Starting phenix.real_space_refine on Tue Feb 3 14:35:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mtx_48615/02_2026/9mtx_48615.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mtx_48615/02_2026/9mtx_48615.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9mtx_48615/02_2026/9mtx_48615.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mtx_48615/02_2026/9mtx_48615.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mtx_48615/02_2026/9mtx_48615.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mtx_48615/02_2026/9mtx_48615.map" } resolution = 3.06 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.036 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: 4 Type Number sf(0) Gaussians S 26 5.16 5 C 2370 2.51 5 N 671 2.21 5 O 695 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3762 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 823 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 110, 817 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 104} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 19 Conformer: "B" Number of residues, atoms: 110, 817 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 104} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 19 bond proxies already assigned to first conformer: 826 Chain: "B" Number of atoms: 2939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 2939 Classifications: {'peptide': 400} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PTRANS': 18, 'TRANS': 381} Chain breaks: 7 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 199 Unresolved non-hydrogen angles: 248 Unresolved non-hydrogen dihedrals: 162 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 8, 'ARG:plan': 8, 'ASN:plan1': 5, 'TRP:plan': 1, 'GLU:plan': 6, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 137 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ASER A 19 " occ=0.67 ... (10 atoms not shown) pdb=" OG BSER A 19 " occ=0.33 Time building chain proxies: 0.81, per 1000 atoms: 0.22 Number of scatterers: 3762 At special positions: 0 Unit cell: (60.32, 83.52, 85.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 26 16.00 O 695 8.00 N 671 7.00 C 2370 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 24 " - pdb=" SG CYS A 97 " distance=2.03 Simple disulfide: pdb=" SG CYS B 224 " - pdb=" SG CYS B 235 " distance=2.03 Simple disulfide: pdb=" SG CYS B 236 " - pdb=" SG CYS B 244 " distance=2.03 Simple disulfide: pdb=" SG CYS B 240 " - pdb=" SG CYS B 252 " distance=2.03 Simple disulfide: pdb=" SG CYS B 255 " - pdb=" SG CYS B 264 " distance=2.03 Simple disulfide: pdb=" SG CYS B 268 " - pdb=" SG CYS B 295 " distance=2.03 Simple disulfide: pdb=" SG CYS B 299 " - pdb=" SG CYS B 311 " distance=2.03 Simple disulfide: pdb=" SG CYS B 342 " - pdb=" SG CYS B 367 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.27 Conformation dependent library (CDL) restraints added in 172.4 milliseconds 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 940 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 10 sheets defined 10.4% alpha, 17.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'A' and resid 88 through 92 removed outlier: 3.760A pdb=" N THR A 92 " --> pdb=" O PRO A 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 48 Processing helix chain 'B' and resid 71 through 75 removed outlier: 3.728A pdb=" N GLN B 75 " --> pdb=" O SER B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 110 Processing helix chain 'B' and resid 361 through 365 Processing helix chain 'B' and resid 377 through 381 removed outlier: 3.590A pdb=" N PHE B 381 " --> pdb=" O PRO B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 401 removed outlier: 3.536A pdb=" N GLN B 398 " --> pdb=" O GLU B 395 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N VAL B 399 " --> pdb=" O GLN B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 426 Processing helix chain 'B' and resid 436 through 439 Processing helix chain 'B' and resid 481 through 485 Processing sheet with id=AA1, first strand: chain 'A' and resid 6 through 9 removed outlier: 3.550A pdb=" N VAL A 80 " --> pdb=" O CYS A 24 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 12 through 14 removed outlier: 5.826A pdb=" N GLY A 12 " --> pdb=" O THR A 112 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR A 95 " --> pdb=" O THR A 109 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 59 through 61 removed outlier: 5.286A pdb=" N TRP A 49 " --> pdb=" O ARG A 40 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N ARG A 40 " --> pdb=" O TRP A 49 