Starting phenix.real_space_refine on Tue Jul 29 19:25:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wca_21604/07_2025/6wca_21604.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wca_21604/07_2025/6wca_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_21604/07_2025/6wca_21604.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wca_21604/07_2025/6wca_21604.map" model { file = "/net/cci-nas-00/data/ceres_data/6wca_21604/07_2025/6wca_21604.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wca_21604/07_2025/6wca_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 6.07, per 1000 atoms: 0.52 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: 3.36 Conformation dependent library (CDL) restraints added in 957.7 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: 0.95 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: 4.36 Time building geometry restraints manager: 3.88 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: 0.110 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: 0.230 Extract box with map and model: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 29.240 Find NCS groups from input model: 0.400 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: 0.010 Load rotamer database and sin/cos tables:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.780 ------------------------------------------------------------------------------- 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= 0.160 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 Details of bonding type rmsd hydrogen bonds : bond 0.11279 ( 452) hydrogen bonds : angle 5.10310 ( 1326) covalent geometry : bond 0.00293 ( 5838) covalent geometry : angle 0.60680 ( 7956) *********************** 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 : 0.994 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: 0.3780 time to fit residues: 56.0682 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 : 0.810 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.169930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.118580 restraints weight = 17501.741| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 2.14 r_work: 0.3046 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 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= 0.156 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 Details of bonding type rmsd hydrogen bonds : bond 0.05698 ( 452) hydrogen bonds : angle 4.11200 ( 1326) covalent geometry : bond 0.00331 ( 5838) covalent geometry : angle 0.57819 ( 7956) *********************** 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 : 0.913 Fit side-chains REVERT: A 142 LEU cc_start: 0.8157 (mt) cc_final: 0.7937 (tp) REVERT: A 162 PHE cc_start: 0.8806 (m-80) cc_final: 0.8333 (m-80) REVERT: A 282 GLU cc_start: 0.5423 (mm-30) cc_final: 0.4064 (mm-30) REVERT: A 335 ARG cc_start: 0.8210 (mtp180) cc_final: 0.7834 (mtp-110) REVERT: A 336 LYS cc_start: 0.8104 (ttpp) cc_final: 0.7859 (mtpp) REVERT: B 142 LEU cc_start: 0.8295 (mt) cc_final: 0.8059 (tp) REVERT: B 162 PHE cc_start: 0.8835 (m-80) cc_final: 0.8375 (m-80) REVERT: B 282 GLU cc_start: 0.5421 (mm-30) cc_final: 0.4091 (mm-30) REVERT: B 335 ARG cc_start: 0.8298 (mtp180) cc_final: 0.7918 (mtp-110) outliers start: 15 outliers final: 11 residues processed: 104 average time/residue: 0.3705 time to fit residues: 51.0274 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 : 0.974 ------------------------------------------------------------------------------- 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 1 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 chunk 68 optimal weight: 5.9990 chunk 61 optimal weight: 10.0000 chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 overall best weight: 3.3388 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.166137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.115114 restraints weight = 18198.959| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 2.19 r_work: 0.2958 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5838 Z= 0.197 Angle : 0.590 4.601 7956 Z= 0.312 Chirality : 0.038 0.136 978 Planarity : 0.005 0.050 976 Dihedral : 5.663 59.547 789 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.42 % Allowed : 16.13 % 