Starting phenix.real_space_refine on Tue Feb 3 16:32:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jxj_61865/02_2026/9jxj_61865.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jxj_61865/02_2026/9jxj_61865.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jxj_61865/02_2026/9jxj_61865.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jxj_61865/02_2026/9jxj_61865.map" model { file = "/net/cci-nas-00/data/ceres_data/9jxj_61865/02_2026/9jxj_61865.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jxj_61865/02_2026/9jxj_61865.cif" } resolution = 3.22 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= 0.005 sd= 0.075 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: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 21 5.16 5 C 3261 2.51 5 N 814 2.21 5 O 862 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 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: 4961 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 4946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4946 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 20, 'TRANS': 575} Chain breaks: 2 Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 15 Unusual residues: {'PO4': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 0.83, per 1000 atoms: 0.17 Number of scatterers: 4961 At special positions: 0 Unit cell: (98.115, 72.795, 101.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 21 16.00 P 3 15.00 O 862 8.00 N 814 7.00 C 3261 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 415 " - pdb=" SG CYS B 440 " 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: 0.26 Conformation dependent library (CDL) restraints added in 240.7 milliseconds 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1144 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 0 sheets defined 79.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'B' and resid 2 through 10 Processing helix chain 'B' and resid 12 through 19 removed outlier: 3.554A pdb=" N ARG B 16 " --> pdb=" O PRO B 13 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N LYS B 17 " --> pdb=" O GLU B 14 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR B 19 " --> pdb=" O ARG B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 35 removed outlier: 3.632A pdb=" N PHE B 25 " --> pdb=" O GLN B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 99 removed outlier: 3.895A pdb=" N LYS B 99 " --> pdb=" O LEU B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 168 Processing helix chain 'B' and resid 170 through 180 Processing helix chain 'B' and resid 181 through 183 No H-bonds generated for 'chain 'B' and resid 181 through 183' Processing helix chain 'B' and resid 190 through 207 removed outlier: 3.557A pdb=" N GLU B 207 " --> pdb=" O THR B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 219 Processing helix chain 'B' and resid 230 through 259 removed outlier: 4.171A pdb=" N LEU B 259 " --> pdb=" O ALA B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 272 Processing helix chain 'B' and resid 272 through 296 removed outlier: 3.640A pdb=" N PHE B 276 " --> pdb=" O TYR B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 304 removed outlier: 3.730A pdb=" N ILE B 302 " --> pdb=" O ASN B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 337 removed outlier: 3.539A pdb=" N LEU B 316 " --> pdb=" O SER B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 360 removed outlier: 3.638A pdb=" N LEU B 349 " --> pdb=" O TYR B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 382 Processing helix chain 'B' and resid 390 through 403 removed outlier: 3.886A pdb=" N ASN B 401 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N SER B 402 " --> pdb=" O ASP B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 420 Processing helix chain 'B' and resid 449 through 471 Proline residue: B 455 - end of helix Processing helix chain 'B' and resid 472 through 478 removed outlier: 4.111A pdb=" N HIS B 476 " --> pdb=" O ARG B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 502 removed outlier: 3.969A pdb=" N THR B 486 " --> pdb=" O LYS B 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 507 through 533 removed outlier: 3.662A pdb=" N ASP B 533 " --> pdb=" O ASP B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 581 removed outlier: 3.519A pdb=" N TYR B 560 " --> pdb=" O LYS B 556 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE B 571 " --> pdb=" O VAL B 567 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TRP B 573 " --> pdb=" O LEU B 569 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR B 574 " --> pdb=" O ARG B 570 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE B 575 " --> pdb=" O PHE B 571 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N GLN B 576 " --> pdb=" O ALA B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 585 through 617 removed outlier: 4.325A pdb=" N ASP B 590 " --> pdb=" O PRO B 586 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ILE B 591 " --> pdb=" O HIS B 587 " (cutoff:3.500A) Proline residue: B 598 - end of helix removed outlier: 3.788A pdb=" N PHE B 609 " --> pdb=" O PHE B 605 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N PHE B 610 " --> pdb=" O VAL B 606 " (cutoff:3.500A) 348 hydrogen bonds defined for protein. 