Starting phenix.real_space_refine on Tue Feb 11 23:30:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rw5_19543/02_2025/8rw5_19543.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rw5_19543/02_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8rw5_19543/02_2025/8rw5_19543.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rw5_19543/02_2025/8rw5_19543.map" model { file = "/net/cci-nas-00/data/ceres_data/8rw5_19543/02_2025/8rw5_19543.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rw5_19543/02_2025/8rw5_19543.cif" } resolution = 2.94 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.013 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 8.80, per 1000 atoms: 1.30 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: 1.38 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.69 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: 2.24 Time building geometry restraints manager: 1.67 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: 14.080 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: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 23.430 Find NCS groups from input model: 0.060 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:13.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.550 ------------------------------------------------------------------------------- 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 6886 Z= 0.222 Angle : 0.536 8.486 9368 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (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 TRP 0.014 0.001 TRP B 974 HIS 0.004 0.001 HIS B 636 PHE 0.019 0.002 PHE B 634 TYR 0.012 0.001 TYR B 422 ARG 0.008 0.000 ARG B 153 *********************** 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 : 0.747 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: 1.4982 time to fit residues: 109.9296 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 : 0.712 ------------------------------------------------------------------------------- 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 73 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 68 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 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 446 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.134209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.109693 restraints weight = 7993.691| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 2.04 r_work: 0.3074 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.0676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 6886 Z= 0.352 Angle : 0.596 8.844 9368 Z= 0.303 Chirality : 0.042 0.139 1058 Planarity : 0.005 0.056 1243 Dihedral : 4.859 63.815 981 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.07 % Allowed : 11.11 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.28), residues: 866 helix: 0.88 (0.22), residues: 547 sheet: -1.44 (0.60), residues: 69 loop : -0.29 (0.37), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 974 HIS 0.005 0.001 HIS B 636 PHE 0.014 0.002 PHE B 634 TYR 0.012 0.001 TYR B 123 ARG 0.006 0.000 ARG B 153 *********************** 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 98 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 77 time to evaluate : 0.779 Fit side-chains REVERT: B 261 GLU cc_start: 0.7354 (OUTLIER) cc_final: 0.6996 (pt0) REVERT: B 338 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7730 (mt) REVERT: B 849 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7507 (tp30) REVERT: B 958 LEU cc_start: 0.7864 (OUTLIER) cc_final: 0.7303 (tm) outliers start: 21 outliers final: 9 residues processed: 88 average time/residue: 1.4064 time to fit residues: 130.2161 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 : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 261 GLU 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 614 VAL Chi-restraints excluded: chain B residue 714 THR 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 958 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 5 optimal weight: 0.9990 chunk 53 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 chunk 68 optimal weight: 0.6980 chunk 86 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 56 optimal weight: 0.5980 chunk 27 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 chunk 82 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 106 GLN B 446 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.134634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.109966 restraints weight = 8118.352| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.06 r_work: 0.3102 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.0814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.115 6886 Z= 0.292 Angle : 0.562 8.645 9368 Z= 0.286 Chirality : 0.040 0.127 1058 Planarity : 0.005 0.055 1243 Dihedral : 4.725 63.387 978 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.07 % Allowed : 13.74 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.28), residues: 866 helix: 1.03 (0.22), residues: 545 sheet: -1.44 (0.59), residues: 69 loop : -0.36 (0.37), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 974 HIS 0.004 0.001 HIS B 636 PHE 0.014 0.002 PHE B 634 TYR 0.013 0.001 TYR B 123 ARG 0.006 0.000 ARG B 153 *********************** 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 97 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 76 time to evaluate : 0.790 Fit side-chains REVERT: B 