Starting phenix.real_space_refine on Sun Dec 29 23:05:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wca_21604/12_2024/6wca_21604.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wca_21604/12_2024/6wca_21604.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6wca_21604/12_2024/6wca_21604.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wca_21604/12_2024/6wca_21604.map" model { file = "/net/cci-nas-00/data/ceres_data/6wca_21604/12_2024/6wca_21604.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wca_21604/12_2024/6wca_21604.cif" } resolution = 3.03 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 ------------------------------------------------------------------------------- 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= 1.000 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: 6 Type Number sf(0) Gaussians K 5 8.98 5 S 38 5.16 5 C 3758 2.51 5 N 940 2.21 5 O 994 1.98 5 H 5910 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 11645 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 5807 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 16, 'TRANS': 350} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 5807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 5807 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 16, 'TRANS': 350} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' K': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' K': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "B" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Time building chain proxies: 5.83, per 1000 atoms: 0.50 Number of scatterers: 11645 At special positions: 0 Unit cell: (107.712, 68.544, 77.248, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 5 19.00 S 38 16.00 O 994 8.00 N 940 7.00 C 3758 6.00 H 5910 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 3.34 Conformation dependent library (CDL) restraints added in 981.4 milliseconds 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1404 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 0 sheets defined 88.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'A' and resid 33 through 50 Processing helix chain 'A' and resid 52 through 57 Processing helix chain 'A' and resid 61 through 65 Processing helix chain 'A' and resid 67 through 103 removed outlier: 3.526A pdb=" N GLN A 71 " --> pdb=" O ASP A 67 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA A 75 " --> pdb=" O GLN A 71 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL A 101 " --> pdb=" O ARG A 97 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY A 103 " --> pdb=" O PHE A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 122 removed outlier: 3.643A pdb=" N PHE A 122 " --> pdb=" O MET A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 133 removed outlier: 4.242A pdb=" N THR A 132 " --> pdb=" O SER A 128 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE A 133 " --> pdb=" O LEU A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 164 removed outlier: 3.545A pdb=" N PHE A 164 " --> pdb=" O TYR A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 168 Processing helix chain 'A' and resid 257 through 285 removed outlier: 3.852A pdb=" N VAL A 285 " --> pdb=" O CYS A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 295 Processing helix chain 'A' and resid 298 through 305 removed outlier: 3.813A pdb=" N ALA A 302 " --> pdb=" O SER A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 333 removed outlier: 3.774A pdb=" N HIS A 333 " --> pdb=" O SER A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 353 Processing helix chain 'A' and resid 354 through 359 Processing helix chain 'A' and resid 371 through 398 removed outlier: 4.046A pdb=" N PHE A 389 " --> pdb=" O LEU A 385 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N GLN A 390 " --> pdb=" O ALA A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 405 Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 415 through 440 removed outlier: 5.047A pdb=" N TYR A 426 " --> pdb=" O LYS A 422 " (cutoff:3.500A) Proline