Starting phenix.real_space_refine on Wed Sep 17 07:47:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rw5_19543/09_2025/8rw5_19543.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rw5_19543/09_2025/8rw5_19543.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8rw5_19543/09_2025/8rw5_19543.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rw5_19543/09_2025/8rw5_19543.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8rw5_19543/09_2025/8rw5_19543.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rw5_19543/09_2025/8rw5_19543.map" } resolution = 2.94 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= 0.000 sd= 0.013 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 18 5.16 5 C 4230 2.51 5 N 1249 2.21 5 O 1256 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6753 Number of models: 1 Model: "" Number of chains: 1 Chain: "B" Number of atoms: 6753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 872, 6753 Classifications: {'peptide': 872} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 45, 'TRANS': 825} Chain breaks: 2 Time building chain proxies: 1.59, per 1000 atoms: 0.24 Number of scatterers: 6753 At special positions: 0 Unit cell: (94.9914, 81.4212, 109.854, 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 18 16.00 O 1256 8.00 N 1249 7.00 C 4230 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 470 " - pdb=" SG CYS B 479 " distance=2.03 Simple disulfide: pdb=" SG CYS B 709 " - pdb=" SG CYS B 763 " 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: 0.68 Conformation dependent library (CDL) restraints added in 493.1 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1646 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 3 sheets defined 65.1% alpha, 5.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'B' and resid 143 through 154 removed outlier: 3.555A pdb=" N SER B 148 " --> pdb=" O LEU B 144 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU B 150 " --> pdb=" O LEU B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 166 removed outlier: 3.636A pdb=" N THR B 166 " --> pdb=" O ALA B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 182 removed outlier: 3.561A pdb=" N ALA B 174 " --> pdb=" O GLU B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 205 removed outlier: 3.558A pdb=" N LYS B 205 " --> pdb=" O TYR B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 230 removed outlier: 4.195A pdb=" N GLU B 214 " --> pdb=" O ALA B 210 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU B 215 " --> pdb=" O ARG B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 247 Processing helix chain 'B' and resid 249 through 264 Processing helix chain 'B' and resid 266 through 281 Processing helix chain 'B' and resid 282 through 304 removed outlier: 3.713A pdb=" N ARG B 286 " --> pdb=" O SER B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 312 Processing helix chain 'B' and resid 313 through 315 No H-bonds generated for 'chain 'B' and resid 313 through 315' Processing helix chain 'B' and resid 319 through 330 Processing helix chain 'B' and resid 333 through 340 removed outlier: 3.588A pdb=" N VAL B 337 " --> pdb=" O SER B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 352 removed outlier: 3.630A pdb=" N VAL B 351 " --> pdb=" O LEU B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 365 Processing helix chain 'B' and resid 368 through 384 removed outlier: 3.517A pdb=" N ARG B 372 " --> pdb=" O ASP B 368 " (cutoff:3.500A) Proline residue: B 374 - end of helix removed outlier: 3.521A pdb=" N GLU B 377 " --> pdb=" O ALA B 373 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLN B 378 " --> pdb=" O PRO B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 401 removed outlier: 4.181A pdb=" N ASP B 393 " --> pdb=" O GLU B 389 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ALA B 394 " --> pdb=" O SER B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 416 removed outlier: 3.645A pdb=" N ALA B 408 " --> pdb=" O GLU B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 430 Processing helix chain 'B' and resid 435 through 453 removed outlier: 3.676A pdb=" N GLN B 453 " --> pdb=" O LEU B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 474 removed outlier: 3.656A pdb=" N LEU B 463 " --> pdb=" O ALA B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 493 removed outlier: 3.609A pdb=" N PHE B 481 " --> pdb=" O TYR B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 511 Processing helix chain 'B' and resid 514 through 532 Processing helix chain 'B' and resid 534 through 549 Processing helix chain 'B' and resid 553 through 570 Processing helix chain 'B' and resid 572 through 585 Processing helix chain 'B' and resid 591 through 602 Processing helix chain 'B' and resid 609 through 