1038 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: 0.70 Time building geometry restraints manager: 0.35 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: 763 1.31 - 1.43: 1515 1.43 - 1.56: 2791 1.56 - 1.68: 0 1.68 - 1.81: 30 Bond restraints: 5099 Sorted by residual: bond pdb=" CA SER B 264 " pdb=" CB SER B 264 " ideal model delta sigma weight residual 1.524 1.451 0.074 1.27e-02 6.20e+03 3.38e+01 bond pdb=" C ASN B 614 " pdb=" O ASN B 614 " ideal model delta sigma weight residual 1.235 1.182 0.053 1.33e-02 5.65e+03 1.61e+01 bond pdb=" CA ALA B 449 " pdb=" CB ALA B 449 " ideal model delta sigma weight residual 1.533 1.479 0.054 1.46e-02 4.69e+03 1.35e+01 bond pdb=" O3 PO4 B 701 " pdb=" P PO4 B 701 " ideal model delta sigma weight residual 1.569 1.503 0.066 2.00e-02 2.50e+03 1.09e+01 bond pdb=" CA ASN B 614 " pdb=" C ASN B 614 " ideal model delta sigma weight residual 1.523 1.477 0.047 1.56e-02 4.11e+03 8.94e+00 ... (remaining 5094 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.54: 6839 3.54 - 7.09: 62 7.09 - 10.63: 9 10.63 - 14.18: 2 14.18 - 17.72: 1 Bond angle restraints: 6913 Sorted by residual: angle pdb=" C ASN B 614 " pdb=" CA ASN B 614 " pdb=" CB ASN B 614 " ideal model delta sigma weight residual 110.37 92.65 17.72 1.78e+00 3.16e-01 9.91e+01 angle pdb=" CA PHE B 394 " pdb=" CB PHE B 394 " pdb=" CG PHE B 394 " ideal model delta sigma weight residual 113.80 121.68 -7.88 1.00e+00 1.00e+00 6.22e+01 angle pdb=" N GLU B 615 " pdb=" CA GLU B 615 " pdb=" C GLU B 615 " ideal model delta sigma weight residual 113.55 103.91 9.64 1.26e+00 6.30e-01 5.85e+01 angle pdb=" C ASN B 618 " pdb=" CA ASN B 618 " pdb=" CB ASN B 618 " ideal model delta sigma weight residual 109.65 96.75 12.90 1.75e+00 3.27e-01 5.43e+01 angle pdb=" N ARG B 448 " pdb=" CA ARG B 448 " pdb=" C ARG B 448 " ideal model delta sigma weight residual 114.12 104.10 10.02 1.39e+00 5.18e-01 5.20e+01 ... (remaining 6908 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.07: 2632 18.07 - 36.14: 265 36.14 - 54.20: 58 54.20 - 72.27: 9 72.27 - 90.34: 3 Dihedral angle restraints: 2967 sinusoidal: 1203 harmonic: 1764 Sorted by residual: dihedral pdb=" C ASN B 614 " pdb=" N ASN B 614 " pdb=" CA ASN B 614 " pdb=" CB ASN B 614 " ideal model delta harmonic sigma weight residual -122.60 -102.82 -19.78 0 2.50e+00 1.60e-01 6.26e+01 dihedral pdb=" C ASN B 618 " pdb=" N ASN B 618 " pdb=" CA ASN B 618 " pdb=" CB ASN B 618 " ideal model delta harmonic sigma weight residual -122.60 -105.95 -16.65 0 2.50e+00 1.60e-01 4.44e+01 dihedral pdb=" CA ALA B 384 " pdb=" C ALA B 384 " pdb=" N PRO B 385 " pdb=" CA PRO B 385 " ideal model delta harmonic sigma weight residual 180.00 149.91 30.09 0 5.00e+00 4.00e-02 3.62e+01 ... (remaining 2964 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 650 0.067 - 0.135: 89 0.135 - 0.202: 9 0.202 - 0.269: 2 0.269 - 0.337: 1 Chirality restraints: 751 Sorted by residual: chirality pdb=" CA ASN B 618 " pdb=" N ASN B 618 " pdb=" C ASN B 618 " pdb=" CB ASN B 618 " both_signs ideal model delta sigma weight residual False 2.51 2.85 -0.34 2.00e-01 2.50e+01 2.83e+00 chirality pdb=" CA CYS B 620 " pdb=" N CYS B 620 " pdb=" C CYS B 620 " pdb=" CB CYS B 620 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.78e+00 chirality pdb=" CA VAL B 447 " pdb=" N VAL B 447 " pdb=" C VAL B 447 " pdb=" CB VAL B 447 " both_signs ideal model delta sigma weight residual False 2.44 2.69 -0.25 2.00e-01 2.50e+01 1.58e+00 ... (remaining 748 not shown) Planarity restraints: 859 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 624 " 0.702 9.50e-02 1.11e+02 3.15e-01 6.07e+01 pdb=" NE ARG B 624 " -0.045 2.00e-02 2.50e+03 pdb=" CZ ARG B 624 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG B 624 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG B 624 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 618 " 0.020 2.00e-02 2.50e+03 3.96e-02 1.57e+01 pdb=" C ASN B 618 " -0.069 2.00e-02 2.50e+03 pdb=" O ASN B 618 " 0.025 2.00e-02 2.50e+03 pdb=" N ASN B 619 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS B 616 " 0.019 2.00e-02 2.50e+03 3.90e-02 1.52e+01 pdb=" C HIS B 616 " -0.067 2.00e-02 2.50e+03 pdb=" O HIS B 616 " 0.025 2.00e-02 2.50e+03 pdb=" N LEU B 617 " 0.023 