338 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7714 (mt) REVERT: B 434 GLU cc_start: 0.7868 (mm-30) cc_final: 0.7260 (mp0) REVERT: B 849 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7505 (tp30) outliers start: 21 outliers final: 8 residues processed: 92 average time/residue: 1.3253 time to fit residues: 128.4026 Evaluate side-chains 84 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 time to evaluate : 0.824 ------------------------------------------------------------------------------- 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 593 HIS 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 21 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 83 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 36 optimal weight: 0.0670 chunk 16 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 75 optimal weight: 0.2980 chunk 41 optimal weight: 1.9990 overall best weight: 0.4718 ------------------------------------------------------------------------------- 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 = 0.3476 r_free = 0.3476 target = 0.136329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.111289 restraints weight = 8204.597| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 2.10 r_work: 0.3145 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.0925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 6886 Z= 0.232 Angle : 0.536 9.485 9368 Z= 0.269 Chirality : 0.039 0.148 1058 Planarity : 0.005 0.056 1243 Dihedral : 4.604 61.983 978 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.51 % Allowed : 14.04 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.28), residues: 866 helix: 1.29 (0.22), residues: 541 sheet: -1.47 (0.59), residues: 71 loop : -0.24 (0.37), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 974 HIS 0.003 0.001 HIS B 636 PHE 0.012 0.002 PHE B 634 TYR 0.013 0.001 TYR B 123 ARG 0.006 0.000 ARG B 153 *********************** 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 98 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 74 time to evaluate : 0.735 Fit side-chains REVERT: B 338 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7710 (mt) REVERT: B 396 LEU cc_start: 0.7774 (OUTLIER) cc_final: 0.7446 (mp) REVERT: B 434 GLU cc_start: 0.7775 (mm-30) cc_final: 0.7216 (mp0) REVERT: B 616 GLN cc_start: 0.7421 (mm-40) cc_final: 0.7055 (mm-40) REVERT: B 849 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7444 (tp30) outliers start: 24 outliers final: 11 residues processed: 93 average time/residue: 1.4456 time to fit residues: 140.8208 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 : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 262 HIS 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 396 LEU 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 944 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 55 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 70 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 36 optimal weight: 0.5980 chunk 14 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 22 optimal weight: 0.4980 chunk 16 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3464 r_free = 0.3464 target = 0.135018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.110487 restraints weight = 8091.576| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 2.05 r_work: 0.3111 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.1005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 6886 Z= 0.286 Angle : 0.560 9.258 9368 Z= 0.281 Chirality : 0.040 0.126 1058 Planarity : 0.005 0.057 1243 Dihedral : 4.678 63.078 978 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.65 % Allowed : 13.89 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.28), residues: 866 helix: 1.22 (0.22), residues: 542 sheet: -1.38 (0.58), residues: 75 loop : -0.25 (0.38), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 974 HIS 0.003 0.001 HIS B 636 PHE 0.011 0.002 PHE B 634 TYR 0.012 0.001 TYR B 123 ARG 0.007 0.000 ARG B 429 *********************** 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 99 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 74 time to evaluate : 0.805 Fit side-chains REVERT: B 211 ARG cc_start: 0.7371 (mtp180) cc_final: 0.6965 (mtm180) REVERT: B 338 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7728 (mt) REVERT: B 381 ARG cc_start: 0.7939 (mtp-110) cc_final: 0.7677 (mtp-110) REVERT: B 396 LEU cc_start: 0.7774 (OUTLIER) cc_final: 0.7482 (mp) REVERT: B 434 GLU cc_start: 0.7851 (mm-30) cc_final: 0.7240 (mp0) REVERT: B 616 GLN cc_start: 0.7482 (mm-40) cc_final: 0.7127 (mm-40) REVERT: B 849 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7514 (tp30) outliers start: 25 outliers final: 13 residues processed: 91 average time/residue: 1.3606 time to fit residues: 130.1923 Evaluate side-chains 89 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 73 time to evaluate : 0.772 ------------------------------------------------------------------------------- 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 396 LEU Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 593 HIS Chi-restraints excluded: chain B residue 620 ARG 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 767 ASP 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 51 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 chunk 66 optimal weight: 0.0770 chunk 70 optimal weight: 0.9990 chunk 77 optimal weight: 0.6980 