residue: A 427 - end of helix Processing helix chain 'A' and resid 443 through 461 Proline residue: A 456 - end of helix Processing helix chain 'A' and resid 461 through 476 Processing helix chain 'B' and resid 33 through 50 Processing helix chain 'B' and resid 52 through 57 Processing helix chain 'B' and resid 61 through 65 Processing helix chain 'B' and resid 67 through 103 removed outlier: 3.526A pdb=" N GLN B 71 " --> pdb=" O ASP B 67 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA B 75 " --> pdb=" O GLN B 71 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL B 101 " --> pdb=" O ARG B 97 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY B 103 " --> pdb=" O PHE B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 122 removed outlier: 3.642A pdb=" N PHE B 122 " --> pdb=" O MET B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 133 removed outlier: 4.242A pdb=" N THR B 132 " --> pdb=" O SER B 128 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE B 133 " --> pdb=" O LEU B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 164 removed outlier: 3.545A pdb=" N PHE B 164 " --> pdb=" O TYR B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 168 Processing helix chain 'B' and resid 257 through 285 removed outlier: 3.852A pdb=" N VAL B 285 " --> pdb=" O CYS B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 295 Processing helix chain 'B' and resid 298 through 305 removed outlier: 3.813A pdb=" N ALA B 302 " --> pdb=" O SER B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 333 removed outlier: 3.772A pdb=" N HIS B 333 " --> pdb=" O SER B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 353 Processing helix chain 'B' and resid 354 through 359 Processing helix chain 'B' and resid 371 through 398 removed outlier: 4.045A pdb=" N PHE B 389 " --> pdb=" O LEU B 385 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N GLN B 390 " --> pdb=" O ALA B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 405 Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 415 through 440 removed outlier: 5.046A pdb=" N TYR B 426 " --> pdb=" O LYS B 422 " (cutoff:3.500A) Proline residue: B 427 - end of helix Processing helix chain 'B' and resid 443 through 461 Proline residue: B 456 - end of helix Processing helix chain 'B' and resid 461 through 476 452 hydrogen bonds defined for protein. 1326 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: 4.12 Time building geometry restraints manager: 3.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 5892 1.03 - 1.22: 18 1.22 - 1.42: 2386 1.42 - 1.62: 3394 1.62 - 1.81: 58 Bond restraints: 11748 Sorted by residual: bond pdb=" CA VAL B 455 " pdb=" CB VAL B 455 " ideal model delta sigma weight residual 1.539 1.530 0.009 5.40e-03 3.43e+04 2.71e+00 bond pdb=" CA VAL A 455 " pdb=" CB VAL A 455 " ideal model delta sigma weight residual 1.539 1.530 0.009 5.40e-03 3.43e+04 2.54e+00 bond pdb=" CB ASP B 371 " pdb=" HB3 ASP B 371 " ideal model delta sigma weight residual 0.970 1.001 -0.031 2.00e-02 2.50e+03 2.41e+00 bond pdb=" CB ASP B 371 " pdb=" HB2 ASP B 371 " ideal model delta sigma weight residual 0.970 0.939 0.031 2.00e-02 2.50e+03 2.35e+00 bond pdb=" CB ASP B 279 " pdb=" CG ASP B 279 " ideal model delta sigma weight residual 1.516 1.548 -0.032 2.50e-02 1.60e+03 1.62e+00 ... (remaining 11743 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.28: 20304 1.28 - 2.56: 891 2.56 - 3.85: 78 3.85 - 5.13: 19 5.13 - 6.41: 6 Bond angle restraints: 21298 Sorted by residual: angle pdb=" CA ARG A 294 " pdb=" CB ARG A 294 " pdb=" CG ARG A 294 " ideal model delta sigma weight residual 114.10 118.83 -4.73 2.00e+00 2.50e-01 5.59e+00 angle pdb=" CA ARG B 294 " pdb=" CB ARG B 294 " pdb=" CG ARG B 294 " ideal model delta sigma weight residual 114.10 118.80 -4.70 2.00e+00 2.50e-01 5.53e+00 angle pdb=" N SER B 441 " pdb=" CA SER B 441 " pdb=" CB SER B 441 " ideal model delta sigma weight residual 114.17 111.58 2.59 1.14e+00 7.69e-01 5.17e+00 angle pdb=" N SER A 441 " pdb=" CA SER A 441 " pdb=" CB SER A 441 " ideal model