621 Processing helix chain 'B' and resid 625 through 644 removed outlier: 4.162A pdb=" N GLU B 642 " --> pdb=" O ARG B 638 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N VAL B 643 " --> pdb=" O ILE B 639 " (cutoff:3.500A) Processing helix chain 'B' and resid 644 through 661 removed outlier: 3.586A pdb=" N ALA B 661 " --> pdb=" O ARG B 657 " (cutoff:3.500A) Processing helix chain 'B' and resid 666 through 687 Processing helix chain 'B' and resid 689 through 701 removed outlier: 3.724A pdb=" N ALA B 693 " --> pdb=" O ASP B 689 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LEU B 701 " --> pdb=" O PHE B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 753 through 761 Processing helix chain 'B' and resid 838 through 842 removed outlier: 3.532A pdb=" N ALA B 842 " --> pdb=" O ASP B 839 " (cutoff:3.500A) Processing helix chain 'B' and resid 843 through 852 removed outlier: 3.721A pdb=" N SER B 852 " --> pdb=" O LEU B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 888 through 894 Processing helix chain 'B' and resid 921 through 930 Processing helix chain 'B' and resid 944 through 960 removed outlier: 4.079A pdb=" N ALA B 948 " --> pdb=" O LEU B 944 " (cutoff:3.500A) Processing helix chain 'B' and resid 962 through 976 Processing helix chain 'B' and resid 980 through 985 removed outlier: 3.763A pdb=" N VAL B 984 " --> pdb=" O ASP B 980 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 731 through 736 removed outlier: 6.574A pdb=" N LEU B 711 " --> pdb=" O LEU B 769 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 833 through 836 removed outlier: 3.923A pdb=" N GLU B 856 " --> pdb=" O THR B 804 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ILE B 857 " --> pdb=" O VAL B 903 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 862 through 865 removed outlier: 4.333A pdb=" N HIS B 862 " --> pdb=" O LEU B 875 " (cutoff:3.500A) 408 hydrogen bonds defined for protein. 1215 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.29 Time building geometry restraints manager: 0.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2369 1.34 - 1.46: 845 1.46 - 1.57: 3642 1.57 - 1.69: 0 1.69 - 1.80: 30 Bond restraints: 6886 Sorted by residual: bond pdb=" CA VAL B 820 " pdb=" CB VAL B 820 " ideal model delta sigma weight residual 1.537 1.524 0.013 1.29e-02 6.01e+03 1.06e+00 bond pdb=" CG LEU B 935 " pdb=" CD1 LEU B 935 " ideal model delta sigma weight residual 1.521 1.494 0.027 3.30e-02 9.18e+02 6.67e-01 bond pdb=" CG GLN B 616 " pdb=" CD GLN B 616 " ideal model delta sigma weight residual 1.516 1.498 0.018 2.50e-02 1.60e+03 5.44e-01 bond pdb=" CG LEU B 396 " pdb=" CD1 LEU B 396 " ideal model delta sigma weight residual 1.521 1.498 0.023 3.30e-02 9.18e+02 4.92e-01 bond pdb=" CB GLU B 518 " pdb=" CG GLU B 518 " ideal model delta sigma weight residual 1.520 1.500 0.020 3.00e-02 1.11e+03 4.59e-01 ... (remaining 6881 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 9203 1.70 - 3.39: 145 3.39 - 5.09: 15 5.09 - 6.79: 2 6.79 - 8.49: 3 Bond angle restraints: 9368 Sorted by residual: angle pdb=" C ASP B 943 " pdb=" N LEU B 944 " pdb=" CA LEU B 944 " ideal model delta sigma weight residual 121.54 127.40 -5.86 1.91e+00 2.74e-01 9.43e+00 angle pdb=" CA LEU B 944 " pdb=" CB LEU B 944 " pdb=" CG LEU B 944 " ideal model delta sigma weight residual 116.30 124.79 -8.49 3.50e+00 8.16e-02 5.88e+00 angle pdb=" CA LEU B 475 " pdb=" CB LEU B 475 " pdb=" CG LEU B 475 " ideal model delta sigma weight residual 116.30 124.00 -7.70 3.50e+00 8.16e-02 4.84e+00 angle pdb=" CA LEU B 612 " pdb=" CB LEU B 612 " pdb=" CG LEU B 612 " ideal model delta sigma weight residual 116.30 123.60 -7.30 3.50e+00 8.16e-02 4.35e+00 angle pdb=" N ARG B 122 " pdb=" CA ARG B 122 " pdb=" C ARG B 122 " ideal model delta sigma weight residual 108.99 105.93 3.06 1.57e+00 4.06e-01 3.80e+00 ... (remaining 9363 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.46: 3673 17.46 - 34.92: 404 34.92 - 52.37: 106 52.37 - 69.83: 11 69.83 - 87.29: 6 Dihedral angle restraints: 4200 sinusoidal: 1665 harmonic: 2535 Sorted by residual: dihedral pdb=" CA LEU B 164 " pdb=" C LEU B 164 " pdb=" N ALA B 165 " pdb=" CA ALA B 165 " ideal model delta harmonic sigma weight residual -180.00 -162.01 -17.99 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CB CYS B 470 " pdb=" SG CYS B 470 " pdb=" SG CYS B 479 " pdb=" CB CYS B 479 " ideal model delta sinusoidal sigma weight residual 93.00 122.74 -29.74 1 1.00e+01 1.00e-02 1.26e+01 dihedral pdb=" CA LEU B 146 " pdb=" C LEU B 146 " pdb=" N LEU B 147 " pdb=" CA LEU B 147 " ideal model delta harmonic sigma weight residual 180.00 162.34 17.66 0 5.00e+00 4.00e-02 1.25e+01 ... (remaining 4197 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 603 0.026 - 0.053: 