Starting phenix.real_space_refine on Thu Jun 5 22:38:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rw5_19543/06_2025/8rw5_19543.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rw5_19543/06_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_19543/06_2025/8rw5_19543.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rw5_19543/06_2025/8rw5_19543.map" model { file = "/net/cci-nas-00/data/ceres_data/8rw5_19543/06_2025/8rw5_19543.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rw5_19543/06_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-5710/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: 8.68, per 1000 atoms: 1.29 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: 1.57 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: 0.78 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: 2.30 Time building geometry restraints manager: 1.88 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: 16.060 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: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 24.320 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.720 ------------------------------------------------------------------------------- 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 (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 Details of bonding type rmsd hydrogen bonds : bond 0.13728 ( 408) hydrogen bonds : angle 5.42942 ( 1215) SS BOND : bond 0.00172 ( 2) SS BOND : angle 1.10784 ( 4) covalent geometry : bond 0.00337 ( 6886) covalent geometry : angle 0.53598 ( 9368) *********************** 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 : 0.777 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: 1.4360 time to fit residues: 105.6404 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 : 0.804 ------------------------------------------------------------------------------- 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 = 39)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.109707 restraints weight = 7993.691| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 2.04 r_work: 0.3075 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 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 6888 Z= 0.220 Angle : 0.596 8.844 9372 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 Details of bonding type rmsd hydrogen bonds : bond 0.05086 ( 408) hydrogen bonds : angle 4.48084 ( 1215) SS BOND : bond 0.00150 ( 2) SS BOND : angle 0.79103 ( 4) covalent geometry : bond 0.00535 ( 6886) covalent geometry : angle 0.59617 ( 9368) *********************** 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 : 0.775 Fit side-chains REVERT: B 261 GLU cc_start: 0.7357 (OUTLIER) cc_final: 0.7001 (pt0) REVERT: B 338 LEU cc_start: 0.8088 (OUTLIER) cc_final: 0.7731 (mt) REVERT: B 849 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7515 (tp30) REVERT: B 958 LEU cc_start: 0.7866 (OUTLIER) cc_final: 0.7306 (tm) outliers start: 21 outliers final: 9 residues processed: 88 average time/residue: 1.3292 time to fit residues: 123.0658 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 : 0.708 ------------------------------------------------------------------------------- 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: 0.5980 chunk 86 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 56 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 chunk 82 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3466 r_free = 0.3466 target = 0.135136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.110426 restraints weight = 8100.869| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.06 r_work: 0.3102 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.0806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.113 6888 Z= 0.175 Angle : 0.571 11.890 9372 Z= 0.290 Chirality : 0.040 0.126 1058 Planarity : 0.005 0.055 1243 Dihedral : 4.705 63.252 978 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.92 % Allowed : 13.89 % 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: 0.57 (0.28), residues: 866 helix: 1.05 (0.22), residues: 545 sheet: -1.44 (0.59), residues: 69 loop : -0.35 (0.37), residues: 252 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 0.014 0.002 PHE B 634 TYR 0.013 0.001 TYR B 123 ARG 0.006 0.000 ARG B 153 Details of bonding type rmsd hydrogen bonds : bond 0.04565 ( 408) hydrogen bonds : angle 4.30225 ( 1215) SS BOND : bond 0.00403 ( 2) SS BOND : angle 5.97892 ( 4) covalent geometry : bond 0.00426 ( 6886) covalent geometry : angle 0.55759 ( 9368) *********************** 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 96 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 76 time to evaluate : 0.766 Fit side-chains REVERT: B 338 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7730 (mt) REVERT: B 434 GLU cc_start: 0.7867 (mm-30) cc_final: 0.7266 (mp0) REVERT: B 849 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7508 (tp30) outliers start: 20 outliers final: 7 residues processed: 91 average time/residue: 1.4784 time to fit residues: 141.8978 Evaluate side-chains 82 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.806 ------------------------------------------------------------------------------- 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 475 LEU Chi-restraints excluded: chain B residue 593 HIS Chi-restraints excluded: chain B residue 722 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 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: 0.9990 chunk 83 optimal weight: 0.6980 chunk 56 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 36 optimal weight: 0.0980 chunk 16 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 