delta sigma weight residual 114.17 111.60 2.57 1.14e+00 7.69e-01 5.08e+00 angle pdb=" CG ASP A 371 " pdb=" CB ASP A 371 " pdb=" HB2 ASP A 371 " ideal model delta sigma weight residual 108.00 114.41 -6.41 3.00e+00 1.11e-01 4.57e+00 ... (remaining 21293 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.52: 4787 16.52 - 33.04: 548 33.04 - 49.56: 127 49.56 - 66.08: 58 66.08 - 82.60: 10 Dihedral angle restraints: 5530 sinusoidal: 2938 harmonic: 2592 Sorted by residual: dihedral pdb=" CA ASP A 283 " pdb=" C ASP A 283 " pdb=" N ASN A 284 " pdb=" CA ASN A 284 " ideal model delta harmonic sigma weight residual 180.00 -154.97 -25.03 0 5.00e+00 4.00e-02 2.51e+01 dihedral pdb=" CA ASP B 283 " pdb=" C ASP B 283 " pdb=" N ASN B 284 " pdb=" CA ASN B 284 " ideal model delta harmonic sigma weight residual -180.00 -154.97 -25.03 0 5.00e+00 4.00e-02 2.51e+01 dihedral pdb=" CA ASP A 287 " pdb=" C ASP A 287 " pdb=" N PRO A 288 " pdb=" CA PRO A 288 " ideal model delta harmonic sigma weight residual -180.00 -158.38 -21.62 0 5.00e+00 4.00e-02 1.87e+01 ... (remaining 5527 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 636 0.026 - 0.052: 179 0.052 - 0.078: 108 0.078 - 0.104: 40 0.104 - 0.130: 15 Chirality restraints: 978 Sorted by residual: chirality pdb=" CA PRO B 288 " pdb=" N PRO B 288 " pdb=" C PRO B 288 " pdb=" CB PRO B 288 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.22e-01 chirality pdb=" CA PRO A 288 " pdb=" N PRO A 288 " pdb=" C PRO A 288 " pdb=" CB PRO A 288 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.06e-01 chirality pdb=" CA PRO B 62 " pdb=" N PRO B 62 " pdb=" C PRO B 62 " pdb=" CB PRO B 62 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.01e-01 ... (remaining 975 not shown) Planarity restraints: 1674 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 455 " -0.031 5.00e-02 4.00e+02 4.69e-02 3.52e+00 pdb=" N PRO A 456 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 456 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 456 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 455 " 0.031 5.00e-02 4.00e+02 4.68e-02 3.50e+00 pdb=" N PRO B 456 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO B 456 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 456 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 53 " 0.020 5.00e-02 4.00e+02 3.06e-02 1.50e+00 pdb=" N PRO A 54 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 54 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 54 " 0.017 5.00e-02 4.00e+02 ... (remaining 1671 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.30: 2189 2.30 - 3.01: 32664 3.01 - 3.72: 44616 3.72 - 4.43: 65194 4.43 - 5.14: 102460 Nonbonded interactions: 247123 Sorted by model distance: nonbonded pdb=" OD2 ASP B 279 " pdb=" H GLN B 361 " model vdw 1.592 2.450 nonbonded pdb=" OD2 ASP A 279 " pdb=" H GLN A 361 " model vdw 1.593 2.450 nonbonded pdb=" HG SER A 61 " pdb=" OE1 GLU A 63 " model vdw 1.596 2.450 nonbonded pdb=" HG SER B 61 " pdb=" OE1 GLU B 63 " model vdw 1.641 2.450 nonbonded pdb=" O PHE B 85 " pdb=" HG1 THR B 89 " model vdw 1.643 2.450 ... (remaining 247118 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 30 through 476 or resid 701 through 702)) selection = chain 'B' } 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: 0.090 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: 0.210 Extract box with map and model: 0.400 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 27.760 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.040 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 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 0.034 5838 Z= 0.189 Angle : 0.607 5.130 7956 Z= 0.342 Chirality : 0.037 0.130 978 Planarity : 0.004 0.047 976 Dihedral : 15.592 82.599 2040 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.94 % Allowed : 16.77 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.15 (0.30), residues: 726 helix: 0.49 (0.21), residues: 584 sheet: None (None), residues: 0 loop : -2.30 (0.50), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 394 