298 0.053 - 0.079: 94 0.079 - 0.106: 43 0.106 - 0.132: 20 Chirality restraints: 1058 Sorted by residual: chirality pdb=" CA LEU B 944 " pdb=" N LEU B 944 " pdb=" C LEU B 944 " pdb=" CB LEU B 944 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.35e-01 chirality pdb=" CA PRO B 512 " pdb=" N PRO B 512 " pdb=" C PRO B 512 " pdb=" CB PRO B 512 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.59e-01 chirality pdb=" CA PRO B 171 " pdb=" N PRO B 171 " pdb=" C PRO B 171 " pdb=" CB PRO B 171 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.52e-01 ... (remaining 1055 not shown) Planarity restraints: 1243 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS B 939 " 0.037 5.00e-02 4.00e+02 5.64e-02 5.09e+00 pdb=" N PRO B 940 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO B 940 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 940 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 753 " -0.031 5.00e-02 4.00e+02 4.69e-02 3.52e+00 pdb=" N PRO B 754 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO B 754 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 754 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 341 " -0.030 5.00e-02 4.00e+02 4.54e-02 3.30e+00 pdb=" N PRO B 342 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO B 342 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 342 " -0.026 5.00e-02 4.00e+02 ... (remaining 1240 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 238 2.72 - 3.27: 6799 3.27 - 3.81: 11556 3.81 - 4.36: 14117 4.36 - 4.90: 24214 Nonbonded interactions: 56924 Sorted by model distance: nonbonded pdb=" OE1 GLU B 856 " pdb=" NH1 ARG B 954 " model vdw 2.179 3.120 nonbonded pdb=" OH TYR B 325 " pdb=" OD2 ASP B 435 " model vdw 2.269 3.040 nonbonded pdb=" OD2 ASP B 121 " pdb=" NE2 GLN B 235 " model vdw 2.294 3.120 nonbonded pdb=" O ALA B 672 " pdb=" OG SER B 676 " model vdw 2.301 3.040 nonbonded pdb=" NE2 HIS B 805 " pdb=" OD2 ASP B 858 " model vdw 2.316 3.120 ... (remaining 56919 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: 24.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.870 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6888 Z= 0.144 Angle : 0.536 8.486 9372 Z= 0.269 Chirality : 0.038 0.132 1058 Planarity : 0.005 0.056 1243 Dihedral : 15.685 87.288 2548 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.29 % Allowed : 13.01 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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 aren not related in a simple way. whole: 0.66 (0.28), residues: 866 helix: 1.10 (0.22), residues: 534 sheet: -1.53 (0.59), residues: 75 loop : -0.14 (0.37), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 153 TYR 0.012 0.001 TYR B 422 PHE 0.019 0.002 PHE B 634 TRP 0.014 0.001 TRP B 974 HIS 0.004 0.001 HIS B 636 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 6886) covalent geometry : angle 0.53598 ( 9368) SS BOND : bond 0.00172 ( 2) SS BOND : angle 1.10784 ( 4) hydrogen bonds : bond 0.13728 ( 408) hydrogen bonds : angle 5.42942 ( 1215) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 69 time to evaluate : 0.295 Fit side-chains REVERT: B 170 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.7281 (mt-10) outliers start: 2 outliers final: 0 residues processed: 70 average time/residue: 0.7578 time to fit residues: 55.6467 Evaluate side-chains 69 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 68 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 170 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.0980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.4980 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3467 r_free = 0.3467 target = 0.135324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.110685 restraints weight = 8122.351| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 2.07 r_work: 0.3089 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.0603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6888 Z= 0.185 Angle : 0.565 8.830 9372 Z= 0.287 Chirality : 0.040 0.128 1058 Planarity : 0.005 0.056 1243 Dihedral : 4.762 62.716 981 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.34 % Allowed : 11.70 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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 aren not related in a simple way. whole: 0.62 (0.28), residues: 866 helix: 1.07 (0.22), residues: 541 sheet: -1.65 (0.57), residues: 73 loop : -0.14 (0.37), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 153 TYR 0.012 0.001 TYR B 123 PHE 0.015 0.002 PHE B 634 TRP 0.015 0.002 TRP B 974 HIS 0.004 0.001 HIS B 636 Details of bonding type rmsd covalent geometry : bond 0.00444 ( 6886) covalent geometry : angle 0.56524 ( 9368) SS BOND : bond 0.00170 ( 2) SS BOND : angle 0.74291 ( 4) hydrogen bonds : bond 0.04950 ( 408) hydrogen bonds : angle 4.42463 ( 1215) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 76 time to evaluate : 0.310 Fit side-chains REVERT: B 338 LEU cc_start: 0.8068 (OUTLIER) cc_final: 0.7741 (mt) REVERT: B 849 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7488 (tp30) outliers start: 16 outliers final: 7 residues processed: 86 average time/residue: 0.7120 time to fit residues: 64.0907 Evaluate side-chains 84 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 75 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 614 VAL Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 741 SER Chi-restraints excluded: chain B residue 748 MET Chi-restraints excluded: chain B residue 765 LEU Chi-restraints excluded: chain B residue 849 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 8 optimal weight: 0.7980 chunk 85 optimal weight: 0.5980 chunk 77 optimal weight: 0.4980 chunk 55 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 63 optimal weight: 0.0470 chunk 26 optimal weight: 0.9990 chunk 62 optimal weight: 0.0270 chunk 71 optimal weight: 0.2980 chunk 86 optimal weight: 0.3980 chunk 51 optimal weight: 0.4980 overall best weight: 0.2536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 158 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.138464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.113628 restraints weight = 8052.012| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.08 r_work: 0.3182 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.0828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6888 Z= 0.109 Angle : 0.499 8.448 9372 Z= 0.251 Chirality : 0.037 0.118 1058 Planarity : 0.005 0.055 1243 Dihedral : 4.393 60.445 978 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.49 % Allowed : 13.45 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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 aren not related in a simple way. whole: 0.99 (0.28), residues: 866 helix: 1.40 (0.22), residues: 542 sheet: -1.56 (0.58), residues: 73 loop : -0.10 (0.37), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 153 TYR 0.012 0.001 TYR B 123 PHE 0.014 0.001 PHE B 634 TRP 0.012 0.001 TRP B 238 HIS 0.002 0.000 HIS B 636 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 6886) covalent geometry : angle 0.49847 ( 9368) SS BOND : bond 0.00122 ( 2) SS BOND : angle 0.82204 ( 4) hydrogen bonds : bond 0.03864 ( 408) hydrogen bonds : angle 4.11466 ( 1215) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 78 time to evaluate : 0.316 Fit side-chains REVERT: B 338 LEU cc_start: 0.8041 (OUTLIER) cc_final: 0.7739 (mt) REVERT: B 381 ARG cc_start: 0.7887 (mtp-110) cc_final: 0.7602 (mtp-110) REVERT: B 434 GLU cc_start: 0.7730 (mm-30) cc_final: 0.7150 (mp0) REVERT: B 849 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7471 (tp30) outliers start: 17 outliers final: 7 residues processed: 90 average time/residue: 0.7463 time to fit residues: 70.1301 Evaluate side-chains 80 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 262 HIS Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 593 HIS Chi-restraints excluded: chain B residue 748 MET Chi-restraints excluded: chain B residue 765 LEU Chi-restraints excluded: chain B residue 849 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 50 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 chunk 20 optimal weight: 0.0060 chunk 81 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 106 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.135705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.110881 restraints weight = 8138.745| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 2.08 r_work: 0.3088 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.0909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6888 Z= 0.161 Angle : 0.549 9.783 9372 Z= 0.272 Chirality : 0.039 0.144 1058 Planarity : 0.005 0.058 1243 Dihedral : 4.497 61.023 978 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.92 % Allowed : 14.04 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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 aren not related in a simple way. whole: 0.95 (0.28), residues: 866 helix: 1.37 (0.22), residues: 543 sheet: -1.46 (0.56), residues: 77 loop : -0.14 (0.38), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 153 TYR 0.011 0.001 TYR B 123 PHE 0.011 0.002 PHE B 634 TRP 0.013 0.001 TRP B 974 HIS 0.003 0.001 HIS B 636 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 6886) covalent geometry : angle 0.54925 ( 9368) SS BOND : bond 0.00185 ( 2) SS BOND : angle 0.70510 ( 4) hydrogen bonds : bond 0.04223 ( 408) hydrogen bonds : angle 4.14409 ( 1215) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 74 time to evaluate : 0.282 Fit side-chains