2.00e-02 2.50e+03 ... (remaining 856 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.25: 7 2.25 - 2.91: 2126 2.91 - 3.57: 7370 3.57 - 4.24: 11383 4.24 - 4.90: 19770 Nonbonded interactions: 40656 Sorted by model distance: nonbonded pdb=" NH1 ARG B 611 " pdb=" SG CYS B 620 " model vdw 1.585 3.480 nonbonded pdb=" OE1 GLU B 615 " pdb=" NH2 ARG B 624 " model vdw 1.608 3.120 nonbonded pdb=" SD MET B 408 " pdb=" NE2 GLN B 452 " model vdw 1.633 3.480 nonbonded pdb=" CE MET B 408 " pdb=" CG2 THR B 580 " model vdw 1.881 3.880 nonbonded pdb=" OE1 GLN B 18 " pdb=" CD1 PHE B 72 " model vdw 2.148 3.340 ... (remaining 40651 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.000 Find NCS groups from input model: 0.010 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:0.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 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 0.074 5100 Z= 0.378 Angle : 0.888 17.723 6915 Z= 0.577 Chirality : 0.050 0.337 751 Planarity : 0.012 0.315 859 Dihedral : 15.079 90.340 1820 Min Nonbonded Distance : 1.585 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 0.19 % Allowed : 12.85 % Favored : 86.96 % Cbeta Deviations : 0.35 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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: -1.37 (0.31), residues: 590 helix: -0.03 (0.22), residues: 438 sheet: None (None), residues: 0 loop : -3.42 (0.41), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 624 TYR 0.015 0.002 TYR B 148 PHE 0.014 0.002 PHE B 54 TRP 0.038 0.002 TRP B 395 HIS 0.015 0.002 HIS B 616 Details of bonding type rmsd covalent geometry : bond 0.00720 ( 5099) covalent geometry : angle 0.88779 ( 6913) SS BOND : bond 0.00452 ( 1) SS BOND : angle 0.59851 ( 2) hydrogen bonds : bond 0.13038 ( 348) hydrogen bonds : angle 5.84860 ( 1038) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 119 time to evaluate : 0.179 Fit side-chains revert: symmetry clash REVERT: B 213 LYS cc_start: 0.7966 (ttmm) cc_final: 0.7761 (mttp) REVERT: B 272 TYR cc_start: 0.8998 (m-80) cc_final: 0.8403 (m-80) REVERT: B 448 ARG cc_start: 0.7600 (ttm110) cc_final: 0.7070 (mtm180) REVERT: B 468 ARG cc_start: 0.7814 (tmt170) cc_final: 0.7151 (mtt180) REVERT: B 469 ASP cc_start: 0.7893 (t0) cc_final: 0.7062 (t0) REVERT: B 498 THR cc_start: 0.8192 (p) cc_final: 0.7988 (p) REVERT: B 613 GLU cc_start: 0.8542 (tt0) cc_final: 0.7681 (tt0) outliers start: 1 outliers final: 1 residues processed: 120 average time/residue: 0.0833 time to fit residues: 12.1444 Evaluate side-chains 68 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 67 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 394 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 54 optimal weight: 0.5980 chunk 24 optimal weight: 0.5980 chunk 48 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 0.4980 chunk 31 optimal weight: 0.5980 chunk 25 optimal weight: 0.4980 chunk 58 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 GLN B 614 ASN ** B 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 619 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.166718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.122008 restraints weight = 5959.124| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 1.76 r_work: 0.3104 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5100 Z= 0.141 Angle : 0.568 10.071 6915 Z= 0.305 Chirality : 0.039 0.158 751 Planarity : 0.005 0.054 859 Dihedral : 4.844 29.016 654 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 1.13 % Allowed : 14.37 % Favored : 84.50 % 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: 0.71 (0.35), residues: 590 helix: 1.59 (0.24), residues: 440 sheet: None (None), residues: 0 loop : -3.09 (0.47), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 217 TYR 0.016 0.001 TYR B 352 PHE 0.016 0.001 PHE B 394 TRP 0.015 0.001 TRP B 395 HIS 0.010 0.001 HIS B 616 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 5099) covalent geometry : angle 0.56767 ( 6913) SS BOND : bond 0.00134 ( 1) SS BOND : angle 0.76163 ( 2) hydrogen bonds : bond 0.04403 ( 348) hydrogen bonds : angle 4.07268 ( 1038) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 79 time to evaluate : 0.140 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.6681 (pmm) cc_final: 0.6040 (pmm) REVERT: B 171 ARG cc_start: 0.8086 (mtp180) cc_final: 0.7785 (mtp-110) REVERT: B 272 TYR cc_start: 0.9134 (m-80) cc_final: 0.8541 (m-80) REVERT: B 448 ARG cc_start: 0.7967 (ttm110) cc_final: 0.6980 (mtm-85) REVERT: B 468 ARG cc_start: 0.8180 (tmt170) cc_final: 0.6441 (mtt180) REVERT: B 472 ARG cc_start: 0.8253 (mtp85) cc_final: 0.7778 (mtp85) REVERT: B 613 GLU cc_start: 0.8566 (tt0) cc_final: 0.8177 (tt0) outliers start: 6 outliers final: 1 residues processed: 