HIS 0.003 0.001 HIS B 328 PHE 0.010 0.001 PHE A 99 TYR 0.016 0.002 TYR B 125 ARG 0.003 0.000 ARG A 294 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 125 is missing expected H atoms. Skipping. Residue TYR 125 is missing expected H atoms. Skipping. Evaluate side-chains 113 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 101 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 PHE cc_start: 0.8621 (m-80) cc_final: 0.8305 (m-80) REVERT: A 282 GLU cc_start: 0.5094 (mm-30) cc_final: 0.3769 (mm-30) REVERT: A 335 ARG cc_start: 0.7987 (mtp180) cc_final: 0.7736 (mtp-110) REVERT: B 142 LEU cc_start: 0.8401 (mt) cc_final: 0.8098 (tp) REVERT: B 162 PHE cc_start: 0.8685 (m-80) cc_final: 0.8353 (m-80) REVERT: B 282 GLU cc_start: 0.5079 (mm-30) cc_final: 0.3804 (mm-30) REVERT: B 335 ARG cc_start: 0.8035 (mtp180) cc_final: 0.7824 (mtp-110) outliers start: 12 outliers final: 8 residues processed: 113 average time/residue: 0.3857 time to fit residues: 57.3036 Evaluate side-chains 99 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 91 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 SER Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 303 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 60 optimal weight: 0.8980 chunk 54 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 chunk 36 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 56 optimal weight: 7.9990 chunk 21 optimal weight: 4.9990 chunk 34 optimal weight: 7.9990 chunk 42 optimal weight: 0.9980 chunk 65 optimal weight: 6.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 GLN A 368 GLN B 173 GLN B 368 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5838 Z= 0.215 Angle : 0.578 4.653 7956 Z= 0.302 Chirality : 0.037 0.143 978 Planarity : 0.004 0.047 976 Dihedral : 6.533 59.006 792 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.42 % Allowed : 15.32 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.61 (0.31), residues: 726 helix: 1.71 (0.21), residues: 600 sheet: None (None), residues: 0 loop : -2.07 (0.52), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 394 HIS 0.004 0.001 HIS A 328 PHE 0.014 0.001 PHE A 99 TYR 0.013 0.002 TYR B 313 ARG 0.003 0.000 ARG A 294 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 125 is missing expected H atoms. Skipping. Residue TYR 125 is missing expected H atoms. Skipping. Evaluate side-chains 104 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 0.830 Fit side-chains REVERT: A 142 LEU cc_start: 0.8286 (mt) cc_final: 0.8036 (tp) REVERT: A 162 PHE cc_start: 0.8730 (m-80) cc_final: 0.8388 (m-80) REVERT: A 282 GLU cc_start: 0.5072 (mm-30) cc_final: 0.3861 (mm-30) REVERT: A 335 ARG cc_start: 0.8051 (mtp180) cc_final: 0.7831 (mtp-110) REVERT: B 142 LEU cc_start: 0.8459 (mt) cc_final: 0.8208 (tp) REVERT: B 162 PHE cc_start: 0.8774 (m-80) cc_final: 0.8421 (m-80) REVERT: B 282 GLU cc_start: 0.5060 (mm-30) cc_final: 0.3866 (mm-30) REVERT: B 335 ARG cc_start: 0.8081 (mtp180) cc_final: 0.7865 (mtp-110) outliers start: 15 outliers final: 11 residues processed: 104 average time/residue: 0.3801 time to fit residues: 51.9806 Evaluate side-chains 97 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 86 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 468 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 36 optimal weight: 5.9990 chunk 20 optimal weight: 7.9990 chunk 54 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 58 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 449 HIS B 449 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5838 Z= 0.225 Angle : 0.552 4.509 7956 Z= 0.287 Chirality : 0.037 0.130 978 Planarity : 0.005 0.047 976 Dihedral : 5.540 59.912 789 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.74 % Allowed : 15.81 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.40 (0.32), residues: 726 helix: 2.25 (0.21), residues: 600 sheet: None (None), residues: 0 loop : -1.80 (0.50), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 394 HIS 0.005 0.001 HIS B 328 PHE 0.018 0.002 PHE A 99 TYR 0.012 0.002 TYR