REVERT: B 338 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7762 (mt) REVERT: B 434 GLU cc_start: 0.7788 (mm-30) cc_final: 0.7215 (mp0) REVERT: B 616 GLN cc_start: 0.7472 (mm-40) cc_final: 0.7168 (mm-40) REVERT: B 849 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7450 (tp30) outliers start: 20 outliers final: 11 residues processed: 87 average time/residue: 0.7056 time to fit residues: 64.2796 Evaluate side-chains 86 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 73 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 384 SER Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 593 HIS Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 741 SER Chi-restraints excluded: chain B residue 748 MET Chi-restraints excluded: chain B residue 765 LEU Chi-restraints excluded: chain B residue 849 GLU Chi-restraints excluded: chain B residue 935 LEU Chi-restraints excluded: chain B residue 984 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 68 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 85 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 67 optimal weight: 0.0570 chunk 9 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 overall best weight: 0.6500 ------------------------------------------------------------------------------- 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 = 0.3471 r_free = 0.3471 target = 0.135694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.110909 restraints weight = 8212.412| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 2.07 r_work: 0.3109 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.0955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.117 6888 Z= 0.179 Angle : 0.590 16.666 9372 Z= 0.293 Chirality : 0.040 0.125 1058 Planarity : 0.005 0.055 1243 Dihedral : 4.638 61.504 978 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.22 % Allowed : 13.74 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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 aren not related in a simple way. whole: 0.86 (0.28), residues: 866 helix: 1.29 (0.22), residues: 542 sheet: -1.44 (0.56), residues: 77 loop : -0.19 (0.38), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 153 TYR 0.012 0.001 TYR B 123 PHE 0.011 0.002 PHE B 634 TRP 0.014 0.001 TRP B 974 HIS 0.003 0.001 HIS B 636 Details of bonding type rmsd covalent geometry : bond 0.00442 ( 6886) covalent geometry : angle 0.56361 ( 9368) SS BOND : bond 0.00953 ( 2) SS BOND : angle 8.43532 ( 4) hydrogen bonds : bond 0.04354 ( 408) hydrogen bonds : angle 4.17210 ( 1215) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 78 time to evaluate : 0.285 Fit side-chains REVERT: B 211 ARG cc_start: 0.7388 (mtp180) cc_final: 0.6984 (mtm180) REVERT: B 338 LEU cc_start: 0.8092 (OUTLIER) cc_final: 0.7747 (mt) REVERT: B 381 ARG cc_start: 0.7948 (mtp-110) cc_final: 0.7683 (mtp-110) REVERT: B 434 GLU cc_start: 0.7850 (mm-30) cc_final: 0.7253 (mp0) REVERT: B 616 GLN cc_start: 0.7486 (mm-40) cc_final: 0.7174 (mm-40) REVERT: B 849 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7469 (tp30) outliers start: 22 outliers final: 12 residues processed: 94 average time/residue: 0.7564 time to fit residues: 74.3676 Evaluate side-chains 87 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 73 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 384 SER Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 593 HIS Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 741 SER Chi-restraints excluded: chain B residue 748 MET Chi-restraints excluded: chain B residue 765 LEU Chi-restraints excluded: chain B residue 767 ASP Chi-restraints excluded: chain B residue 849 GLU Chi-restraints excluded: chain B residue 935 LEU Chi-restraints excluded: chain B residue 944 LEU Chi-restraints excluded: chain B residue 984 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 29 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 13 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 83 optimal weight: 0.0870 overall best weight: 0.6760 ------------------------------------------------------------------------------- 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 = 0.3459 r_free = 0.3459 target = 0.134854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.110019 restraints weight = 8201.670| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.08 r_work: 0.3080 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.1038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 6888 Z= 0.178 Angle : 0.569 9.938 9372 Z= 0.284 Chirality : 0.040 0.127 1058 Planarity : 0.005 0.054 1243 Dihedral : 4.644 62.289 978 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.07 % Allowed : 14.62 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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 