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 25 through 26 Processing sheet with id=AA5, first strand: chain 'B' and resid 60 through 63 removed outlier: 5.166A pdb=" N GLY B 152 " --> pdb=" O TYR B 112 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 258 through 260 Processing sheet with id=AA7, first strand: chain 'B' and resid 289 through 291 Processing sheet with id=AA8, first strand: chain 'B' and resid 304 through 305 Processing sheet with id=AA9, first strand: chain 'B' and resid 369 through 370 Processing sheet with id=AB1, first strand: chain 'B' and resid 374 through 376 removed outlier: 4.971A pdb=" N TYR B 441 " --> pdb=" O LEU B 465 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N LEU B 467 " --> pdb=" O TYR B 441 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N LEU B 443 " --> pdb=" O LEU B 467 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N HIS B 469 " --> pdb=" O LEU B 443 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N LEU B 445 " --> pdb=" O HIS B 469 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ALA B 466 " --> pdb=" O LEU B 494 " (cutoff:3.500A) 81 hydrogen bonds defined for protein. 159 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.44 Time building geometry restraints manager: 0.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 615 1.31 - 1.43: 1031 1.43 - 1.56: 2156 1.56 - 1.69: 2 1.69 - 1.81: 31 Bond restraints: 3835 Sorted by residual: bond pdb=" C ASN A 45 " pdb=" N GLN A 46 " ideal model delta sigma weight residual 1.330 1.612 -0.282 1.31e-02 5.83e+03 4.62e+02 bond pdb=" C GLN B 46 " pdb=" N ARG B 47 " ideal model delta sigma weight residual 1.335 1.578 -0.243 1.34e-02 5.57e+03 3.29e+02 bond pdb=" C GLN B 46 " pdb=" O GLN B 46 " ideal model delta sigma weight residual 1.237 1.180 0.056 1.16e-02 7.43e+03 2.37e+01 bond pdb=" C ARG A 88 " pdb=" O ARG A 88 " ideal model delta sigma weight residual 1.240 1.180 0.060 1.29e-02 6.01e+03 2.18e+01 bond pdb=" C GLN A 46 " pdb=" N ARG A 47 " ideal model delta sigma weight residual 1.332 1.282 0.051 1.40e-02 5.10e+03 1.31e+01 ... (remaining 3830 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 5158 2.08 - 4.16: 60 4.16 - 6.24: 6 6.24 - 8.32: 3 8.32 - 10.39: 1 Bond angle restraints: 5228 Sorted by residual: angle pdb=" CA GLN B 46 " pdb=" C GLN B 46 " pdb=" N ARG B 47 " ideal model delta sigma weight residual 117.17 106.78 10.39 1.18e+00 7.18e-01 7.76e+01 angle pdb=" O GLN B 46 " pdb=" C GLN B 46 " pdb=" N ARG B 47 " ideal model delta sigma weight residual 122.09 128.94 -6.85 1.08e+00 8.57e-01 4.02e+01 angle pdb=" C ASN A 45 " pdb=" N GLN A 46 " pdb=" CA GLN A 46 " ideal model delta sigma weight residual 120.94 113.99 6.95 1.57e+00 4.06e-01 1.96e+01 angle pdb=" O ARG A 88 " pdb=" C ARG A 88 " pdb=" N PRO A 89 " ideal model delta sigma weight residual 121.94 117.36 4.58 1.05e+00 9.07e-01 1.90e+01 angle pdb=" CA LEU A 87 " pdb=" C LEU A 87 " pdb=" N ARG A 88 " ideal model delta sigma weight residual 115.56 110.10 5.46 1.30e+00 5.92e-01 1.77e+01 ... (remaining 5223 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.24: 1944 16.24 - 32.48: 244 32.48 - 48.73: 69 48.73 - 64.97: 12 64.97 - 81.21: 3 Dihedral angle restraints: 2272 sinusoidal: 812 harmonic: 1460 Sorted by residual: dihedral pdb=" CA HIS B 473 " pdb=" C HIS B 473 " pdb=" N LEU B 474 " pdb=" CA LEU B 474 " ideal model delta harmonic sigma weight residual 180.00 -159.63 -20.37 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" CA MET B 347 " pdb=" C MET B 347 " pdb=" N GLU B 348 " pdb=" CA GLU B 348 " ideal model delta harmonic sigma weight residual 180.00 159.88 20.12 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" CB CYS B 240 " pdb=" SG CYS B 240 " pdb=" SG CYS B 252 " pdb=" CB CYS B 252 " ideal model delta sinusoidal sigma weight residual -86.00 -53.65 -32.35 1 1.00e+01 1.00e-02 1.49e+01 ... (remaining 2269 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 353 0.030 - 0.059: 173 0.059 - 0.089: 49 0.089 - 0.119: 31 0.119 - 0.148: 8 Chirality restraints: 614 Sorted by residual: chirality pdb=" CA ILE B 86 " pdb=" N ILE B 86 " pdb=" C ILE B 86 " pdb=" CB ILE B 86 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.50e-01 chirality pdb=" CA ILE B 431 " pdb=" N ILE B 431 " pdb=" C ILE B 431 " pdb=" CB ILE B 431 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.15e-01 chirality pdb=" CA ILE B 155 " pdb=" N ILE B 155 " pdb=" C ILE B 155 " pdb=" CB ILE B 155 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.01e-01 ... (remaining 611 not shown) Planarity restraints: 675 