A 125 ARG 0.004 0.000 ARG A 309 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 125 is missing expected H atoms. Skipping. Residue TYR 125 is missing expected H atoms. Skipping. Evaluate side-chains 107 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 90 time to evaluate : 0.879 Fit side-chains REVERT: A 162 PHE cc_start: 0.8792 (m-80) cc_final: 0.8400 (m-80) REVERT: A 282 GLU cc_start: 0.5072 (mm-30) cc_final: 0.3897 (mm-30) REVERT: A 359 TYR cc_start: 0.7936 (m-80) cc_final: 0.7710 (m-10) REVERT: B 162 PHE cc_start: 0.8847 (m-80) cc_final: 0.8445 (m-80) REVERT: B 282 GLU cc_start: 0.4931 (mm-30) cc_final: 0.3806 (mm-30) REVERT: B 359 TYR cc_start: 0.7957 (m-80) cc_final: 0.7680 (m-10) outliers start: 17 outliers final: 11 residues processed: 107 average time/residue: 0.3934 time to fit residues: 55.7653 Evaluate side-chains 99 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 436 SER Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 468 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 64 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 33 optimal weight: 8.9990 chunk 7 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 69 optimal weight: 8.9990 chunk 34 optimal weight: 0.9990 chunk 62 optimal weight: 10.0000 chunk 18 optimal weight: 8.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 284 ASN B 284 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 5838 Z= 0.304 Angle : 0.576 4.433 7956 Z= 0.305 Chirality : 0.038 0.132 978 Planarity : 0.005 0.048 976 Dihedral : 5.346 57.831 788 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.94 % Allowed : 16.29 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.35 (0.31), residues: 726 helix: 2.20 (0.21), residues: 600 sheet: None (None), residues: 0 loop : -1.72 (0.51), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 394 HIS 0.006 0.001 HIS B 328 PHE 0.016 0.002 PHE A 99 TYR 0.012 0.002 TYR A 313 ARG 0.002 0.000 ARG B 375 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 125 is missing expected H atoms. Skipping. Residue TYR 125 is missing expected H atoms. Skipping. Evaluate side-chains 101 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 89 time to evaluate : 0.961 Fit side-chains REVERT: A 162 PHE cc_start: 0.8868 (m-80) cc_final: 0.8448 (m-80) REVERT: A 282 GLU cc_start: 0.5112 (mm-30) cc_final: 0.4050 (mm-30) REVERT: A 359 TYR cc_start: 0.8020 (m-80) cc_final: 0.7812 (m-10) REVERT: B 282 GLU cc_start: 0.4963 (mm-30) cc_final: 0.3945 (mm-30) REVERT: B 359 TYR cc_start: 0.8054 (m-80) cc_final: 0.7849 (m-10) outliers start: 12 outliers final: 12 residues processed: 101 average time/residue: 0.4164 time to fit residues: 54.4034 Evaluate side-chains 97 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 436 SER Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 468 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 57 optimal weight: 4.9990 chunk 39 optimal weight: 7.9990 chunk 1 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 59 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 62 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 284 ASN B 284 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5838 Z= 0.202 Angle : 0.527 4.414 7956 Z= 0.272 Chirality : 0.036 0.120 978 Planarity : 0.005 0.047 976 Dihedral : 5.161 55.790 788 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.58 % Allowed : 15.81 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.75 (0.32), residues: 726 helix: 2.46 (0.21), residues: 600 sheet: None (None), residues: 0 loop : -1.53 (0.52), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 394 HIS 0.004 0.001 HIS A 449 PHE 0.014 0.001 PHE B 99 TYR 0.013 0.002 TYR A 125 ARG 0.002 0.000 ARG B 294 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 125 is missing expected H atoms. Skipping. Residue TYR 125 is missing expected H atoms. Skipping. Evaluate side-chains 105 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 89 time to evaluate : 0.946 Fit side-chains REVERT: A 162 PHE cc_start: 0.8857 (m-80) cc_final: 