82 average time/residue: 0.0923 time to fit residues: 9.1534 Evaluate side-chains 69 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 68 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 11 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 21 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 44 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 52 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 499 HIS ** B 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.165487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.120093 restraints weight = 5847.799| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 1.94 r_work: 0.3053 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5100 Z= 0.160 Angle : 0.539 5.854 6915 Z= 0.290 Chirality : 0.040 0.139 751 Planarity : 0.004 0.054 859 Dihedral : 4.673 28.431 652 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 1.70 % Allowed : 15.69 % Favored : 82.61 % 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: 1.40 (0.35), residues: 590 helix: 2.14 (0.24), residues: 438 sheet: None (None), residues: 0 loop : -2.94 (0.47), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 502 TYR 0.019 0.002 TYR B 186 PHE 0.012 0.001 PHE B 3 TRP 0.013 0.001 TRP B 395 HIS 0.009 0.001 HIS B 616 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 5099) covalent geometry : angle 0.53875 ( 6913) SS BOND : bond 0.00010 ( 1) SS BOND : angle 0.33101 ( 2) hydrogen bonds : bond 0.04225 ( 348) hydrogen bonds : angle 3.88294 ( 1038) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 77 time to evaluate : 0.197 Fit side-chains revert: symmetry clash REVERT: B 213 LYS cc_start: 0.8552 (ttmm) cc_final: 0.8230 (mtpp) REVERT: B 272 TYR cc_start: 0.9178 (m-80) cc_final: 0.8508 (m-80) REVERT: B 288 ASN cc_start: 0.8917 (OUTLIER) cc_final: 0.8670 (m-40) REVERT: B 369 LYS cc_start: 0.8878 (mmmm) cc_final: 0.8637 (mmtt) REVERT: B 423 TRP cc_start: 0.8538 (m100) cc_final: 0.8298 (m100) REVERT: B 448 ARG cc_start: 0.8166 (ttm110) cc_final: 0.7034 (mtm-85) REVERT: B 468 ARG cc_start: 0.8064 (tmt170) cc_final: 0.6205 (mtt180) REVERT: B 472 ARG cc_start: 0.8242 (mtp85) cc_final: 0.7782 (mtp85) REVERT: B 539 LYS cc_start: 0.8236 (mmtt) cc_final: 0.7875 (mmtm) REVERT: B 584 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8246 (mt) REVERT: B 613 GLU cc_start: 0.8661 (tt0) cc_final: 0.8317 (tt0) REVERT: B 614 ASN cc_start: 0.8620 (t0) cc_final: 0.8209 (t0) outliers start: 9 outliers final: 5 residues processed: 82 average time/residue: 0.1025 time to fit residues: 10.2610 Evaluate side-chains 77 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 288 ASN Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 532 MET Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 618 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 22 optimal weight: 0.5980 chunk 8 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 chunk 41 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 499 HIS B 614 ASN B 616 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.165342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.119107 restraints weight = 5871.752| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 1.94 r_work: 0.2979 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5100 Z= 0.135 Angle : 0.499 5.714 6915 Z= 0.267 Chirality : 0.038 0.128 751 Planarity : 0.004 0.053 859 Dihedral : 4.481 28.269 652 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.89 % Allowed : 17.58 % Favored : 80.53 % 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: 1.84 (0.36), residues: 590 helix: 2.45 (0.24), residues: 439 sheet: None (None), residues: 0 loop : -2.75 (0.47), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 502 TYR 0.020 0.001 TYR B 148 PHE 0.011 0.001 PHE B 3 TRP 0.010 0.001 TRP B 395 HIS 0.009 0.001 HIS B 616 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 5099) covalent geometry : angle 0.49934 ( 6913) SS BOND : bond 0.00076 ( 1) SS BOND : angle 0.46872 ( 2) hydrogen bonds : bond 0.03939 ( 348) hydrogen bonds : angle 3.73293 ( 1038) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 time to evaluate : 0.112 Fit side-chains revert: symmetry clash REVERT: B 171 ARG cc_start: 0.8203 (mtp180) cc_final: 0.7943 (mtp-110) REVERT: B 272 TYR cc_start: 0.9132 (m-80) cc_final: 0.8448 (m-80) REVERT: B 288 ASN cc_start: 0.8867 (OUTLIER) cc_final: 0.8623 (m-40) REVERT: B 423 TRP cc_start: 0.8513 (m100) cc_final: 0.8029 (m100) REVERT: B 448 ARG cc_start: 0.8062 (ttm110) cc_final: 0.7035 (mtm-85) REVERT: B 468 ARG cc_start: 0.8097 (tmt170) cc_final: 0.6212 (mtt180) REVERT: B 472 ARG cc_start: 0.8129 (mtp85) cc_final: 0.7701 (mtp85) REVERT: B 539 LYS cc_start: 0.8263 (mmtt) cc_final: 0.7863 (mmtm) REVERT: B 