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 88 " 0.012 2.00e-02 2.50e+03 2.29e-02 5.25e+00 pdb=" C ARG A 88 " -0.040 2.00e-02 2.50e+03 pdb=" O ARG A 88 " 0.015 2.00e-02 2.50e+03 pdb=" N PRO A 89 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 46 " -0.007 2.00e-02 2.50e+03 1.53e-02 2.35e+00 pdb=" C GLN B 46 " 0.026 2.00e-02 2.50e+03 pdb=" O GLN B 46 " -0.012 2.00e-02 2.50e+03 pdb=" N ARG B 47 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 46 " 0.007 2.00e-02 2.50e+03 1.41e-02 2.00e+00 pdb=" C GLN A 46 " -0.024 2.00e-02 2.50e+03 pdb=" O GLN A 46 " 0.009 2.00e-02 2.50e+03 pdb=" N ARG A 47 " 0.009 2.00e-02 2.50e+03 ... (remaining 672 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 468 2.75 - 3.29: 3472 3.29 - 3.83: 5900 3.83 - 4.36: 7396 4.36 - 4.90: 13009 Nonbonded interactions: 30245 Sorted by model distance: nonbonded pdb=" NH2 ARG A 68 " pdb=" OD2 ASP A 91 " model vdw 2.218 3.120 nonbonded pdb=" O CYS B 367 " pdb=" OG1 THR B 402 " model vdw 2.224 3.040 nonbonded pdb=" OE2 GLU B 404 " pdb=" NE2 GLN B 429 " model vdw 2.234 3.120 nonbonded pdb=" O GLN B 426 " pdb=" OG SER B 457 " model vdw 2.243 3.040 nonbonded pdb=" O LEU B 161 " pdb=" NE2 GLN B 164 " model vdw 2.319 3.120 ... (remaining 30240 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.33 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: 0.880 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: 0.040 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 4.810 Find NCS groups from input model: 0.020 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:0.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 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 : 0.007 0.282 3843 Z= 0.494 Angle : 0.587 10.394 5244 Z= 0.352 Chirality : 0.043 0.148 614 Planarity : 0.004 0.028 675 Dihedral : 15.674 81.211 1308 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 0.53 % Allowed : 24.54 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.78 (0.37), residues: 495 helix: -3.66 (0.88), residues: 19 sheet: -1.62 (0.47), residues: 107 loop : -0.92 (0.33), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 34 TYR 0.007 0.001 TYR B 409 PHE 0.005 0.001 PHE B 371 TRP 0.008 0.001 TRP B 452 HIS 0.006 0.001 HIS B 349 Details of bonding type rmsd covalent geometry : bond 0.00692 ( 3835) covalent geometry : angle 0.58636 ( 5228) SS BOND : bond 0.00194 ( 8) SS BOND : angle 0.77340 ( 16) hydrogen bonds : bond 0.24722 ( 81) hydrogen bonds : angle 9.04019 ( 159) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 57 time to evaluate : 0.095 Fit side-chains REVERT: B 354 ARG cc_start: 0.7202 (OUTLIER) cc_final: 0.5668 (mtp-110) outliers start: 1 outliers final: 0 residues processed: 57 average time/residue: 0.0475 time to fit residues: 3.4289 Evaluate side-chains 58 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 57 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 354 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 24 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 26 optimal weight: 9.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 5.9990 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 50 optimal weight: 0.2980 chunk 19 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN A 107 GLN B 469 HIS B 470 HIS B 478 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.176689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.144606 restraints weight = 9884.631| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 4.56 r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3667 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3667 r_free = 0.3667 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3667 r_free = 0.3667 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3667 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.0837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3843 Z= 0.141 Angle : 0.546 5.309 5244 Z= 0.288 Chirality : 0.044 0.148 614 Planarity : 0.004 0.039 675 Dihedral : 5.030 39.925 548 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 5.28 % Allowed : 21.90 % Favored : 72.82 % 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: -1.57 (0.37), residues: 495 helix: -3.11 (1.01), residues: 19 sheet: -1.25 (0.55), residues: 91 loop : -0.92 (0.32), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 88 TYR 0.010 0.001 TYR A 95 PHE 0.006 0.001 PHE B 381 TRP 0.007 0.001 TRP B 482 HIS 0.007 0.001 HIS B 42 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 3835) covalent geometry : angle 0.54539 ( 5228) SS BOND : bond 0.00248 ( 8) SS BOND : angle 0.76912 ( 