75 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 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 158 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.134912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.110243 restraints weight = 8200.652| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.06 r_work: 0.3217 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.0924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 6888 Z= 0.177 Angle : 0.573 10.448 9372 Z= 0.287 Chirality : 0.040 0.131 1058 Planarity : 0.005 0.057 1243 Dihedral : 4.698 62.841 978 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.65 % Allowed : 14.04 % 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 (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: 0.69 (0.28), residues: 866 helix: 1.17 (0.22), residues: 540 sheet: -1.44 (0.57), residues: 75 loop : -0.30 (0.37), residues: 251 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 0.012 0.002 PHE B 634 TYR 0.013 0.001 TYR B 123 ARG 0.005 0.000 ARG B 153 Details of bonding type rmsd hydrogen bonds : bond 0.04429 ( 408) hydrogen bonds : angle 4.24966 ( 1215) SS BOND : bond 0.00218 ( 2) SS BOND : angle 5.24504 ( 4) covalent geometry : bond 0.00433 ( 6886) covalent geometry : angle 0.56267 ( 9368) *********************** 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 102 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 77 time to evaluate : 0.776 Fit side-chains REVERT: B 338 LEU cc_start: 0.8111 (OUTLIER) cc_final: 0.7729 (mt) REVERT: B 434 GLU cc_start: 0.7839 (mm-30) cc_final: 0.7260 (mp0) REVERT: B 616 GLN cc_start: 0.7506 (mm-40) cc_final: 0.7146 (mm-40) REVERT: B 849 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7527 (tp30) outliers start: 25 outliers final: 12 residues processed: 96 average time/residue: 1.3864 time to fit residues: 139.8378 Evaluate side-chains 90 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 76 time to evaluate : 0.750 ------------------------------------------------------------------------------- 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 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: 0.9980 chunk 70 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 36 optimal weight: 0.2980 chunk 14 optimal weight: 0.9990 chunk 17 optimal weight: 0.4980 chunk 22 optimal weight: 0.1980 chunk 16 optimal weight: 0.5980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 = 0.3473 r_free = 0.3473 target = 0.135965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.111292 restraints weight = 8084.117| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.06 r_work: 0.3115 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.1003 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= 0.145 Angle : 0.542 9.657 9372 Z= 0.271 Chirality : 0.038 0.120 1058 Planarity : 0.005 0.056 1243 Dihedral : 4.596 61.797 978 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.22 % Allowed : 14.18 % Favored : 82.60 % 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: 0.85 (0.28), residues: 866 helix: 1.29 (0.22), residues: 542 sheet: -1.42 (0.60), residues: 71 loop : -0.24 (0.37), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 974 HIS 0.002 0.001 HIS B 636 PHE 0.011 0.001 PHE B 634 TYR 0.012 0.001 TYR B 123 ARG 0.006 0.000 ARG B 153 Details of bonding type rmsd hydrogen bonds : bond 0.04050 ( 408) hydrogen bonds : angle 4.12076 ( 1215) SS BOND : bond 0.00158 ( 2) SS BOND : angle 4.85145 ( 4) covalent geometry : bond 0.00352 ( 6886) covalent geometry : angle 0.53279 ( 9368) *********************** 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 98 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 76 time to evaluate : 0.707 Fit side-chains REVERT: B 211 ARG cc_start: 0.7359 (mtp180) cc_final: 0.6954 (mtm180) REVERT: B 338 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7714 (mt) REVERT: B 381 ARG cc_start: 0.7918 (mtp-110) cc_final: 0.7663 (mtp-110) REVERT: B 396 LEU cc_start: 0.7758 (OUTLIER) cc_final: 0.7378 (mp) REVERT: B 434 GLU cc_start: 0.7843 (mm-30) cc_final: 0.7232 (mp0) REVERT: B 616 GLN cc_start: 0.7432 (mm-40) cc_final: 0.7085 (mm-40) REVERT: B 849 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7509 (tp30) outliers start: 22 outliers final: 12 residues processed: 92 average time/residue: 1.3796 time to fit residues: 133.1598 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 : 0.759 ------------------------------------------------------------------------------- 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 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 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 51 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 86 optimal weight: 0.9980 chunk 66 optimal weight: 0.0980 chunk 70 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 17 optimal weight: 0.0770 chunk 20 optimal weight: 0.0670 chunk 5 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 overall best weight: 0.3276 ------------------------------------------------------------------------------- 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 = 0.3501 r_free = 0.3501 target = 0.138275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.113552 restraints weight = 8049.851| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.07 r_work: 0.3146 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.1123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 6888 Z= 0.122 Angle : 0.527 10.423 9372 Z= 0.262 Chirality : 0.037 0.118 1058 Planarity : 0.005 0.054 1243 Dihedral : 4.473 59.813 978 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.92 % Allowed : 14.47 % Favored : 82.60 % 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: 1.03 (0.28), residues: 866 helix: 1.44 (0.22), residues: 543 sheet: -1.45 (0.59), residues: 73 loop : -0.15 (0.37), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 974 HIS 0.002 0.000 HIS B 593 PHE 0.010 0.001 PHE B 634 TYR 0.012 0.001 TYR B 123 ARG 0.008 0.000 ARG B 429 Details of bonding type rmsd hydrogen bonds : bond 0.03727 ( 408) hydrogen bonds : angle 3.97264 ( 1215) SS BOND : bond 0.00141 ( 2) SS BOND : angle 5.22270 ( 4) covalent geometry : bond 0.00290 ( 6886) covalent geometry : angle 0.51641 ( 9368) *********************** 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: 20 poor density : 75 time to evaluate : 0.745 Fit side-chains REVERT: B 211 ARG cc_start: 0.7352 (mtp180) cc_final: 0.6956 (mtm180) REVERT: B 338 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7770 (mt) REVERT: B 434 GLU cc_start: 0.7785 (mm-30) cc_final: 0.7223 (mp0) REVERT: B 849 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7463 (tp30) outliers start: 20 outliers final: 12 residues processed: 89 average time/residue: 1.3430 time to fit residues: 125.9798 Evaluate side-chains 88 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 74 time to evaluate : 0.678 ------------------------------------------------------------------------------- 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 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 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: 0.5980 chunk 6 optimal weight: 0.9980 chunk 29 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 58 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3474 r_free = 0.3474 target = 0.135788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.111002 restraints weight = 8113.032| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 2.06 r_work: 0.3132 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.1146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 6888 Z= 0.164 Angle : 0.556 9.085 9372 Z= 0.276 Chirality : 0.039 0.126 1058 Planarity : 0.005 0.054 1243 Dihedral : 4.554 61.452 978 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.22 % Allowed : 14.33 % 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: 0.95 (0.28), residues: 866 helix: 1.36 (0.22), residues: 543 sheet: -1.34 (0.57), residues: 75 loop : -0.18 (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 0.011 0.001 TYR B 123 ARG 0.008 0.000 ARG B 153 Details of bonding type rmsd hydrogen bonds : bond 0.04114 ( 408) hydrogen bonds : angle 4.03000 ( 1215) SS BOND : bond 0.00256 ( 2) SS BOND : angle 4.57281 ( 4) covalent geometry : bond 0.00401 ( 6886) covalent geometry : angle 0.54758 ( 9368) *********************** 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 98 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 76 time to evaluate : 0.686 Fit side-chains REVERT: B 211 ARG cc_start: 0.7355 (mtp180) cc_final: 0.6972 (mtm180) REVERT: B 338 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7754 (mt) REVERT: B 434 GLU cc_start: 0.7845 (mm-30) cc_final: 0.7288 (mp0) REVERT: B 849 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.7502 (tp30) outliers start: 22 outliers final: 12 residues processed: 91 average time/residue: 1.3666 time to fit residues: 130.5258 Evaluate side-chains 88 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 74 time to evaluate : 0.710 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 2 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 56 optimal weight: 0.9990 chunk 46 optimal weight: 0.6980 chunk 37 optimal weight: 0.4980 chunk 48 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 = 0.3465 r_free = 0.3465 target = 0.134992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.110366 restraints weight = 8132.708| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.05 r_work: 0.3250 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.1169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 6888 Z= 0.186 Angle : 0.594 14.025 9372 Z= 0.295 Chirality : 0.040 0.128 1058 Planarity : 0.005 0.054 1243 Dihedral : 4.679 62.730 978 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.19 % Allowed : 15.64 % 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: 0.82 (0.28), residues: 866 helix: 1.25 (0.22), residues: 543 sheet: -1.37 (0.57), residues: 75 loop : -0.21 (0.38), residues: 248 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 Details of bonding type rmsd hydrogen bonds : bond 0.04319 ( 408) hydrogen bonds : angle 4.07831 ( 1215) SS BOND : bond 0.00492 ( 2) SS BOND : angle 7.04587 ( 4) covalent geometry : bond 0.00458 ( 6886) covalent geometry : angle 0.57581 ( 9368) *********************** 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 90 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 75 time to evaluate : 0.716 Fit side-chains REVERT: B 211 ARG cc_start: 0.7446 (mtp180) cc_final: 0.7077 (mtm180) REVERT: B 338 LEU cc_start: 0.8116 (OUTLIER) cc_final: 0.7902 (mm) REVERT: B 434 GLU cc_start: 0.7826 (mm-30) cc_final: 0.7316 (mp0) REVERT: B 849 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7565 (tp30) outliers start: 15 outliers final: 12 residues processed: 85 average time/residue: 1.2967 time to fit residues: 116.1814 Evaluate side-chains 89 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 0.705 ------------------------------------------------------------------------------- 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 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: 0.9990 chunk 13 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 6 optimal weight: 0.6980 chunk 66 