584 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8250 (mt) REVERT: B 613 GLU cc_start: 0.8643 (tt0) cc_final: 0.8219 (tt0) outliers start: 10 outliers final: 6 residues processed: 81 average time/residue: 0.1020 time to fit residues: 9.8924 Evaluate side-chains 75 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 288 ASN Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 532 MET Chi-restraints excluded: chain B residue 584 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 21 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 57 optimal weight: 0.5980 chunk 24 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 22 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 40 optimal weight: 0.0020 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.166036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.119685 restraints weight = 5978.022| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 1.97 r_work: 0.2972 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5100 Z= 0.118 Angle : 0.480 5.575 6915 Z= 0.259 Chirality : 0.038 0.124 751 Planarity : 0.004 0.052 859 Dihedral : 4.327 27.751 652 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.27 % Allowed : 17.01 % Favored : 80.72 % 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: 2.12 (0.36), residues: 590 helix: 2.69 (0.24), residues: 437 sheet: None (None), residues: 0 loop : -2.75 (0.45), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 502 TYR 0.014 0.001 TYR B 496 PHE 0.011 0.001 PHE B 3 TRP 0.008 0.001 TRP B 395 HIS 0.003 0.001 HIS B 616 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 5099) covalent geometry : angle 0.47965 ( 6913) SS BOND : bond 0.00095 ( 1) SS BOND : angle 0.50893 ( 2) hydrogen bonds : bond 0.03745 ( 348) hydrogen bonds : angle 3.63281 ( 1038) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 74 time to evaluate : 0.191 Fit side-chains revert: symmetry clash REVERT: B 171 ARG cc_start: 0.8272 (mtp180) cc_final: 0.8056 (mtp-110) REVERT: B 272 TYR cc_start: 0.9117 (m-80) cc_final: 0.8368 (m-80) REVERT: B 288 ASN cc_start: 0.8828 (OUTLIER) cc_final: 0.8596 (m-40) REVERT: B 316 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8674 (mm) REVERT: B 423 TRP cc_start: 0.8494 (m100) cc_final: 0.8001 (m100) REVERT: B 448 ARG cc_start: 0.8073 (ttm110) cc_final: 0.6983 (mtm-85) REVERT: B 468 ARG cc_start: 0.8130 (tmt170) cc_final: 0.6252 (mtt180) REVERT: B 472 ARG cc_start: 0.8156 (mtp85) cc_final: 0.7763 (mtp85) REVERT: B 477 LEU cc_start: 0.8306 (mt) cc_final: 0.7928 (mt) REVERT: B 539 LYS cc_start: 0.8246 (mmtt) cc_final: 0.7872 (mmtm) REVERT: B 584 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8316 (mt) REVERT: B 613 GLU cc_start: 0.8617 (tt0) cc_final: 0.8293 (tt0) REVERT: B 615 GLU cc_start: 0.8345 (tp30) cc_final: 0.7934 (tp30) outliers start: 12 outliers final: 8 residues processed: 83 average time/residue: 0.1090 time to fit residues: 10.9344 Evaluate side-chains 81 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 288 ASN Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 484 SER Chi-restraints excluded: chain B residue 532 MET Chi-restraints excluded: chain B residue 584 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 40 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 33 optimal weight: 0.2980 chunk 32 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 5 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 476 HIS ** B 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.164952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.119735 restraints weight = 6084.699| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 2.06 r_work: 0.3101 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.3417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5100 Z= 0.144 Angle : 0.496 5.759 6915 Z= 0.266 Chirality : 0.038 0.134 751 Planarity : 0.004 0.053 859 Dihedral : 4.324 27.632 652 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.65 % Allowed : 16.64 % Favored : 80.72 % 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: 2.18 (0.35), residues: 590 helix: 2.70 (0.24), residues: 438 sheet: None (None), residues: 0 loop : -2.62 (0.45), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 502 TYR 0.023 0.002 TYR B 186 PHE 0.011 0.001 PHE B 3 TRP 0.007 0.001 TRP B 266 HIS 0.003 0.001 HIS B 616 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 5099) covalent geometry : angle 0.49591 ( 6913) SS BOND : bond 0.00055 ( 1) SS BOND : angle 0.44997 ( 2) hydrogen bonds : bond 0.03920 ( 348) hydrogen bonds : angle 3.64713 ( 1038) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 72 time to evaluate : 0.210 Fit side-chains revert: symmetry clash REVERT: B 213 LYS cc_start: 0.8644 (ttmm) cc_final: 