16) hydrogen bonds : bond 0.04261 ( 81) hydrogen bonds : angle 6.03259 ( 159) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 60 time to evaluate : 0.140 Fit side-chains REVERT: B 460 GLU cc_start: 0.7624 (tt0) cc_final: 0.7271 (tt0) outliers start: 19 outliers final: 16 residues processed: 71 average time/residue: 0.0370 time to fit residues: 3.5376 Evaluate side-chains 75 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 59 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 139 GLU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 342 CYS Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 469 HIS Chi-restraints excluded: chain B residue 496 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 49 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 28 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN B 469 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.176777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.144382 restraints weight = 7129.924| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 3.49 r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3694 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3694 r_free = 0.3694 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3694 r_free = 0.3694 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3694 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.1045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 3843 Z= 0.220 Angle : 0.622 6.352 5244 Z= 0.322 Chirality : 0.047 0.153 614 Planarity : 0.004 0.042 675 Dihedral : 5.059 22.971 544 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 8.71 % Allowed : 17.41 % Favored : 73.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.75 (0.37), residues: 495 helix: -3.59 (0.86), residues: 19 sheet: -1.47 (0.54), residues: 91 loop : -1.00 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 88 TYR 0.017 0.002 TYR B 409 PHE 0.007 0.001 PHE B 381 TRP 0.010 0.002 TRP B 482 HIS 0.009 0.002 HIS B 42 Details of bonding type rmsd covalent geometry : bond 0.00531 ( 3835) covalent geometry : angle 0.62100 ( 5228) SS BOND : bond 0.00399 ( 8) SS BOND : angle 0.92879 ( 16) hydrogen bonds : bond 0.04336 ( 81) hydrogen bonds : angle 6.19552 ( 159) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 56 time to evaluate : 0.085 Fit side-chains revert: symmetry clash REVERT: B 266 LEU cc_start: 0.7806 (OUTLIER) cc_final: 0.7568 (tt) REVERT: B 460 GLU cc_start: 0.7559 (tt0) cc_final: 0.7256 (tt0) outliers start: 32 outliers final: 20 residues processed: 78 average time/residue: 0.0454 time to fit residues: 4.5992 Evaluate side-chains 78 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 57 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 139 GLU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 342 CYS Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 496 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 46 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 35 optimal weight: 0.3980 chunk 22 optimal weight: 0.5980 chunk 47 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 44 optimal weight: 0.3980 chunk 50 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN A 83 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.179263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.146307 restraints weight = 5409.539| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 2.52 r_work: 0.3425 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3423 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3423 r_free = 0.3423 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3423 r_free = 0.3423 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3423 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.1145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3843 Z= 0.113 Angle : 0.500 4.242 5244 Z= 0.269 Chirality : 0.043 0.157 614 Planarity : 0.004 0.039 675 Dihedral : 4.605 19.527 544 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 6.86 % Allowed : 19.26 % Favored : 73.