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: 2.09 (0.31), residues: 726 helix: 2.04 (0.21), residues: 600 sheet: None (None), residues: 0 loop : -1.93 (0.50), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 394 HIS 0.007 0.002 HIS B 328 PHE 0.019 0.002 PHE A 99 TYR 0.011 0.002 TYR A 313 ARG 0.003 0.001 ARG A 309 Details of bonding type rmsd hydrogen bonds : bond 0.06004 ( 452) hydrogen bonds : angle 4.06081 ( 1326) covalent geometry : bond 0.00444 ( 5838) covalent geometry : angle 0.59006 ( 7956) *********************** 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 106 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 91 time to evaluate : 0.788 Fit side-chains REVERT: A 162 PHE cc_start: 0.8880 (m-80) cc_final: 0.8363 (m-80) REVERT: A 282 GLU cc_start: 0.5427 (mm-30) cc_final: 0.4158 (mm-30) REVERT: A 335 ARG cc_start: 0.8251 (mtp180) cc_final: 0.7998 (mtp-110) REVERT: A 336 LYS cc_start: 0.8230 (ttpp) cc_final: 0.8011 (mtpp) REVERT: A 359 TYR cc_start: 0.8267 (m-80) cc_final: 0.7996 (m-10) REVERT: B 282 GLU cc_start: 0.5223 (mm-30) cc_final: 0.4016 (mm-30) REVERT: B 335 ARG cc_start: 0.8254 (mtp180) cc_final: 0.7987 (mtp-110) REVERT: B 359 TYR cc_start: 0.8280 (m-80) cc_final: 0.7930 (m-10) outliers start: 15 outliers final: 11 residues processed: 106 average time/residue: 0.4180 time to fit residues: 57.6484 Evaluate side-chains 100 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 89 time to evaluate : 0.814 ------------------------------------------------------------------------------- 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 7 optimal weight: 4.9990 chunk 3 optimal weight: 0.6980 chunk 34 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 46 optimal weight: 4.9990 chunk 61 optimal weight: 6.9990 chunk 0 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.163713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.112077 restraints weight = 18009.692| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 2.21 r_work: 0.2946 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 5838 Z= 0.164 Angle : 0.548 4.281 7956 Z= 0.286 Chirality : 0.037 0.133 978 Planarity : 0.005 0.048 976 Dihedral : 5.332 57.275 788 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.90 % Allowed : 15.32 % 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: 2.47 (0.32), residues: 726 helix: 2.28 (0.21), residues: 600 sheet: None (None), residues: 0 loop : -1.70 (0.51), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 394 HIS 0.004 0.001 HIS A 328 PHE 0.013 0.001 PHE B 99 TYR 0.015 0.002 TYR B 125 ARG 0.002 0.000 ARG A 294 Details of bonding type rmsd hydrogen bonds : bond 0.05329 ( 452) hydrogen bonds : angle 3.91844 ( 1326) covalent geometry : bond 0.00372 ( 5838) covalent geometry : angle 0.54772 ( 7956) *********************** 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 110 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 92 time to evaluate : 0.931 Fit side-chains revert: symmetry clash REVERT: A 162 PHE cc_start: 0.8879 (m-80) cc_final: 0.8343 (m-80) REVERT: A 282 GLU cc_start: 0.5238 (mm-30) cc_final: 0.4128 (mm-30) REVERT: A 336 LYS cc_start: 0.8278 (ttpp) cc_final: 0.8035 (mtpp) REVERT: B 282 GLU cc_start: 0.5153 (mm-30) cc_final: 0.4105 (mm-30) REVERT: B 335 ARG cc_start: 0.8232 (mtp180) cc_final: 0.8017 (mtp-110) REVERT: B 359 TYR cc_start: 0.8086 (m-80) cc_final: 0.7868 (m-10) outliers start: 18 outliers final: 13 residues processed: 110 average time/residue: 0.3967 time to fit residues: 57.0857 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 : 0.808 ------------------------------------------------------------------------------- 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 14 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 15 optimal weight: 0.9980 chunk 54 optimal weight: 6.9990 chunk 70 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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 = 0.3871 r_free = 0.3871 target = 0.166508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.115636 restraints weight = 17912.114| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.16 r_work: 0.3004 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5838 Z= 0.145 Angle : 0.527 4.275 7956 Z= 0.274 Chirality : 