0.7802 (tptm) REVERT: B 272 TYR cc_start: 0.9139 (m-80) cc_final: 0.8460 (m-80) REVERT: B 316 LEU cc_start: 0.9231 (OUTLIER) cc_final: 0.8785 (mm) REVERT: B 423 TRP cc_start: 0.8557 (m100) cc_final: 0.8085 (m100) REVERT: B 448 ARG cc_start: 0.8121 (ttm110) cc_final: 0.7169 (mtm-85) REVERT: B 468 ARG cc_start: 0.8307 (tmt170) cc_final: 0.6509 (mtt180) REVERT: B 472 ARG cc_start: 0.8146 (mtp85) cc_final: 0.7894 (mtp85) REVERT: B 477 LEU cc_start: 0.8393 (mt) cc_final: 0.8028 (mt) REVERT: B 539 LYS cc_start: 0.8204 (mmtt) cc_final: 0.7772 (mmtm) REVERT: B 584 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8258 (mt) REVERT: B 613 GLU cc_start: 0.8616 (tt0) cc_final: 0.8242 (tt0) REVERT: B 615 GLU cc_start: 0.8411 (tp30) cc_final: 0.8053 (tp30) outliers start: 14 outliers final: 8 residues processed: 81 average time/residue: 0.1053 time to fit residues: 10.2836 Evaluate side-chains 79 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 532 MET Chi-restraints excluded: chain B residue 584 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 10 optimal weight: 0.5980 chunk 43 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 37 optimal weight: 0.4980 chunk 21 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 chunk 46 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 32 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 chunk 39 optimal weight: 0.1980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 193 GLN B 476 HIS ** B 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.166576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.123438 restraints weight = 6005.244| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 1.94 r_work: 0.3108 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.3616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5100 Z= 0.118 Angle : 0.480 5.796 6915 Z= 0.259 Chirality : 0.037 0.126 751 Planarity : 0.004 0.051 859 Dihedral : 4.243 27.235 652 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.46 % Allowed : 17.77 % Favored : 79.77 % 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: 2.31 (0.35), residues: 590 helix: 2.82 (0.24), residues: 437 sheet: None (None), residues: 0 loop : -2.62 (0.45), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 502 TYR 0.016 0.001 TYR B 186 PHE 0.019 0.001 PHE B 372 TRP 0.010 0.001 TRP B 607 HIS 0.002 0.001 HIS B 499 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 5099) covalent geometry : angle 0.47995 ( 6913) SS BOND : bond 0.00079 ( 1) SS BOND : angle 0.43756 ( 2) hydrogen bonds : bond 0.03709 ( 348) hydrogen bonds : angle 3.61274 ( 1038) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.189 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 48 LYS cc_start: 0.9002 (mmtm) cc_final: 0.8779 (mtmt) REVERT: B 171 ARG cc_start: 0.8597 (mmm-85) cc_final: 0.7946 (mtm110) REVERT: B 272 TYR cc_start: 0.9135 (m-80) cc_final: 0.8421 (m-80) REVERT: B 316 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8720 (mm) REVERT: B 423 TRP cc_start: 0.8435 (m100) cc_final: 0.7964 (m100) REVERT: B 427 LYS cc_start: 0.8787 (mmtm) cc_final: 0.8221 (mmtp) REVERT: B 448 ARG cc_start: 0.7988 (ttm110) cc_final: 0.7000 (mtm-85) REVERT: B 468 ARG cc_start: 0.8196 (tmt170) cc_final: 0.6383 (mtt180) REVERT: B 472 ARG cc_start: 0.8102 (mtp85) cc_final: 0.7848 (mtp85) REVERT: B 477 LEU cc_start: 0.8314 (mt) cc_final: 0.7793 (mt) REVERT: B 539 LYS cc_start: 0.8175 (mmtt) cc_final: 0.7752 (mmtm) REVERT: B 584 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8210 (mt) REVERT: B 613 GLU cc_start: 0.8581 (tt0) cc_final: 0.8240 (tt0) REVERT: B 615 GLU cc_start: 0.8374 (tp30) cc_final: 0.7978 (tp30) outliers start: 13 outliers final: 10 residues processed: 82 average time/residue: 0.1190 time to fit residues: 11.6537 Evaluate side-chains 84 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 532 MET Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 584 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 45 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 46 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 18 optimal weight: 5.9990 chunk 30 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 476 HIS ** B 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.165426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.115983 restraints weight = 6091.673| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 1.99 r_work: 0.2914 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.3670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5100 Z= 0.134 Angle : 0.492 5.716 6915 Z= 0.264 Chirality : 0.038 0.153 751 Planarity : 0.004 0.052 859 Dihedral : 4.242 27.170 652 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.46 % Allowed : 18.53 