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.42 (0.37), residues: 495 helix: -3.11 (1.01), residues: 19 sheet: -1.09 (0.52), residues: 103 loop : -0.80 (0.32), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 88 TYR 0.014 0.001 TYR B 409 PHE 0.004 0.001 PHE B 381 TRP 0.008 0.001 TRP B 452 HIS 0.005 0.001 HIS B 42 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 3835) covalent geometry : angle 0.49976 ( 5228) SS BOND : bond 0.00165 ( 8) SS BOND : angle 0.66683 ( 16) hydrogen bonds : bond 0.03306 ( 81) hydrogen bonds : angle 5.63252 ( 159) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 58 time to evaluate : 0.113 Fit side-chains revert: symmetry clash REVERT: B 266 LEU cc_start: 0.7648 (OUTLIER) cc_final: 0.7361 (tt) REVERT: B 404 GLU cc_start: 0.6832 (OUTLIER) cc_final: 0.6441 (tp30) REVERT: B 460 GLU cc_start: 0.7702 (tt0) cc_final: 0.7433 (tt0) outliers start: 25 outliers final: 15 residues processed: 76 average time/residue: 0.0535 time to fit residues: 5.1594 Evaluate side-chains 75 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 58 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 139 GLU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 342 CYS Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 404 GLU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 469 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 28 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 18 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 34 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 chunk 15 optimal weight: 0.5980 chunk 3 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.179384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.153844 restraints weight = 13397.681| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 4.18 r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3799 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3799 r_free = 0.3799 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3799 r_free = 0.3799 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3799 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.1208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3843 Z= 0.134 Angle : 0.519 4.208 5244 Z= 0.276 Chirality : 0.044 0.155 614 Planarity : 0.004 0.038 675 Dihedral : 4.660 20.297 544 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 7.12 % Allowed : 18.73 % Favored : 74.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.37), residues: 495 helix: -3.23 (0.98), residues: 19 sheet: -1.08 (0.52), residues: 103 loop : -0.81 (0.32), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 88 TYR 0.012 0.001 TYR B 409 PHE 0.006 0.001 PHE B 258 TRP 0.007 0.001 TRP B 482 HIS 0.005 0.001 HIS B 42 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 3835) covalent geometry : angle 0.51840 ( 5228) SS BOND : bond 0.00256 ( 8) SS BOND : angle 0.70687 ( 16) hydrogen bonds : bond 0.03368 ( 81) hydrogen bonds : angle 5.68979 ( 159) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 61 time to evaluate : 0.135 Fit side-chains revert: symmetry clash REVERT: B 142 LEU cc_start: 0.7373 (OUTLIER) cc_final: 0.6968 (mt) REVERT: B 266 LEU cc_start: 0.7718 (OUTLIER) cc_final: 0.7469 (tt) REVERT: B 404 GLU cc_start: 0.6557 (OUTLIER) cc_final: 0.6219 (tp30) outliers start: 26 outliers final: 19 residues processed: 81 average time/residue: 0.0540 time to fit residues: 5.5957 Evaluate side-chains 80 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 58 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 139 GLU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 342 CYS Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 404 GLU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 469 HIS Chi-restraints excluded: chain B residue 496 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 49 optimal weight: 0.1980 chunk 1 optimal weight: 0.0870 chunk 16 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 35 optimal weight: 0.0980 chunk 20 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 48 optimal weight: 0.9990 chunk 34 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 overall best weight: 0.3358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN A 85 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.183130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.148534 restraints weight = 9229.548| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 4.84 r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3728 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3728 r_free = 0.3728 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3728 r_free = 0.3728 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3728 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 3843 Z= 0.090 Angle : 0.464 3.991 5244 Z= 0.252 Chirality : 0.043 0.151 614 Planarity : 0.003 0.036 675 Dihedral : 4.293 18.305 544 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 6.33 % Allowed : 20.32 % Favored : 73.