chunk 60 optimal weight: 0.5980 chunk 17 optimal weight: 0.0670 chunk 20 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 overall best weight: 0.4076 ------------------------------------------------------------------------------- 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 = 0.3491 r_free = 0.3491 target = 0.137521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.112764 restraints weight = 8065.210| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 2.07 r_work: 0.3224 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.1094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 6886 Z= 0.210 Angle : 0.526 9.252 9368 Z= 0.262 Chirality : 0.038 0.120 1058 Planarity : 0.005 0.055 1243 Dihedral : 4.548 61.385 978 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.92 % Allowed : 14.62 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.28), residues: 866 helix: 1.39 (0.22), residues: 543 sheet: -1.37 (0.58), residues: 77 loop : -0.13 (0.38), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 974 HIS 0.002 0.001 HIS B 593 PHE 0.010 0.001 PHE B 634 TYR 0.013 0.001 TYR B 123 ARG 0.007 0.000 ARG B 153 *********************** 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 96 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 76 time to evaluate : 0.718 Fit side-chains REVERT: B 211 ARG cc_start: 0.7352 (mtp180) cc_final: 0.6955 (mtm180) REVERT: B 338 LEU cc_start: 0.8075 (OUTLIER) cc_final: 0.7740 (mt) REVERT: B 434 GLU cc_start: 0.7791 (mm-30) cc_final: 0.7228 (mp0) REVERT: B 849 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7476 (tp30) outliers start: 20 outliers final: 13 residues processed: 90 average time/residue: 1.5527 time to fit residues: 146.7067 Evaluate side-chains 87 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 620 ARG Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 654 GLU 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 11 optimal weight: 0.5980 chunk 4 optimal weight: 0.5980 chunk 85 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 29 optimal weight: 0.3980 chunk 15 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 chunk 58 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3477 r_free = 0.3477 target = 0.136233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.111444 restraints weight = 8125.482| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 2.07 r_work: 0.3221 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.1107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 6886 Z= 0.255 Angle : 0.548 9.424 9368 Z= 0.272 Chirality : 0.039 0.125 1058 Planarity : 0.005 0.054 1243 Dihedral : 4.578 61.654 978 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.92 % Allowed : 14.91 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.28), residues: 866 helix: 1.34 (0.22), residues: 543 sheet: -1.36 (0.57), residues: 75 loop : -0.16 (0.38), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 974 HIS 0.003 0.001 HIS B 636 PHE 0.010 0.002 PHE B 634 TYR 0.012 0.001 TYR B 123 ARG 0.007 0.000 ARG B 153 *********************** 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 95 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 75 time to evaluate : 0.798 Fit side-chains REVERT: B 211 ARG cc_start: 0.7354 (mtp180) cc_final: 0.6970 (mtm180) REVERT: B 338 LEU cc_start: 0.8088 (OUTLIER) cc_final: 0.7739 (mt) REVERT: B 434 GLU cc_start: 0.7809 (mm-30) cc_final: 0.7258 (mp0) REVERT: B 849 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7490 (tp30) outliers start: 20 outliers final: 14 residues processed: 89 average time/residue: 1.2870 time to fit residues: 121.0702 Evaluate side-chains 89 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 73 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 168 VAL 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 68 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 46 optimal weight: 0.5980 chunk 37 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.134269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.109786 restraints weight = 8150.770| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 2.04 r_work: 0.3095 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.1189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.101 6886 Z= 0.325 Angle : 0.583 9.657 9368 Z= 0.291 Chirality : 0.041 0.135 1058 Planarity : 0.005 0.054 1243 Dihedral : 4.726 63.054 978 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.49 % Allowed : 16.08 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.28), residues: 866 helix: 1.17 (0.22), residues: 541 sheet: -1.38 (0.57), residues: 75 loop : -0.25 (0.37), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 974 HIS 0.003 0.001 HIS B 636 PHE 0.010 0.002 PHE B 634 TYR 0.013 0.001 TYR B 123 ARG 0.007 0.000 ARG B 153 *********************** 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 93 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 76 time to evaluate : 0.758 Fit side-chains REVERT: B 211 ARG cc_start: 0.7323 (mtp180) cc_final: 0.6952 (mtm180) REVERT: B 338 LEU cc_start: 0.8121 (OUTLIER) cc_final: 0.7872 (mm) REVERT: B 434 GLU cc_start: 0.7825 (mm-30) cc_final: 0.7270 (mp0) REVERT: B 849 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7538 (tp30) outliers start: 17 outliers final: 13 residues processed: 87 average time/residue: 1.4526 time to fit residues: 132.6467 Evaluate side-chains 90 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 