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.31 (0.35), residues: 590 helix: 2.80 (0.24), residues: 437 sheet: None (None), residues: 0 loop : -2.55 (0.46), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 502 TYR 0.021 0.002 TYR B 148 PHE 0.018 0.001 PHE B 54 TRP 0.008 0.001 TRP B 607 HIS 0.003 0.001 HIS B 499 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 5099) covalent geometry : angle 0.49215 ( 6913) SS BOND : bond 0.00059 ( 1) SS BOND : angle 0.43413 ( 2) hydrogen bonds : bond 0.03811 ( 348) hydrogen bonds : angle 3.61825 ( 1038) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 73 time to evaluate : 0.199 Fit side-chains revert: symmetry clash REVERT: B 48 LYS cc_start: 0.9029 (mmtm) cc_final: 0.8807 (mtmt) REVERT: B 56 GLU cc_start: 0.8544 (mt-10) cc_final: 0.8183 (tp30) REVERT: B 171 ARG cc_start: 0.8757 (mmm-85) cc_final: 0.8331 (mtp-110) REVERT: B 213 LYS cc_start: 0.8518 (ttmm) cc_final: 0.7585 (tptm) REVERT: B 272 TYR cc_start: 0.9113 (m-80) cc_final: 0.8341 (m-80) REVERT: B 316 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8551 (mm) REVERT: B 423 TRP cc_start: 0.8401 (m100) cc_final: 0.7887 (m100) REVERT: B 427 LYS cc_start: 0.8820 (mmtm) cc_final: 0.8166 (mmtp) REVERT: B 448 ARG cc_start: 0.8014 (ttm110) cc_final: 0.6903 (mtm-85) REVERT: B 468 ARG cc_start: 0.8081 (tmt170) cc_final: 0.6278 (mtt180) REVERT: B 472 ARG cc_start: 0.8066 (mtp85) cc_final: 0.7774 (mtp85) REVERT: B 477 LEU cc_start: 0.8286 (mt) cc_final: 0.7757 (mt) REVERT: B 539 LYS cc_start: 0.8261 (mmtt) cc_final: 0.7832 (mmtm) REVERT: B 584 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8263 (mt) REVERT: B 613 GLU cc_start: 0.8668 (tt0) cc_final: 0.8354 (tt0) REVERT: B 615 GLU cc_start: 0.8407 (tp30) cc_final: 0.8003 (tp30) outliers start: 13 outliers final: 8 residues processed: 81 average time/residue: 0.1141 time to fit residues: 11.0582 Evaluate side-chains 82 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 532 MET Chi-restraints excluded: chain B residue 584 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 48 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 51 optimal weight: 0.1980 chunk 3 optimal weight: 8.9990 chunk 36 optimal weight: 2.9990 chunk 18 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 55 optimal weight: 6.9990 chunk 53 optimal weight: 0.6980 chunk 54 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 476 HIS ** B 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.165613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.122667 restraints weight = 6024.333| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 1.95 r_work: 0.3051 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.3767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5100 Z= 0.134 Angle : 0.489 5.762 6915 Z= 0.263 Chirality : 0.038 0.144 751 Planarity : 0.004 0.051 859 Dihedral : 4.254 27.127 652 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.46 % Allowed : 18.34 % Favored : 79.21 % 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: 2.32 (0.35), residues: 590 helix: 2.77 (0.24), residues: 438 sheet: None (None), residues: 0 loop : -2.45 (0.46), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 502 TYR 0.014 0.001 TYR B 352 PHE 0.018 0.001 PHE B 372 TRP 0.010 0.001 TRP B 266 HIS 0.003 0.001 HIS B 499 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 5099) covalent geometry : angle 0.48905 ( 6913) SS BOND : bond 0.00067 ( 1) SS BOND : angle 0.38683 ( 2) hydrogen bonds : bond 0.03800 ( 348) hydrogen bonds : angle 3.61086 ( 1038) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 0.141 Fit side-chains REVERT: B 30 TYR cc_start: 0.8313 (m-10) cc_final: 0.7960 (m-10) REVERT: B 55 GLU cc_start: 0.8552 (mt-10) cc_final: 0.8284 (mm-30) REVERT: B 56 GLU cc_start: 0.8567 (mt-10) cc_final: 0.8234 (tp30) REVERT: B 171 ARG cc_start: 0.8773 (mmm-85) cc_final: 0.8533 (mmm-85) REVERT: B 213 LYS cc_start: 0.8588 (ttmm) cc_final: 0.7655 (tptm) REVERT: B 272 TYR cc_start: 0.9141 (m-80) cc_final: 0.8418 (m-80) REVERT: B 316 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8617 (mm) REVERT: B 423 TRP cc_start: 0.8450 (m100) cc_final: 0.7964 (m100) REVERT: B 427 LYS cc_start: 0.8773 (mmtm) cc_final: 0.8133 (mmtp) REVERT: B 448 ARG cc_start: 0.8021 (ttm110) cc_final: 0.6977 (mtm-85) REVERT: B 468 ARG cc_start: 0.8081 (tmt170) cc_final: 0.6189 (mtt180) REVERT: B 477 LEU cc_start: 0.8342 (mt) cc_final: 0.7825 (mt) REVERT: B 504 HIS cc_start: 0.6760 (t70) cc_final: 0.6381 (t70) REVERT: B 539 LYS cc_start: 0.8263 (mmtt) cc_final: 0.7828 (mmtm) REVERT: B 584 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8155 (mt) REVERT: B 613 GLU cc_start: 0.8605 (tt0) cc_final: 0.8207 (tt0) REVERT: B 615 GLU cc_start: 0.8430 (tp30) cc_final: 0.8037 (tp30) outliers start: 13 outliers final: 8 residues processed: 84 average time/residue: 0.1057 time to fit residues: 10.5859 Evaluate side-chains 81 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 532 MET Chi-restraints excluded: chain B residue 584 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 24 optimal weight: 1.9990 chunk 51 optimal weight: 0.0070 chunk 26 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 chunk 57 optimal weight: 0.5980 chunk 58 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 3 optimal weight: 7.9990 chunk 7 optimal weight: 0.9990 overall best weight: 0.7002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 476 HIS ** B 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.166826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.123561 restraints weight = 6019.443| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 1.97 r_work: 0.3027 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.3809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5100 Z= 0.136 Angle : 0.507 6.107 6915 Z= 0.273 Chirality : 0.039 0.145 751 Planarity : 0.004 0.054 859 Dihedral : 4.256 27.168 652 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.89 % Allowed : 19.28 % Favored : 78.83 % 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: 2.27 (0.35), residues: 590 helix: 2.72 (0.24), residues: 438 sheet: None (None), residues: 0 loop : -2.42 (0.46), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 502 TYR 0.022 0.002 TYR B 148 PHE 0.023 0.001 PHE B 54 TRP 0.008 0.001 TRP B 607 HIS 0.003 0.001 HIS B 499 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 5099) covalent geometry : angle 0.50660 ( 6913) SS BOND : bond 0.00053 ( 1) SS BOND : angle 0.38335 ( 2) hydrogen bonds : bond 0.03861 ( 348) hydrogen bonds : angle 3.66447 ( 1038) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 0.158 Fit side-chains REVERT: B 55 GLU cc_start: 0.8528 (mt-10) cc_final: 0.8277 (mm-30) REVERT: B 56 GLU cc_start: 0.8566 (mt-10) cc_final: 0.8239 (tp30) REVERT: B 89 ASN cc_start: 0.8549 (m-40) cc_final: 0.8338 (m-40) REVERT: B 171 ARG cc_start: 0.8789 (mmm-85) cc_final: 0.8530 (mmm-85) REVERT: B 213 LYS cc_start: 0.8585 (ttmm) cc_final: 0.7649 (tptm) REVERT: B 272 TYR cc_start: 0.9137 (m-80) cc_final: 0.8412 (m-80) REVERT: B 316 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8612 (mm) REVERT: B 423 TRP cc_start: 0.8461 (m100) cc_final: 0.8041 (m100) REVERT: B 427 LYS cc_start: 0.8773 (mmtm) cc_final: 0.8230 (mmtp) REVERT: B 448 ARG cc_start: 0.8007 (ttm110) cc_final: 0.6984 (mtm-85) REVERT: B 468 ARG cc_start: 0.8079 (tmt170) cc_final: 0.6192 (mtt180) REVERT: B 477 LEU cc_start: 0.8336 (mt) cc_final: 0.7819 (mt) REVERT: B 539 LYS cc_start: 0.8251 (mmtt) cc_final: 0.7824 (mmtm) REVERT: B 584 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8230 (mt) REVERT: B 613 GLU cc_start: 0.8611 (tt0) cc_final: 0.8220 (tt0) REVERT: B 615 GLU cc_start: 0.8371 (tp30) cc_final: 0.7976 (tp30) outliers start: 10 outliers final: 7 residues processed: 76 average time/residue: 0.0970 time to fit residues: 8.7895 Evaluate side-chains 77 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 532 MET Chi-restraints excluded: chain B residue 584 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 5 optimal weight: 7.9990 chunk 8 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 51 optimal weight: 0.4980 chunk 19 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 476 HIS ** B 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.164932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.115407 restraints weight = 6092.236| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 1.98 r_work: 0.2963 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.3892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5100 Z= 0.142 Angle : 0.510 6.047 6915 Z= 0.275 Chirality : 0.039 0.146 751 Planarity : 0.004 0.056 859 Dihedral : 4.291 27.311 652 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.89 % Allowed : 19.85 % Favored : 78.26 % 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: 2.22 (0.35), residues: 590 helix: 2.65 (0.24), residues: 438 sheet: None (None), residues: 0 loop : -2.35 (0.46), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 502 TYR 0.016 0.001 TYR B 496 PHE 0.021 0.001 PHE B 54 TRP 0.009 0.001 TRP B 266 HIS 0.004 0.001 HIS B 499 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 5099) covalent geometry : angle 0.50961 ( 6913) SS BOND : bond 0.00032 ( 1) SS BOND : angle 0.36624 ( 2) hydrogen bonds : bond 0.03915 ( 348) hydrogen bonds : angle 3.68479 ( 1038) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1464.52 seconds wall clock time: 25 minutes 40.54 seconds (1540.54 seconds total)