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.38), residues: 495 helix: -2.72 (1.12), residues: 19 sheet: -0.93 (0.55), residues: 98 loop : -0.70 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 88 TYR 0.011 0.001 TYR B 409 PHE 0.021 0.001 PHE B 258 TRP 0.008 0.001 TRP B 452 HIS 0.004 0.001 HIS B 260 Details of bonding type rmsd covalent geometry : bond 0.00213 ( 3835) covalent geometry : angle 0.46453 ( 5228) SS BOND : bond 0.00137 ( 8) SS BOND : angle 0.43280 ( 16) hydrogen bonds : bond 0.02819 ( 81) hydrogen bonds : angle 5.33726 ( 159) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 66 time to evaluate : 0.138 Fit side-chains REVERT: A 34 ARG cc_start: 0.7252 (OUTLIER) cc_final: 0.6917 (mtp180) REVERT: A 88 ARG cc_start: 0.7623 (mtm110) cc_final: 0.7411 (mmt-90) REVERT: B 266 LEU cc_start: 0.7685 (OUTLIER) cc_final: 0.7481 (tt) REVERT: B 404 GLU cc_start: 0.6607 (OUTLIER) cc_final: 0.6252 (tp30) outliers start: 23 outliers final: 17 residues processed: 83 average time/residue: 0.0491 time to fit residues: 5.2329 Evaluate side-chains 80 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 60 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 26 CYS Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 139 GLU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 342 CYS Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 404 GLU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 469 HIS Chi-restraints excluded: chain B residue 496 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 28 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 41 optimal weight: 0.3980 chunk 37 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 49 optimal weight: 0.5980 chunk 3 optimal weight: 0.5980 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 78 ASN B 349 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.180417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.153152 restraints weight = 12633.397| |-----------------------------------------------------------------------------| r_work (start): 0.3787 rms_B_bonded: 4.56 r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3787 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3787 r_free = 0.3787 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3787 r_free = 0.3787 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3787 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3843 Z= 0.128 Angle : 0.505 4.215 5244 Z= 0.269 Chirality : 0.044 0.153 614 Planarity : 0.004 0.035 675 Dihedral : 4.491 19.783 544 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 7.12 % Allowed : 20.05 % Favored : 72.82 % 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: -1.28 (0.38), residues: 495 helix: -2.95 (1.05), residues: 19 sheet: -0.92 (0.52), residues: 103 loop : -0.72 (0.33), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 88 TYR 0.014 0.001 TYR B 409 PHE 0.007 0.001 PHE B 258 TRP 0.007 0.001 TRP B 482 HIS 0.015 0.002 HIS B 349 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 3835) covalent geometry : angle 0.50433 ( 5228) SS BOND : bond 0.00232 ( 8) SS BOND : angle 0.60499 ( 16) hydrogen bonds : bond 0.03099 ( 81) hydrogen bonds : angle 5.54740 ( 159) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 61 time to evaluate : 0.083 Fit side-chains REVERT: A 34 ARG cc_start: 0.7362 (OUTLIER) cc_final: 0.7072 (mtp180) REVERT: B 31 MET cc_start: 0.7632 (OUTLIER) cc_final: 0.7039 (pmm) REVERT: B 142 LEU cc_start: 0.7189 (OUTLIER) cc_final: 0.6798 (mt) REVERT: B 404 GLU cc_start: 0.6517 (OUTLIER) cc_final: 0.6180 (tp30) outliers start: 26 outliers final: 20 residues processed: 81 average time/residue: 0.0353 time to fit residues: 3.7520 Evaluate side-chains 82 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 58 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 26 CYS Chi-restraints excluded: chain B residue 31 MET Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 139 GLU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 342 CYS Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 404 GLU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 469 HIS Chi-restraints excluded: chain B residue 496 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 21 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 35 optimal weight: 0.4980 chunk 49 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN B 46 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.175700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.141727 restraints weight = 8306.882| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 4.38 r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3661 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3661 r_free = 0.3661 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3661 r_free = 0.3661 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3661 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 3843 Z= 0.242 Angle : 0.634 6.917 5244 Z= 0.327 Chirality : 0.049 0.209 614 Planarity : 0.004 0.038 675 Dihedral : 5.119 23.513 544 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 7.92 % Allowed : 19.53 % Favored : 72.