75 time to evaluate : 0.735 ------------------------------------------------------------------------------- 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 4 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 54 optimal weight: 0.4980 chunk 6 optimal weight: 0.5980 chunk 66 optimal weight: 0.7980 chunk 62 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.135955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.111379 restraints weight = 8107.256| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 2.05 r_work: 0.3098 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.1180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 6886 Z= 0.273 Angle : 0.565 9.561 9368 Z= 0.282 Chirality : 0.039 0.127 1058 Planarity : 0.005 0.054 1243 Dihedral : 4.678 62.798 978 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.49 % Allowed : 16.37 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.28), residues: 866 helix: 1.24 (0.22), residues: 542 sheet: -1.38 (0.57), residues: 75 loop : -0.21 (0.37), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 974 HIS 0.002 0.001 HIS B 636 PHE 0.010 0.002 PHE B 634 TYR 0.013 0.001 TYR B 123 ARG 0.007 0.000 ARG B 153 *********************** 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 94 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 77 time to evaluate : 0.734 Fit side-chains REVERT: B 211 ARG cc_start: 0.7313 (mtp180) cc_final: 0.6943 (mtm180) REVERT: B 338 LEU cc_start: 0.8088 (OUTLIER) cc_final: 0.7833 (mm) REVERT: B 381 ARG cc_start: 0.7855 (mtp-110) cc_final: 0.7487 (mtp-110) REVERT: B 434 GLU cc_start: 0.7790 (mm-30) cc_final: 0.7252 (mp0) REVERT: B 849 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7502 (tp30) outliers start: 17 outliers final: 13 residues processed: 88 average time/residue: 1.3460 time to fit residues: 124.5196 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 : 0.693 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 55 optimal weight: 0.7980 chunk 32 optimal weight: 0.0670 chunk 59 optimal weight: 0.9980 chunk 77 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 chunk 74 optimal weight: 0.8980 chunk 81 optimal weight: 0.9980 chunk 20 optimal weight: 0.2980 chunk 50 optimal weight: 0.7980 chunk 57 optimal weight: 0.1980 overall best weight: 0.3718 ------------------------------------------------------------------------------- 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 = 0.3499 r_free = 0.3499 target = 0.137858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.113170 restraints weight = 8177.056| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 2.06 r_work: 0.3155 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.1271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 6886 Z= 0.200 Angle : 0.528 9.508 9368 Z= 0.264 Chirality : 0.038 0.121 1058 Planarity : 0.005 0.053 1243 Dihedral : 4.549 60.923 978 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.34 % Allowed : 16.67 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.28), residues: 866 helix: 1.40 (0.22), residues: 542 sheet: -1.37 (0.56), residues: 77 loop : -0.14 (0.38), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 974 HIS 0.002 0.000 HIS B 593 PHE 0.011 0.001 PHE B 634 TYR 0.012 0.001 TYR B 123 ARG 0.007 0.000 ARG B 153 ********************** 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 90 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 74 time to evaluate : 0.698 Fit side-chains REVERT: B 211 ARG cc_start: 0.7346 (mtp180) cc_final: 0.6974 (mtm180) REVERT: B 338 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7856 (mm) REVERT: B 381 ARG cc_start: 0.7858 (mtp-110) cc_final: 0.7490 (mtp-110) REVERT: B 434 GLU cc_start: 0.7789 (mm-30) cc_final: 0.7287 (mp0) REVERT: B 849 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7510 (tp30) outliers start: 16 outliers final: 13 residues processed: 85 average time/residue: 1.3883 time to fit residues: 123.8971 Evaluate side-chains 89 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 74 time to evaluate : 0.696 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 11 optimal weight: 0.9990 chunk 29 optimal weight: 0.3980 chunk 14 optimal weight: 0.6980 chunk 72 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 1 optimal weight: 0.0570 overall best weight: 0.5498 ------------------------------------------------------------------------------- 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 = 0.136726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.112144 restraints weight = 8121.012| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 2.05 r_work: 0.3226 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.1240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 6886 Z= 0.253 Angle : 0.555 9.382 9368 Z= 0.277 Chirality : 0.039 0.125 1058 Planarity : 0.005 0.054 1243 Dihedral : 4.584 61.121 978 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.19 % Allowed : 16.81 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.28), residues: 866 helix: 1.33 (0.22), residues: 542 sheet: -1.34 (0.57), residues: 75 loop : -0.20 (0.37), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 974 HIS 0.002 0.001 HIS B 636 PHE 0.010 0.002 PHE B 634 TYR 0.011 0.001 TYR B 123 ARG 0.008 0.000 ARG B 429 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5237.19 seconds wall clock time: 93 minutes 33.69 seconds (5613.69 seconds total)