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3466 r_free = 0.3466 target = 0.134778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.110350 restraints weight = 8090.700| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 2.02 r_work: 0.3186 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.1210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.100 6888 Z= 0.198 Angle : 0.606 13.216 9372 Z= 0.302 Chirality : 0.041 0.134 1058 Planarity : 0.005 0.054 1243 Dihedral : 4.747 63.690 978 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.34 % Allowed : 16.23 % 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: 542 sheet: -1.41 (0.56), residues: 75 loop : -0.25 (0.37), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 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 Details of bonding type rmsd hydrogen bonds : bond 0.04450 ( 408) hydrogen bonds : angle 4.11660 ( 1215) SS BOND : bond 0.00137 ( 2) SS BOND : angle 6.63845 ( 4) covalent geometry : bond 0.00489 ( 6886) covalent geometry : angle 0.59016 ( 9368) *********************** 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 89 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 73 time to evaluate : 0.717 Fit side-chains REVERT: B 211 ARG cc_start: 0.7353 (mtp180) cc_final: 0.6982 (mtm180) REVERT: B 338 LEU cc_start: 0.8131 (OUTLIER) cc_final: 0.7879 (mm) REVERT: B 381 ARG cc_start: 0.7942 (mtp-110) cc_final: 0.7578 (mtp-110) REVERT: B 434 GLU cc_start: 0.7843 (mm-30) cc_final: 0.7297 (mp0) REVERT: B 849 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7554 (tp30) outliers start: 16 outliers final: 12 residues processed: 84 average time/residue: 1.2590 time to fit residues: 111.5671 Evaluate side-chains 85 residues out of total 684 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 71 time to evaluate : 0.768 ------------------------------------------------------------------------------- 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 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: 0.6980 chunk 32 optimal weight: 0.9980 chunk 59 optimal weight: 0.8980 chunk 77 optimal weight: 0.6980 chunk 14 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 chunk 74 optimal weight: 0.9980 chunk 81 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 57 optimal weight: 0.2980 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 = 0.3469 r_free = 0.3469 target = 0.135339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.110631 restraints weight = 8186.010| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.07 r_work: 0.3141 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.1238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 6888 Z= 0.160 Angle : 0.570 11.763 9372 Z= 0.285 Chirality : 0.039 0.125 1058 Planarity : 0.005 0.053 1243 Dihedral : 4.672 62.920 978 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.19 % Allowed : 16.67 % 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: 0.83 (0.28), residues: 866 helix: 1.27 (0.22), residues: 542 sheet: -1.38 (0.57), residues: 75 loop : -0.23 (0.37), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 974 HIS 0.002 0.001 HIS B 636 PHE 0.011 0.002 PHE B 634 TYR 0.013 0.001 TYR B 123 ARG 0.007 0.000 ARG B 153 Details of bonding type rmsd hydrogen bonds : bond 0.04111 ( 408) hydrogen bonds : angle 4.03123 ( 1215) SS BOND : bond 0.00301 ( 2) SS BOND : angle 5.89871 ( 4) covalent geometry : bond 0.00392 ( 6886) covalent geometry : angle 0.55686 ( 9368) ********************** 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: 15 poor density : 72 time to evaluate : 0.848 Fit side-chains REVERT: B 211 ARG cc_start: 0.7316 (mtp180) cc_final: 0.6947 (mtm180) REVERT: B 338 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7848 (mm) REVERT: B 381 ARG cc_start: 0.7889 (mtp-110) cc_final: 0.7507 (mtp-110) REVERT: B 434 GLU cc_start: 0.7821 (mm-30) cc_final: 0.7287 (mp0) REVERT: B 849 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7545 (tp30) outliers start: 15 outliers final: 11 residues processed: 84 average time/residue: 1.7516 time to fit residues: 155.7343 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 : 0.648 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 11 optimal weight: 0.5980 chunk 29 optimal weight: 0.5980 chunk 14 optimal weight: 0.7980 chunk 72 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 59 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3454 r_free = 0.3454 target = 0.134192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.109411 restraints weight = 8128.951| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.07 r_work: 0.3194 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.1256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 6888 Z= 0.191 Angle : 0.600 12.025 9372 Z= 0.299 Chirality : 0.040 0.130 1058 Planarity : 0.005 0.054 1243 Dihedral : 4.740 63.525 978 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.05 % Allowed : 17.25 % Favored : 80.70 % 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: 0.71 (0.28), residues: 866 helix: 1.17 (0.22), residues: 542 sheet: -1.39 (0.56), residues: 75 loop : -0.27 (0.37), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 974 HIS 0.003 0.001 HIS B 636 PHE 0.011 0.002 PHE B 634 TYR 0.013 0.001 TYR B 123 ARG 0.007 0.000 ARG B 153 Details of bonding type rmsd hydrogen bonds : bond 0.04392 ( 408) hydrogen bonds : angle 4.10061 ( 1215) SS BOND : bond 0.00234 ( 2) SS BOND : angle 6.03319 ( 4) covalent geometry : bond 0.00469 ( 6886) covalent geometry : angle 0.58732 ( 9368) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5757.55 seconds wall clock time: 100 minutes 10.64 seconds (6010.64 seconds total)