 (mmt) cc_final: 0.7986 (mmt) REVERT: A 327 GLN cc_start: 0.9230 (tp40) cc_final: 0.8943 (mm110) REVERT: A 377 GLN cc_start: 0.9391 (tm-30) cc_final: 0.9038 (pp30) REVERT: A 449 MET cc_start: 0.7078 (mtt) cc_final: 0.6725 (mmp) REVERT: A 655 MET cc_start: 0.8269 (mpp) cc_final: 0.7180 (mpt) REVERT: B 106 ARG cc_start: 0.8589 (mmt-90) cc_final: 0.7577 (mmt90) REVERT: B 150 PHE cc_start: 0.8804 (OUTLIER) cc_final: 0.8567 (m-80) REVERT: B 245 GLU cc_start: 0.9200 (OUTLIER) cc_final: 0.8692 (mp0) REVERT: B 655 MET cc_start: 0.8806 (mmm) cc_final: 0.8496 (mmm) REVERT: B 656 MET cc_start: 0.9157 (tpp) cc_final: 0.8314 (mpp) outliers start: 11 outliers final: 3 residues processed: 78 average time/residue: 0.4986 time to fit residues: 41.7353 Evaluate side-chains 73 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 68 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 HIS Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain B residue 150 PHE Chi-restraints excluded: chain B residue 245 GLU Chi-restraints excluded: chain B residue 394 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: [13, 82, 5, 64, 44, 41, 91, 49, 47, 62, 46] chunk 13 optimal weight: 0.9980 chunk 82 optimal weight: 0.0070 chunk 5 optimal weight: 0.8980 chunk 64 optimal weight: 0.0470 chunk 44 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 91 optimal weight: 0.0770 chunk 49 optimal weight: 0.1980 chunk 47 optimal weight: 0.6980 chunk 62 optimal weight: 0.5980 chunk 46 optimal weight: 0.5980 overall best weight: 0.1854 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 153 ASN A 170 GLN B 170 GLN B 327 GLN B 586 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.103192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.073804 restraints weight = 46959.324| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 4.29 r_work: 0.2898 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2890 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2890 r_free = 0.2890 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2890 r_free = 0.2890 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2890 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.9497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8200 Z= 0.120 Angle : 0.592 8.935 11137 Z= 0.296 Chirality : 0.040 0.336 1288 Planarity : 0.004 0.038 1298 Dihedral : 7.787 104.330 1498 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.06 % Allowed : 23.64 % Favored : 75.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.27 (0.27), residues: 950 helix: 3.37 (0.17), residues: 774 sheet: None (None), residues: 0 loop : 0.07 (0.50), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 621 TYR 0.017 0.001 TYR B 605 PHE 0.025 0.001 PHE A 461 TRP 0.020 0.001 TRP B 261 HIS 0.007 0.001 HIS B 596 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 ( 8200) covalent geometry : angle 0.59234 / 0.30 (11137) hydrogen bonds : bond 0.03656 / 2.37 ( 638) hydrogen bonds : angle 3.57101 / 2.67 ( 1916) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 0.309 Fit side-chains revert: symmetry clash REVERT: A 105 TRP cc_start: 0.8216 (t60) cc_final: 0.7816 (t-100) REVERT: A 106 ARG cc_start: 0.8576 (mmt-90) cc_final: 0.7619 (mmt90) REVERT: A 187 ASP cc_start: 0.8967 (t0) cc_final: 0.8737 (t0) REVERT: A 244 ASN cc_start: 0.8784 (m110) cc_final: 0.8572 (m110) REVERT: A 303 MET cc_start: 0.8232 (mmt) cc_final: 0.7781 (mmt) REVERT: A 327 GLN cc_start: 0.9218 (tp40) cc_final: 0.8961 (mm110) REVERT: A 377 GLN cc_start: 0.9380 (tm-30) cc_final: 0.9029 (pp30) REVERT: A 449 MET cc_start: 0.7242 (mtt) cc_final: 0.6816 (mmp) REVERT: A 655 MET cc_start: 0.8110 (mpp) cc_final: 0.7188 (mpt) REVERT: B 106 ARG cc_start: 0.8561 (mmt-90) cc_final: 0.7491 (mmt90) REVERT: B 245 GLU cc_start: 0.9150 (OUTLIER) cc_final: 0.8669 (mp0) REVERT: B 655 MET cc_start: 0.8800 (mmm) cc_final: 0.8498 (mmm) REVERT: B 656 MET cc_start: 0.9154 (tpp) cc_final: 0.8280 (mpp) outliers start: 7 outliers final: 1 residues processed: 77 average time/residue: 0.5186 time to fit residues: 42.7280 Evaluate side-chains 70 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 68 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 HIS Chi-restraints excluded: chain B residue 245 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: [54, 22, 95, 24, 71, 67, 76, 19, 65, 6, 7] chunk 54 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 95 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 76 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 6 optimal weight: 0.4980 chunk 7 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 170 GLN B 170 GLN B 586 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.100956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.070655 restraints weight = 48258.041| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 4.38 r_work: 0.2839 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2849 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2849 r_free = 0.2849 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2849 r_free = 0.2849 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2849 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.9573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8200 Z= 0.139 Angle : 0.617 9.834 11137 Z= 0.307 Chirality : 0.042 0.317 1288 Planarity : 0.004 0.039 1298 Dihedral : 7.773 104.816 1498 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 0.83 % Allowed : 24.35 % Favored : 74.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.24 (0.27), residues: 950 helix: 3.34 (0.17), residues: 774 sheet: None (None), residues: 0 loop : 0.10 (0.50), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 621 TYR 0.018 0.001 TYR B 605 PHE 0.017 0.001 PHE A 437 TRP 0.017 0.001 TRP B 441 HIS 0.009 0.001 HIS B 596 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 ( 8200) covalent geometry : angle 0.61745 / 0.31 (11137) hydrogen bonds : bond 0.03883 / 2.50 ( 638) hydrogen bonds : angle 3.62062 / 2.71 ( 1916) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3049.09 seconds wall clock time: 52 minutes 40.34 seconds (3160.34 seconds total)