aren not related in a simple way. whole: 0.85 (0.28), residues: 866 helix: 1.28 (0.22), residues: 542 sheet: -1.30 (0.59), residues: 75 loop : -0.22 (0.37), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 429 TYR 0.013 0.001 TYR B 123 PHE 0.011 0.002 PHE B 634 TRP 0.014 0.001 TRP B 974 HIS 0.003 0.001 HIS B 636 Details of bonding type rmsd covalent geometry : bond 0.00436 ( 6886) covalent geometry : angle 0.55985 ( 9368) SS BOND : bond 0.00320 ( 2) SS BOND : angle 4.99416 ( 4) hydrogen bonds : bond 0.04326 ( 408) hydrogen bonds : angle 4.12988 ( 1215) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 74 time to evaluate : 0.275 Fit side-chains REVERT: B 211 ARG cc_start: 0.7325 (mtp180) cc_final: 0.6929 (mtm180) REVERT: B 338 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7813 (mm) REVERT: B 434 GLU cc_start: 0.7839 (mm-30) cc_final: 0.7238 (mp0) REVERT: B 849 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7492 (tp30) outliers start: 21 outliers final: 13 residues processed: 90 average time/residue: 0.6623 time to fit residues: 62.5075 Evaluate side-chains 88 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 73 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 384 SER Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 593 HIS Chi-restraints excluded: chain B residue 614 VAL Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 741 SER Chi-restraints excluded: chain B residue 748 MET Chi-restraints excluded: chain B residue 765 LEU Chi-restraints excluded: chain B residue 767 ASP Chi-restraints excluded: chain B residue 849 GLU Chi-restraints excluded: chain B residue 935 LEU Chi-restraints excluded: chain B residue 944 LEU Chi-restraints excluded: chain B residue 984 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 7 optimal weight: 0.8980 chunk 64 optimal weight: 0.0980 chunk 17 optimal weight: 0.9980 chunk 14 optimal weight: 0.5980 chunk 46 optimal weight: 0.0980 chunk 67 optimal weight: 0.7980 chunk 21 optimal weight: 0.0970 chunk 78 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 81 optimal weight: 0.5980 chunk 77 optimal weight: 0.8980 overall best weight: 0.2978 ------------------------------------------------------------------------------- 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 = 0.3537 r_free = 0.3537 target = 0.140446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.115375 restraints weight = 8022.973| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 2.13 r_work: 0.3157 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 6888 Z= 0.119 Angle : 0.523 11.085 9372 Z= 0.261 Chirality : 0.037 0.119 1058 Planarity : 0.005 0.054 1243 Dihedral : 4.479 59.719 978 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.34 % Allowed : 15.35 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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 aren not related in a simple way. whole: 1.10 (0.28), residues: 866 helix: 1.49 (0.22), residues: 543 sheet: -1.32 (0.61), residues: 66 loop : -0.19 (0.37), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 153 TYR 0.012 0.001 TYR B 123 PHE 0.011 0.001 PHE B 634 TRP 0.014 0.001 TRP B 238 HIS 0.002 0.000 HIS B 593 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 6886) covalent geometry : angle 0.51034 ( 9368) SS BOND : bond 0.00221 ( 2) SS BOND : angle 5.55401 ( 4) hydrogen bonds : bond 0.03633 ( 408) hydrogen bonds : angle 3.92160 ( 1215) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 71 time to evaluate : 0.235 Fit side-chains REVERT: B 211 ARG cc_start: 0.7263 (mtp180) cc_final: 0.6887 (mtm180) REVERT: B 338 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7738 (mt) REVERT: B 381 ARG cc_start: 0.7802 (mtp-110) cc_final: 0.7584 (mtp-110) REVERT: B 434 GLU cc_start: 0.7759 (mm-30) cc_final: 0.7188 (mp0) REVERT: B 849 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7450 (tp30) outliers start: 16 outliers final: 10 residues processed: 80 average time/residue: 0.6905 time to fit residues: 57.9165 Evaluate side-chains 82 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 593 HIS Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 748 MET Chi-restraints excluded: chain B residue 765 LEU Chi-restraints excluded: chain B residue 849 GLU Chi-restraints excluded: chain B residue 935 LEU Chi-restraints excluded: chain B residue 944 LEU Chi-restraints excluded: chain B residue 984 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 9 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 78 optimal weight: 0.0870 chunk 26 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 24 optimal weight: 0.0770 chunk 36 optimal weight: 0.7980 chunk 51 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 overall best weight: 0.5116 ------------------------------------------------------------------------------- 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 = 0.3486 r_free = 0.3486 target = 0.136981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.112170 restraints weight = 8188.698| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.08 r_work: 0.3182 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.1162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 6888 Z= 0.148 Angle : 0.545 10.757 9372 Z= 0.271 Chirality : 0.038 0.124 1058 Planarity : 0.005 0.053 1243 Dihedral : 4.494 60.017 978 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.05 % Allowed : 15.64 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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 aren not related in a simple way. whole: 1.06 (0.28), residues: 866 helix: 1.45 (0.22), residues: 543 sheet: -1.38 (0.56), residues: 77 loop : -0.09 (0.38), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 153 TYR 0.011 0.001 TYR B 123 PHE 0.010 0.002 PHE B 634 TRP 0.013 0.001 TRP B 974 HIS 0.002 0.001 HIS B 636 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 6886) covalent geometry : angle 0.53396 ( 9368) SS BOND : bond 0.00167 ( 2) SS BOND : angle 5.39612 ( 4) hydrogen bonds : bond 0.03950 ( 408) hydrogen bonds : angle 3.96107 ( 1215) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 72 time to evaluate : 0.288 Fit side-chains REVERT: B 211 ARG cc_start: 0.7354 (mtp180) cc_final: 0.6980 (mtm180) REVERT: B 338 LEU cc_start: 0.8084 (OUTLIER) cc_final: 0.7750 (mt) REVERT: B 434 GLU cc_start: 0.7767 (mm-30) cc_final: 0.7219 (mp0) REVERT: B 849 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7495 (tp30) outliers start: 14 outliers final: 11 residues processed: 82 average time/residue: 0.7175 time to fit residues: 61.4891 Evaluate side-chains 85 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 72 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 593 HIS Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 748 MET Chi-restraints excluded: chain B residue 765 LEU Chi-restraints excluded: chain B residue 767 ASP Chi-restraints excluded: chain B residue 849 GLU Chi-restraints excluded: chain B residue 935 LEU Chi-restraints excluded: chain B residue 944 LEU Chi-restraints excluded: chain B residue 984 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 17 optimal weight: 0.9990 chunk 4 optimal weight: 0.5980 chunk 76 optimal weight: 2.9990 chunk 37 optimal weight: 0.0870 chunk 68 optimal weight: 0.4980 chunk 16 optimal weight: 0.5980 chunk 59 optimal weight: 0.0070 chunk 74 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 11 optimal weight: 0.2980 overall best weight: 0.2976 ------------------------------------------------------------------------------- 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 = 0.3514 r_free = 0.3514 target = 0.139143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.114541 restraints weight = 8120.599| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 2.05 r_work: 0.3163 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.1229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 6888 Z= 0.116 Angle : 0.514 9.098 9372 Z= 0.256 Chirality : 0.037 0.120 1058 Planarity : 0.005 0.053 1243 Dihedral : 4.377 58.129 978 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.19 % Allowed : 15.79 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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 aren not related in a simple way. whole: 1.22 (0.29), residues: 866 helix: 1.60 (0.22), residues: 542 sheet: -1.34 (0.58), residues: 71 loop : -0.13 (0.38), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 153 TYR 0.011 0.001 TYR B 123 PHE 0.010 0.001 PHE B 634 TRP 0.013 0.001 TRP B 238 HIS 0.002 0.000 HIS B 593 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 6886) covalent geometry : angle 0.50751 ( 9368) SS BOND : bond 0.00134 ( 2) SS BOND : angle 3.95186 ( 4) hydrogen bonds : bond 0.03570 ( 408) hydrogen bonds : angle 3.86009 ( 1215) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 78 time to evaluate : 0.318 Fit side-chains REVERT: B 211 ARG cc_start: 0.7307 (mtp180) cc_final: 0.6939 (mtm180) REVERT: B 338 LEU cc_start: 0.8092 (OUTLIER) cc_final: 0.7798 (mt) REVERT: B 434 GLU cc_start: 0.7775 (mm-30) cc_final: 0.7224 (mp0) REVERT: B 849 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7478 (tp30) outliers start: 15 outliers final: 11 residues processed: 88 average time/residue: 0.7103 time to fit residues: 65.4915 Evaluate side-chains 84 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 71 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 593 HIS Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 748 MET Chi-restraints