0.036 0.123 978 Planarity : 0.004 0.047 976 Dihedral : 5.196 56.104 788 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.26 % Allowed : 16.61 % Favored : 81.13 % 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: 2.74 (0.32), residues: 726 helix: 2.46 (0.21), residues: 600 sheet: None (None), residues: 0 loop : -1.52 (0.52), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 394 HIS 0.004 0.001 HIS A 328 PHE 0.015 0.001 PHE B 99 TYR 0.013 0.002 TYR A 125 ARG 0.002 0.000 ARG A 294 Details of bonding type rmsd hydrogen bonds : bond 0.05089 ( 452) hydrogen bonds : angle 3.81514 ( 1326) covalent geometry : bond 0.00327 ( 5838) covalent geometry : angle 0.52691 ( 7956) *********************** 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 101 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 0.803 Fit side-chains REVERT: A 162 PHE cc_start: 0.8871 (m-80) cc_final: 0.8355 (m-80) REVERT: A 169 SER cc_start: 0.8311 (OUTLIER) cc_final: 0.7351 (p) REVERT: A 282 GLU cc_start: 0.5068 (mm-30) cc_final: 0.4027 (mm-30) REVERT: A 336 LYS cc_start: 0.8270 (ttpp) cc_final: 0.8031 (mtpp) REVERT: B 282 GLU cc_start: 0.5025 (mm-30) cc_final: 0.4053 (mm-30) REVERT: B 335 ARG cc_start: 0.8305 (mtp180) cc_final: 0.8066 (mtp-110) REVERT: B 359 TYR cc_start: 0.8165 (m-80) cc_final: 0.7941 (m-10) outliers start: 14 outliers final: 12 residues processed: 101 average time/residue: 0.3920 time to fit residues: 51.9314 Evaluate side-chains 98 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.797 ------------------------------------------------------------------------------- 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 373 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 65 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 17 optimal weight: 0.9990 chunk 18 optimal weight: 10.0000 chunk 45 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 3 optimal weight: 8.9990 chunk 6 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 overall best weight: 2.3588 ------------------------------------------------------------------------------- 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 = 0.3826 r_free = 0.3826 target = 0.163287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.110492 restraints weight = 18113.594| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 2.19 r_work: 0.2991 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.3014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5838 Z= 0.158 Angle : 0.529 4.321 7956 Z= 0.276 Chirality : 0.036 0.122 978 Planarity : 0.005 0.047 976 Dihedral : 5.087 54.155 788 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % 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: 2.79 (0.32), residues: 726 helix: 2.49 (0.21), residues: 600 sheet: None (None), residues: 0 loop : -1.51 (0.53), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 394 HIS 0.005 0.001 HIS A 328 PHE 0.014 0.001 PHE A 99 TYR 0.016 0.002 TYR B 125 ARG 0.003 0.000 ARG A 309 Details of bonding type rmsd hydrogen bonds : bond 0.05095 ( 452) hydrogen bonds : angle 3.79794 ( 1326) covalent geometry : bond 0.00358 ( 5838) covalent geometry : angle 0.52927 ( 7956) *********************** 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 109 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 0.837 Fit side-chains revert: symmetry clash REVERT: A 43 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8627 (tt) REVERT: A 162 PHE cc_start: 0.8900 (m-80) cc_final: 0.8382 (m-80) REVERT: A 169 SER cc_start: 0.8379 (OUTLIER) cc_final: 0.7450 (p) REVERT: A 282 GLU cc_start: 0.5060 (mm-30) cc_final: 0.4067 (mm-30) REVERT: A 336 LYS cc_start: 0.8307 (ttpp) cc_final: 0.8071 (mtpp) REVERT: B 43 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8665 (tt) REVERT: B 282 GLU cc_start: 0.4979 (mm-30) cc_final: 0.4022 (mm-30) REVERT: B 335 ARG cc_start: 0.8309 (mtp180) cc_final: 0.8089 (mtp-110) REVERT: B 359 TYR cc_start: 0.8153 (m-80) cc_final: 0.7923 (m-10) outliers start: 16 outliers final: 13 residues processed: 109 average time/residue: 0.3957 time to fit residues: 56.1384 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 : 0.950 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 17 optimal weight: 3.9990 chunk 30 optimal weight: 