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.64 (0.37), residues: 495 helix: -3.57 (0.89), residues: 19 sheet: -1.19 (0.51), residues: 103 loop : -0.95 (0.32), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 226 TYR 0.016 0.002 TYR B 409 PHE 0.008 0.001 PHE B 381 TRP 0.011 0.002 TRP B 482 HIS 0.008 0.002 HIS B 42 Details of bonding type rmsd covalent geometry : bond 0.00582 ( 3835) covalent geometry : angle 0.63171 ( 5228) SS BOND : bond 0.00473 ( 8) SS BOND : angle 1.07389 ( 16) hydrogen bonds : bond 0.03844 ( 81) hydrogen bonds : angle 6.14045 ( 159) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 57 time to evaluate : 0.086 Fit side-chains revert: symmetry clash REVERT: B 142 LEU cc_start: 0.7480 (OUTLIER) cc_final: 0.7135 (mt) REVERT: B 260 HIS cc_start: 0.7733 (t70) cc_final: 0.7264 (t-90) REVERT: B 404 GLU cc_start: 0.6768 (OUTLIER) cc_final: 0.6398 (tp30) outliers start: 29 outliers final: 24 residues processed: 79 average time/residue: 0.0410 time to fit residues: 4.2694 Evaluate side-chains 83 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 57 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain B residue 26 CYS Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 139 GLU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 342 CYS Chi-restraints excluded: chain B residue 350 LEU Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 404 GLU Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 469 HIS Chi-restraints excluded: chain B residue 496 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 23 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 27 optimal weight: 7.9990 chunk 25 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN B 260 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.177648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.144966 restraints weight = 10564.164| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 5.00 r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3694 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3694 r_free = 0.3694 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3694 r_free = 0.3694 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3694 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3843 Z= 0.168 Angle : 0.553 4.960 5244 Z= 0.291 Chirality : 0.046 0.154 614 Planarity : 0.004 0.036 675 Dihedral : 4.893 21.601 544 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 8.18 % Allowed : 19.26 % Favored : 72.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.59 (0.37), residues: 495 helix: -3.53 (0.91), residues: 19 sheet: -1.21 (0.51), residues: 103 loop : -0.90 (0.32), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 34 TYR 0.015 0.002 TYR B 409 PHE 0.007 0.001 PHE B 258 TRP 0.009 0.002 TRP B 482 HIS 0.007 0.001 HIS B 42 Details of bonding type rmsd covalent geometry : bond 0.00403 ( 3835) covalent geometry : angle 0.55172 ( 5228) SS BOND : bond 0.00320 ( 8) SS BOND : angle 0.82207 ( 16) hydrogen bonds : bond 0.03411 ( 81) hydrogen bonds : angle 5.87214 ( 159) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 58 time to evaluate : 0.097 Fit side-chains revert: symmetry clash REVERT: B 142 LEU cc_start: 0.7204 (OUTLIER) cc_final: 0.6841 (mt) REVERT: B 260 HIS cc_start: 0.7680 (t-90) cc_final: 0.7241 (t-90) REVERT: B 404 GLU cc_start: 0.6678 (OUTLIER) cc_final: 0.6286 (tp30) outliers start: 30 outliers final: 24 residues processed: 81 average time/residue: 0.0486 time to fit residues: 5.0905 Evaluate side-chains 82 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 56 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain A residue 78 ASN Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain B residue 26 CYS Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 139 GLU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 342 CYS Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 404 GLU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 469 HIS Chi-restraints excluded: chain B residue 496 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 23 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 7 optimal weight: 0.0170 chunk 50 