excluded: chain B residue 765 LEU Chi-restraints excluded: chain B residue 767 ASP Chi-restraints excluded: chain B residue 849 GLU Chi-restraints excluded: chain B residue 935 LEU Chi-restraints excluded: chain B residue 944 LEU Chi-restraints excluded: chain B residue 984 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 3 optimal weight: 0.4980 chunk 42 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 84 optimal weight: 0.0070 chunk 56 optimal weight: 1.9990 chunk 24 optimal weight: 0.2980 chunk 50 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 overall best weight: 0.4598 ------------------------------------------------------------------------------- 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 = 0.3504 r_free = 0.3504 target = 0.138205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.113589 restraints weight = 8127.025| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 2.06 r_work: 0.3233 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.1250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 6888 Z= 0.142 Angle : 0.556 13.825 9372 Z= 0.276 Chirality : 0.038 0.123 1058 Planarity : 0.005 0.053 1243 Dihedral : 4.460 58.645 978 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.90 % Allowed : 16.08 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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 aren not related in a simple way. whole: 1.12 (0.28), residues: 866 helix: 1.50 (0.22), residues: 542 sheet: -1.37 (0.56), residues: 77 loop : -0.06 (0.38), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 153 TYR 0.011 0.001 TYR B 123 PHE 0.010 0.002 PHE B 634 TRP 0.013 0.001 TRP B 974 HIS 0.002 0.001 HIS B 636 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 6886) covalent geometry : angle 0.53740 ( 9368) SS BOND : bond 0.00589 ( 2) SS BOND : angle 6.97135 ( 4) hydrogen bonds : bond 0.03830 ( 408) hydrogen bonds : angle 3.90702 ( 1215) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.266 Fit side-chains REVERT: B 211 ARG cc_start: 0.7327 (mtp180) cc_final: 0.6959 (mtm180) REVERT: B 338 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7774 (mt) REVERT: B 381 ARG cc_start: 0.7851 (mtp-110) cc_final: 0.7532 (mtp-110) REVERT: B 434 GLU cc_start: 0.7770 (mm-30) cc_final: 0.7242 (mp0) REVERT: B 849 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7479 (tp30) outliers start: 13 outliers final: 11 residues processed: 81 average time/residue: 0.6674 time to fit residues: 56.7758 Evaluate side-chains 87 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 593 HIS Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 748 MET Chi-restraints excluded: chain B residue 765 LEU Chi-restraints excluded: chain B residue 767 ASP Chi-restraints excluded: chain B residue 849 GLU Chi-restraints excluded: chain B residue 935 LEU Chi-restraints excluded: chain B residue 944 LEU Chi-restraints excluded: chain B residue 984 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 29 optimal weight: 0.6980 chunk 67 optimal weight: 0.9990 chunk 22 optimal weight: 0.3980 chunk 48 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 17 optimal weight: 0.0040 chunk 65 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 3 optimal weight: 0.0170 chunk 14 optimal weight: 0.6980 overall best weight: 0.3630 ------------------------------------------------------------------------------- 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 = 0.3513 r_free = 0.3513 target = 0.138969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.114380 restraints weight = 8125.395| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 2.06 r_work: 0.3243 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.1287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 6888 Z= 0.126 Angle : 0.540 12.371 9372 Z= 0.269 Chirality : 0.038 0.121 1058 Planarity : 0.005 0.053 1243 Dihedral : 4.413 57.993 978 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.19 % Allowed : 15.79 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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 aren not related in a simple way. whole: 1.18 (0.28), residues: 866 helix: 1.55 (0.22), residues: 542 sheet: -1.31 (0.57), residues: 71 loop : -0.12 (0.38), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 153 TYR 0.011 0.001 TYR B 123 PHE 0.010 0.001 PHE B 634 TRP 0.013 0.001 TRP B 974 HIS 0.002 0.000 HIS B 593 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 6886) covalent geometry : angle 0.52490 ( 9368) SS BOND : bond 0.00324 ( 2) SS BOND : angle 6.21655 ( 4) hydrogen bonds : bond 0.03648 ( 408) hydrogen bonds : angle 3.86043 ( 1215) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2905.40 seconds wall clock time: 50 minutes 26.25 seconds (3026.25 seconds total)