0.8438 (m-80) REVERT: A 169 SER cc_start: 0.8426 (OUTLIER) cc_final: 0.7729 (p) REVERT: A 282 GLU cc_start: 0.4950 (mm-30) cc_final: 0.3955 (mm-30) REVERT: A 309 ARG cc_start: 0.5541 (mtt180) cc_final: 0.5334 (mtt180) REVERT: B 162 PHE cc_start: 0.8875 (m-80) cc_final: 0.8479 (m-80) REVERT: B 282 GLU cc_start: 0.4829 (mm-30) cc_final: 0.3878 (mm-30) outliers start: 16 outliers final: 11 residues processed: 105 average time/residue: 0.3826 time to fit residues: 53.2492 Evaluate side-chains 96 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 436 SER Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 468 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 23 optimal weight: 4.9990 chunk 62 optimal weight: 8.9990 chunk 13 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 69 optimal weight: 7.9990 chunk 57 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 chunk 36 optimal weight: 5.9990 chunk 67 optimal weight: 0.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.2995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5838 Z= 0.204 Angle : 0.519 4.236 7956 Z= 0.269 Chirality : 0.035 0.119 978 Planarity : 0.004 0.046 976 Dihedral : 5.050 54.474 788 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.10 % Allowed : 17.10 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.94 (0.32), residues: 726 helix: 2.58 (0.21), residues: 600 sheet: None (None), residues: 0 loop : -1.40 (0.53), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 394 HIS 0.004 0.001 HIS A 328 PHE 0.014 0.001 PHE B 99 TYR 0.014 0.002 TYR B 125 ARG 0.002 0.000 ARG A 294 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 125 is missing expected H atoms. Skipping. Residue TYR 125 is missing expected H atoms. Skipping. Evaluate side-chains 103 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 90 time to evaluate : 0.866 Fit side-chains REVERT: A 162 PHE cc_start: 0.8872 (m-80) cc_final: 0.8459 (m-80) REVERT: A 169 SER cc_start: 0.8453 (OUTLIER) cc_final: 0.7787 (p) REVERT: A 282 GLU cc_start: 0.4781 (mm-30) cc_final: 0.3830 (mm-30) REVERT: B 43 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8645 (tt) REVERT: B 282 GLU cc_start: 0.4688 (mm-30) cc_final: 0.3783 (mm-30) outliers start: 13 outliers final: 11 residues processed: 103 average time/residue: 0.4060 time to fit residues: 54.7689 Evaluate side-chains 100 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 436 SER Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 468 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 7 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 chunk 50 optimal weight: 6.9990 chunk 58 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 69 optimal weight: 6.9990 chunk 43 optimal weight: 4.9990 chunk 42 optimal weight: 0.6980 chunk 32 optimal weight: 7.9990 chunk 27 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5838 Z= 0.205 Angle : 0.526 5.358 7956 Z= 0.269 Chirality : 0.036 0.120 978 Planarity : 0.004 0.046 976 Dihedral : 4.972 53.771 788 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.42 % Allowed : 16.77 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.00 (0.32), residues: 726 helix: 2.63 (0.21), residues: 600 sheet: None (None), residues: 0 loop : -1.41 (0.53), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 394 HIS 0.004 0.001 HIS B 328 PHE 0.014 0.001 PHE B 99 TYR 0.014 0.002 TYR B 125 ARG 0.001 0.000 ARG A 294 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 125 is missing expected H atoms. Skipping. Residue TYR 125 is missing expected H atoms. Skipping. Evaluate side-chains 109 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 94 time to evaluate : 0.836 Fit side-chains REVERT: A 43 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8665 (tt) REVERT: A 74 LEU cc_start: 0.7067 (OUTLIER) cc_final: 0.6781 (tp) REVERT: A 162 PHE cc_start: 0.8881 (m-80) cc_final: 0.8461 (m-80) REVERT: A 169 SER cc_start: 0.8455 (OUTLIER) cc_final: 0.7790 (p) REVERT: A 282 GLU cc_start: 0.4516 (mm-30) cc_final: 0.3602 (mm-30) REVERT: B 43 