0.4980 chunk 28 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 14 optimal weight: 8.9990 chunk 32 optimal weight: 7.9990 chunk 7 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 chunk 20 optimal weight: 7.9990 chunk 10 optimal weight: 0.5980 overall best weight: 2.0186 ------------------------------------------------------------------------------- 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 = 0.3825 r_free = 0.3825 target = 0.163241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.110901 restraints weight = 18007.935| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.17 r_work: 0.2994 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.3163 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= 0.142 Angle : 0.520 4.859 7956 Z= 0.268 Chirality : 0.036 0.119 978 Planarity : 0.004 0.046 976 Dihedral : 4.953 51.886 788 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.58 % Allowed : 16.13 % 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: 2.92 (0.32), residues: 726 helix: 2.56 (0.21), residues: 602 sheet: None (None), residues: 0 loop : -1.42 (0.54), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 394 HIS 0.004 0.001 HIS B 328 PHE 0.014 0.001 PHE A 99 TYR 0.015 0.002 TYR B 125 ARG 0.002 0.000 ARG A 309 Details of bonding type rmsd hydrogen bonds : bond 0.04868 ( 452) hydrogen bonds : angle 3.73451 ( 1326) covalent geometry : bond 0.00321 ( 5838) covalent geometry : angle 0.52028 ( 7956) *********************** 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 105 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 89 time to evaluate : 0.815 Fit side-chains revert: symmetry clash REVERT: A 74 LEU cc_start: 0.6739 (OUTLIER) cc_final: 0.6475 (tp) REVERT: A 162 PHE cc_start: 0.8859 (m-80) cc_final: 0.8332 (m-80) REVERT: A 169 SER cc_start: 0.8371 (OUTLIER) cc_final: 0.7433 (p) REVERT: A 282 GLU cc_start: 0.4932 (mm-30) cc_final: 0.3988 (mm-30) REVERT: B 43 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8603 (tt) REVERT: B 74 LEU cc_start: 0.6734 (OUTLIER) cc_final: 0.6484 (tp) REVERT: B 169 SER cc_start: 0.8316 (OUTLIER) cc_final: 0.7367 (p) REVERT: B 282 GLU cc_start: 0.4800 (mm-30) cc_final: 0.3900 (mm-30) REVERT: B 335 ARG cc_start: 0.8270 (mtp180) cc_final: 0.8036 (mtp-110) REVERT: B 359 TYR cc_start: 0.8121 (m-80) cc_final: 0.7906 (m-10) outliers start: 16 outliers final: 11 residues processed: 105 average time/residue: 0.3821 time to fit residues: 52.7053 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 : 0.860 ------------------------------------------------------------------------------- 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 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 169 SER 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 47 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 54 optimal weight: 7.9990 chunk 30 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 64 optimal weight: 0.7980 overall best weight: 1.7588 ------------------------------------------------------------------------------- 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 = 0.3838 r_free = 0.3838 target = 0.164275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.112079 restraints weight = 17916.867| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 2.17 r_work: 0.2972 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.3294 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= 0.132 Angle : 0.509 4.780 7956 Z= 0.262 Chirality : 0.035 0.118 978 Planarity : 0.004 0.046 976 Dihedral : 4.855 50.828 788 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % 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: 3.03 (0.32), residues: 726 helix: 2.63 (0.21), residues: 604 sheet: None (None), residues: 0 loop : -1.47 (0.55), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 394 HIS 0.004 0.001 HIS B 328 PHE 0.014 0.001 PHE B 99 TYR 0.017 0.002 TYR B 125 ARG 0.001 0.000 ARG A 474 Details of bonding type rmsd hydrogen bonds : bond 0.04641 ( 452) hydrogen bonds : angle 3.68161 ( 1326) covalent geometry : bond 0.00297 ( 5838) covalent geometry : angle 0.50948 ( 7956) *********************** 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 110 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 