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 12 optimal weight: 0.0770 chunk 36 optimal weight: 0.0020 chunk 18 optimal weight: 0.0670 chunk 17 optimal weight: 2.9990 chunk 28 optimal weight: 0.0980 overall best weight: 0.0522 ------------------------------------------------------------------------------- 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 = 0.4030 r_free = 0.4030 target = 0.177406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.145485 restraints weight = 10857.667| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 4.89 r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3709 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3709 r_free = 0.3709 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3709 r_free = 0.3709 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3709 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 3843 Z= 0.221 Angle : 1.186 59.199 5244 Z= 0.715 Chirality : 0.049 0.474 614 Planarity : 0.004 0.046 675 Dihedral : 5.101 33.797 544 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.27 % Favored : 95.53 % Rotamer: Outliers : 7.12 % Allowed : 20.32 % Favored : 72.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.37), residues: 495 helix: -3.50 (0.91), residues: 19 sheet: -1.19 (0.51), residues: 103 loop : -0.90 (0.32), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 100 TYR 0.014 0.001 TYR B 409 PHE 0.010 0.001 PHE B 258 TRP 0.009 0.001 TRP B 482 HIS 0.006 0.001 HIS B 42 Details of bonding type rmsd covalent geometry : bond 0.00398 ( 3835) covalent geometry : angle 1.18644 ( 5228) SS BOND : bond 0.00260 ( 8) SS BOND : angle 0.82334 ( 16) hydrogen bonds : bond 0.03274 ( 81) hydrogen bonds : angle 5.88274 ( 159) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 990 Ramachandran restraints generated. 495 Oldfield, 0 Emsley, 495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 56 time to evaluate : 0.092 Fit side-chains revert: symmetry clash REVERT: A 78 ASN cc_start: 0.7973 (OUTLIER) cc_final: 0.7398 (p0) REVERT: B 142 LEU cc_start: 0.7250 (OUTLIER) cc_final: 0.6880 (mt) REVERT: B 260 HIS cc_start: 0.7704 (t-90) cc_final: 0.7271 (t-90) REVERT: B 404 GLU cc_start: 0.6667 (OUTLIER) cc_final: 0.6283 (tp30) outliers start: 26 outliers final: 23 residues processed: 77 average time/residue: 0.0533 time to fit residues: 5.2538 Evaluate side-chains 82 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 56 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain A residue 78 ASN Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 26 CYS Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 139 GLU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 342 CYS Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 404 GLU Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 469 HIS Chi-restraints excluded: chain B residue 496 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 40 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 7 optimal weight: 9.9990 chunk 20 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 1 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4046 r_free = 0.4046 target = 0.178762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.147101 restraints weight = 10177.559| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 4.72 r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3707 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3707 r_free = 0.3707 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3707 r_free = 0.3707 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3707 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 3843 Z= 0.221 Angle : 1.186 59.199 5244 Z= 0.715 Chirality : 0.049 0.474 614 Planarity : 0.004 0.046 675 Dihedral : 5.101 33.797 544 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.27 % Favored : 95.53 % Rotamer: Outliers : 7.12 % Allowed : 20.58 % Favored : 72.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.37), residues: 495 helix: -3.50 (0.91), residues: 19 sheet: -1.19 (0.51), residues: 103 loop : -0.90 (0.32), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 100 TYR 0.014 0.001 TYR B 409 PHE 0.010 0.001 PHE B 258 TRP 0.009 0.001 TRP B 482 HIS 0.006 0.001 HIS B 42 Details of bonding type rmsd covalent geometry : bond 0.00398 ( 3835) covalent geometry : angle 1.18644 ( 5228) SS BOND : bond 0.00260 ( 8) SS BOND : angle 0.82334 ( 16) hydrogen bonds : bond 0.03274 ( 81) hydrogen bonds : angle 5.88274 ( 159) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 816.35 seconds wall clock time: 14 minutes 41.84 seconds (881.84 seconds total)