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8647 (tt) REVERT: B 74 LEU cc_start: 0.7048 (OUTLIER) cc_final: 0.6745 (tp) REVERT: B 282 GLU cc_start: 0.4660 (mm-30) cc_final: 0.3775 (mm-30) outliers start: 15 outliers final: 10 residues processed: 109 average time/residue: 0.4043 time to fit residues: 57.8126 Evaluate side-chains 107 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 436 SER Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 468 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 20 optimal weight: 6.9990 chunk 13 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 34 optimal weight: 0.1980 chunk 6 optimal weight: 3.9990 chunk 54 optimal weight: 8.9990 chunk 63 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.3225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5838 Z= 0.174 Angle : 0.508 4.803 7956 Z= 0.258 Chirality : 0.035 0.118 978 Planarity : 0.004 0.045 976 Dihedral : 4.864 52.577 788 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.42 % Allowed : 17.26 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.16 (0.32), residues: 726 helix: 2.74 (0.21), residues: 602 sheet: None (None), residues: 0 loop : -1.40 (0.54), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 394 HIS 0.003 0.001 HIS B 328 PHE 0.013 0.001 PHE B 99 TYR 0.017 0.002 TYR B 125 ARG 0.001 0.000 ARG A 474 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 125 is missing expected H atoms. Skipping. Residue TYR 125 is missing expected H atoms. Skipping. Evaluate side-chains 111 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 96 time to evaluate : 0.792 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 43 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8611 (tt) REVERT: A 74 LEU cc_start: 0.6988 (OUTLIER) cc_final: 0.6676 (tp) REVERT: A 162 PHE cc_start: 0.8896 (m-80) cc_final: 0.8499 (m-80) REVERT: A 169 SER cc_start: 0.8435 (OUTLIER) cc_final: 0.7770 (p) REVERT: A 282 GLU cc_start: 0.4502 (mm-30) cc_final: 0.3628 (mm-30) REVERT: B 43 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8625 (tt) REVERT: B 74 LEU cc_start: 0.7028 (OUTLIER) cc_final: 0.6731 (tp) REVERT: B 162 PHE cc_start: 0.8896 (m-80) cc_final: 0.8500 (m-80) REVERT: B 282 GLU cc_start: 0.4571 (mm-30) cc_final: 0.3696 (mm-30) outliers start: 15 outliers final: 10 residues processed: 111 average time/residue: 0.3912 time to fit residues: 57.4840 Evaluate side-chains 111 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 96 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 436 SER Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 468 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 66 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 50 optimal weight: 8.9990 chunk 19 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 61 optimal weight: 10.0000 chunk 64 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 68 optimal weight: 8.9990 chunk 41 optimal weight: 0.8980 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.3326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5838 Z= 0.227 Angle : 0.532 5.165 7956 Z= 0.273 Chirality : 0.036 0.121 978 Planarity : 0.004 0.046 976 Dihedral : 4.851 51.836 788 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.58 % Allowed : 16.77 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.02 (0.32), residues: 726 helix: 2.64 (0.21), residues: 602 sheet: None (None), residues: 0 loop : -1.43 (0.55), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 324 HIS 0.005 0.001 HIS A 328 PHE 0.015 0.001 PHE A 99 TYR 0.017 0.002 TYR B 125 ARG 0.001 0.000 ARG A 294 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 125 is missing expected H atoms. Skipping. Residue TYR 125 is missing expected H atoms. Skipping. Evaluate side-chains 113 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 0.769 Fit side-chains revert: symmetry clash REVERT: A 43 LEU cc_start: 0.9131 (OUTLIER) cc_final: 0.8665 (tt) REVERT: A 74 LEU cc_start: 0.7018 (OUTLIER) cc_final: 0.6676 (tp) REVERT: A 162 PHE cc_start: 0.8891 (m-80) cc_final: 0.8462 (m-80) REVERT: A 169 SER cc_start: 0.8471 (OUTLIER) cc_final: 0.7813 (p) REVERT: A 282 GLU cc_start: 0.4571 (mm-30) cc_final: 0.3636 (mm-30) REVERT: B 43 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8670 (tt) REVERT: B 74 LEU cc_start: 0.7108 (OUTLIER) cc_final: 0.6789 (tp) REVERT: B 162 PHE cc_start: 0.8913 (m-80) cc_final: 0.8494 (m-80) REVERT: B 282 GLU cc_start: 0.4547 (mm-30) cc_final: 0.3674 (mm-30) outliers start: 16 outliers final: 11 residues processed: 113 average time/residue: 0.4588 time to fit residues: 66.1832 Evaluate side-chains 112 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 436 SER Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 468 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 32 optimal weight: 7.9990 chunk 47 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 66 optimal weight: 0.6980 chunk 57 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 44 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 chunk 60 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.3443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 5838 Z= 0.152 Angle : 0.506 5.420 7956 Z= 0.253 Chirality : 0.035 0.116 978 Planarity : 0.005 0.078 976 Dihedral : 4.714 50.093 788 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.58 % Allowed : 16.94 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.37 (0.32), residues: 726 helix: 2.86 (0.21), residues: 604 sheet: None (None), residues: 0 loop : -1.28 (0.56), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 394 HIS 0.003 0.001 HIS A 449 PHE 0.010 0.001 PHE B 99 TYR 0.018 0.002 TYR B 125 ARG 0.012 0.000 ARG A 375 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 125 is missing expected H atoms. Skipping. Residue TYR 125 is missing expected H atoms. Skipping. Evaluate side-chains 116 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 100 time to evaluate : 0.886 Fit side-chains REVERT: A 43 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8561 (tt) REVERT: A 74 LEU cc_start: 0.7007 (OUTLIER) cc_final: 0.6670 (tp) REVERT: A 162 PHE cc_start: 0.8885 (m-80) cc_final: 0.8480 (m-80) REVERT: A 282 GLU cc_start: 0.4402 (mm-30) cc_final: 0.3541 (mm-30) REVERT: B 31 GLN cc_start: 0.7976 (mt0) cc_final: 0.7625 (mt0) REVERT: B 43 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8568 (tt) REVERT: B 74 LEU cc_start: 0.7047 (OUTLIER) cc_final: 0.6733 (tp) REVERT: B 162 PHE cc_start: 0.8881 (m-80) cc_final: 0.8482 (m-80) REVERT: B 282 GLU cc_start: 0.4455 (mm-30) cc_final: 0.3613 (mm-30) outliers start: 16 outliers final: 10 residues processed: 116 average time/residue: 0.4237 time to fit residues: 63.4225 Evaluate side-chains 111 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 97 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 436 SER Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 468 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 52 optimal weight: 0.7980 chunk 8 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 3 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.164613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.112245 restraints weight = 17759.402| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 2.16 r_work: 0.2989 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.3507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5838 Z= 0.172 Angle : 0.517 5.843 7956 Z= 0.260 Chirality : 0.035 0.119 978 Planarity : 0.005 0.049 976 Dihedral : 4.687 49.517 788 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.26 % Allowed : 17.26 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.36 (0.32), residues: 726 helix: 2.85 (0.21), residues: 604 sheet: None (None), residues: 0 loop : -1.28 (0.56), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 324 HIS 0.003 0.001 HIS B 328 PHE 0.013 0.001 PHE B 99 TYR 0.008 0.002 TYR A 125 ARG 0.008 0.000 ARG A 375 =============================================================================== Job complete usr+sys time: 2895.87 seconds wall clock time: 52 minutes 52.16 seconds (3172.16 seconds total)