93 time to evaluate : 0.845 Fit side-chains revert: symmetry clash REVERT: A 43 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8690 (tt) REVERT: A 74 LEU cc_start: 0.6683 (OUTLIER) cc_final: 0.6427 (tp) REVERT: A 162 PHE cc_start: 0.8917 (m-80) cc_final: 0.8422 (m-80) REVERT: A 169 SER cc_start: 0.8402 (OUTLIER) cc_final: 0.7479 (p) REVERT: A 282 GLU cc_start: 0.4829 (mm-30) cc_final: 0.3933 (mm-30) REVERT: A 414 ARG cc_start: 0.7904 (mtp180) cc_final: 0.7676 (ttm110) REVERT: B 43 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8682 (tt) REVERT: B 74 LEU cc_start: 0.6776 (OUTLIER) cc_final: 0.6556 (tp) REVERT: B 162 PHE cc_start: 0.8918 (m-80) cc_final: 0.8416 (m-80) REVERT: B 169 SER cc_start: 0.8372 (OUTLIER) cc_final: 0.7450 (p) REVERT: B 282 GLU cc_start: 0.4734 (mm-30) cc_final: 0.3865 (mm-30) REVERT: B 335 ARG cc_start: 0.8324 (mtp180) cc_final: 0.8081 (mtp-110) outliers start: 17 outliers final: 11 residues processed: 110 average time/residue: 0.4623 time to fit residues: 65.5144 Evaluate side-chains 109 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 92 time to evaluate : 0.916 ------------------------------------------------------------------------------- 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 169 SER 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 3 optimal weight: 7.9990 chunk 8 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 53 optimal weight: 7.9990 chunk 21 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 69 optimal weight: 10.0000 chunk 22 optimal weight: 3.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- 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 = 0.3818 r_free = 0.3818 target = 0.162574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.110286 restraints weight = 17913.799| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 2.16 r_work: 0.3008 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.3398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5838 Z= 0.154 Angle : 0.527 4.912 7956 Z= 0.272 Chirality : 0.036 0.122 978 Planarity : 0.005 0.069 976 Dihedral : 4.839 49.359 788 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.06 % Allowed : 15.32 % 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: 2.94 (0.32), residues: 726 helix: 2.57 (0.21), residues: 604 sheet: None (None), residues: 0 loop : -1.45 (0.55), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 324 HIS 0.005 0.001 HIS B 328 PHE 0.014 0.001 PHE A 99 TYR 0.017 0.002 TYR B 125 ARG 0.011 0.000 ARG A 375 Details of bonding type rmsd hydrogen bonds : bond 0.04879 ( 452) hydrogen bonds : angle 3.69873 ( 1326) covalent geometry : bond 0.00353 ( 5838) covalent geometry : angle 0.52696 ( 7956) *********************** 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 117 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 98 time to evaluate : 0.825 Fit side-chains revert: symmetry clash REVERT: A 43 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8635 (tt) REVERT: A 74 LEU cc_start: 0.6824 (OUTLIER) cc_final: 0.6542 (tp) REVERT: A 162 PHE cc_start: 0.8907 (m-80) cc_final: 0.8395 (m-80) REVERT: A 169 SER cc_start: 0.8392 (OUTLIER) cc_final: 0.7470 (p) REVERT: A 282 GLU cc_start: 0.4859 (mm-30) cc_final: 0.3941 (mm-30) REVERT: A 414 ARG cc_start: 0.7915 (mtp180) cc_final: 0.7680 (ttm110) REVERT: B 43 LEU cc_start: 0.9095 (OUTLIER) cc_final: 0.8618 (tt) REVERT: B 74 LEU cc_start: 0.6813 (OUTLIER) cc_final: 0.6546 (tp) REVERT: B 162 PHE cc_start: 0.8897 (m-80) cc_final: 0.8388 (m-80) REVERT: B 169 SER cc_start: 0.8398 (OUTLIER) cc_final: 0.7459 (p) REVERT: B 282 GLU cc_start: 0.4787 (mm-30) cc_final: 0.3888 (mm-30) REVERT: B 335 ARG cc_start: 0.8333 (mtp180) cc_final: 0.8118 (mtp-110) outliers start: 19 outliers final: 11 residues processed: 117 average time/residue: 0.4928 time to fit residues: 71.1888 Evaluate side-chains 114 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 97 time to evaluate : 0.690 ------------------------------------------------------------------------------- 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 169 SER 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 37 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 47 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 chunk 38 optimal weight: 0.0030 chunk 40 optimal weight: 1.9990 overall best weight: 1.7396 ------------------------------------------------------------------------------- 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 = 0.3820 r_free = 0.3820 target = 0.162855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.110504 restraints weight = 17812.702| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 2.16 r_work: 0.2969 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2822 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.3472 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= 0.131 Angle : 0.516 5.199 7956 Z= 0.265 Chirality : 0.035 0.120 978 Planarity : 0.005 0.066 976 Dihedral : 4.786 47.711 788 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.74 % Allowed : 15.48 % 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: 3.08 (0.32), residues: 726 helix: 2.66 (0.21), residues: 604 sheet: None (None), residues: 0 loop : -1.40 (0.56), residues: 122 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 A 99 TYR 0.018 0.002 TYR B 125 ARG 0.010 0.000 ARG B 375 Details of bonding type rmsd hydrogen bonds : bond 0.04630 ( 452) hydrogen bonds : angle 3.66785 ( 1326) covalent geometry : bond 0.00297 ( 5838) covalent geometry : angle 0.51616 ( 7956) ********************** 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 112 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 95 time to evaluate : 0.819 Fit side-chains revert: symmetry clash REVERT: A 43 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8636 (tt) REVERT: A 74 LEU cc_start: 0.6717 (OUTLIER) cc_final: 0.6441 (tp) REVERT: A 162 PHE cc_start: 0.8906 (m-80) cc_final: 0.8387 (m-80) REVERT: A 169 SER cc_start: 0.8384 (OUTLIER) cc_final: 0.7481 (p) REVERT: A 282 GLU cc_start: 0.4822 (mm-30) cc_final: 0.3893 (mm-30) REVERT: A 414 ARG cc_start: 0.7900 (mtp180) cc_final: 0.7670 (ttm110) REVERT: B 43 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8678 (tt) REVERT: B 74 LEU cc_start: 0.6807 (OUTLIER) cc_final: 0.6570 (tp) REVERT: B 83 MET cc_start: 0.8312 (mtt) cc_final: 0.8064 (mtp) REVERT: B 162 PHE cc_start: 0.8913 (m-80) cc_final: 0.8408 (m-80) REVERT: B 169 SER cc_start: 0.8387 (OUTLIER) cc_final: 0.7462 (p) REVERT: B 282 GLU cc_start: 0.4864 (mm-30) cc_final: 0.3916 (mm-30) REVERT: B 335 ARG cc_start: 0.8359 (mtp180) cc_final: 0.8135 (mtp-110) outliers start: 17 outliers final: 11 residues processed: 112 average time/residue: 0.4964 time to fit residues: 69.6057 Evaluate side-chains 112 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 95 time to evaluate : 0.966 ------------------------------------------------------------------------------- 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 169 SER 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 3 optimal weight: 5.9990 chunk 55 optimal weight: 7.9990 chunk 33 optimal weight: 9.9990 chunk 65 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 9 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 = 0.3826 r_free = 0.3826 target = 0.163425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.111041 restraints weight = 17856.420| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 2.17 r_work: 0.2983 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.3545 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= 0.133 Angle : 0.518 5.108 7956 Z= 0.265 Chirality : 0.036 0.122 978 Planarity : 0.005 0.059 976 Dihedral : 4.707 45.992 788 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.74 % Allowed : 15.65 % 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: 3.09 (0.32), residues: 726 helix: 2.67 (0.21), residues: 604 sheet: None (None), residues: 0 loop : -1.40 (0.56), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 394 HIS 0.004 0.001 HIS B 328 PHE 0.014 0.001 PHE A 99 TYR 0.008 0.002 TYR A 125 ARG 0.007 0.000 ARG A 375 Details of bonding type rmsd hydrogen bonds : bond 0.04570 ( 452) hydrogen bonds : angle 3.63045 ( 1326) covalent geometry : bond 0.00303 ( 5838) covalent geometry : angle 0.51785 ( 7956) =============================================================================== Job complete usr+sys time: 6811.82 seconds wall clock time: 118 minutes 17.73 seconds (7097.73 seconds total)