Starting phenix.real_space_refine on Fri Dec 27 13:06:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ezv_31391/12_2024/7ezv_31391.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ezv_31391/12_2024/7ezv_31391.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ezv_31391/12_2024/7ezv_31391.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ezv_31391/12_2024/7ezv_31391.map" model { file = "/net/cci-nas-00/data/ceres_data/7ezv_31391/12_2024/7ezv_31391.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ezv_31391/12_2024/7ezv_31391.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.049 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 22 5.16 5 C 3131 2.51 5 N 835 2.21 5 O 949 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 4937 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1465 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 9, 'TRANS': 173} Chain: "H" Number of atoms: 912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 912 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "L" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 805 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 6, 'TRANS': 99} Chain: "M" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 927 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "N" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 828 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Time building chain proxies: 4.60, per 1000 atoms: 0.93 Number of scatterers: 4937 At special positions: 0 Unit cell: (99.36, 90.72, 98.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 22 16.00 O 949 8.00 N 835 7.00 C 3131 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 96 " distance=2.03 Simple disulfide: pdb=" SG CYS M 101 " - pdb=" SG CYS M 106 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 89 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.18 Conformation dependent library (CDL) restraints added in 588.5 milliseconds 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1152 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 13 sheets defined 9.3% alpha, 34.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 385 through 390 removed outlier: 4.025A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.752A pdb=" N THR H 91 " --> pdb=" O ALA H 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.698A pdb=" N VAL L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 28 through 31 Processing helix chain 'M' and resid 73 through 76 Processing helix chain 'M' and resid 101 through 105 removed outlier: 3.778A pdb=" N GLY M 104 " --> pdb=" O CYS M 101 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR M 105 " --> pdb=" O SER M 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 101 through 105' Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.501A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 10 through 12 Processing sheet with id=AA5, first strand: chain 'H' and resid 18 through 23 Processing sheet with id=AA6, first strand: chain 'L' and resid 4 through 5 Processing sheet with id=AA7, first strand: chain 'L' and resid 10 through 12 Processing sheet with id=AA8, first strand: chain 'L' and resid 44 through 48 removed outlier: 6.378A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'M' and resid 3 through 5 Processing sheet with id=AB1, first strand: chain 'M' and resid 57 through 60 removed outlier: 6.725A pdb=" N TRP M 36 " --> pdb=" O ILE M 48 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N TRP M 50 " --> pdb=" O VAL M 34 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL M 34 " --> pdb=" O TRP M 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'M' and resid 57 through 60 removed outlier: 6.725A pdb=" N TRP M 36 " --> pdb=" O ILE M 48 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N TRP M 50 " --> pdb=" O VAL M 34 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL M 34 " --> pdb=" O TRP M 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'N' and resid 5 through 6 Processing sheet with id=AB4, first strand: chain 'N' and resid 10 through 13 removed outlier: 6.029A pdb=" N LEU N 11 " --> pdb=" O GLU N 106 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR N 103 " --> pdb=" O TYR N 87 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N TRP N 36 " --> pdb=" O LEU N 48 " (cutoff:3.500A) 175 hydrogen bonds defined for protein. 411 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.28 Time building geometry restraints manager: 1.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 867 1.32 - 1.45: 1451 1.45 - 1.57: 2715 1.57 - 1.69: 0 1.69 - 1.81: 27 Bond restraints: 5060 Sorted by residual: bond pdb=" CA ALA A 475 " pdb=" CB ALA A 475 " ideal model delta sigma weight residual 1.532 1.490 0.042 1.53e-02 4.27e+03 7.58e+00 bond pdb=" N THR A 478 " pdb=" CA THR A 478 " ideal model delta sigma weight residual 1.453 1.483 -0.030 1.16e-02 7.43e+03 6.64e+00 bond pdb=" C PRO A 479 " pdb=" O PRO A 479 " ideal model delta sigma weight residual 1.233 1.205 0.028 1.16e-02 7.43e+03 5.93e+00 bond pdb=" CA SER A 477 " pdb=" CB SER A 477 " ideal model delta sigma weight residual 1.530 1.491 0.038 1.63e-02 3.76e+03 5.56e+00 bond pdb=" N ASN A 481 " pdb=" CA ASN A 481 " ideal model delta sigma weight residual 1.460 1.488 -0.028 1.39e-02 5.18e+03 3.97e+00 ... (remaining 5055 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.80: 6660 1.80 - 3.60: 176 3.60 - 5.40: 32 5.40 - 7.21: 3 7.21 - 9.01: 2 Bond angle restraints: 6873 Sorted by residual: angle pdb=" C PRO A 479 " pdb=" CA PRO A 479 " pdb=" CB PRO A 479 " ideal model delta sigma weight residual 111.46 105.43 6.03 1.29e+00 6.01e-01 2.18e+01 angle pdb=" C GLY A 482 " pdb=" N VAL A 483 " pdb=" CA VAL A 483 " ideal model delta sigma weight residual 123.13 118.95 4.18 1.34e+00 5.57e-01 9.74e+00 angle pdb=" CA SER A 477 " pdb=" C SER A 477 " pdb=" O SER A 477 " ideal model delta sigma weight residual 120.55 117.27 3.28 1.07e+00 8.73e-01 9.39e+00 angle pdb=" C ALA L 51 " pdb=" N SER L 52 " pdb=" CA SER L 52 " ideal model delta sigma weight residual 121.54 127.33 -5.79 1.91e+00 2.74e-01 9.20e+00 angle pdb=" N ALA A 475 " pdb=" CA ALA A 475 " pdb=" C ALA A 475 " ideal model delta sigma weight residual 113.41 109.71 3.70 1.22e+00 6.72e-01 9.18e+00 ... (remaining 6868 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.47: 2692 17.47 - 34.93: 233 34.93 - 52.40: 45 52.40 - 69.87: 7 69.87 - 87.33: 3 Dihedral angle restraints: 2980 sinusoidal: 1160 harmonic: 1820 Sorted by residual: dihedral pdb=" CB CYS N 23 " pdb=" SG CYS N 23 " pdb=" SG CYS N 89 " pdb=" CB CYS N 89 " ideal model delta sinusoidal sigma weight residual 93.00 156.07 -63.07 1 1.00e+01 1.00e-02 5.25e+01 dihedral pdb=" CA ALA L 94 " pdb=" C ALA L 94 " pdb=" N PRO L 95 " pdb=" CA PRO L 95 " ideal model delta harmonic sigma weight residual -180.00 -143.91 -36.09 0 5.00e+00 4.00e-02 5.21e+01 dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 88 " pdb=" CB CYS L 88 " ideal model delta sinusoidal sigma weight residual 93.00 147.80 -54.80 1 1.00e+01 1.00e-02 4.07e+01 ... (remaining 2977 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 521 0.040 - 0.081: 144 0.081 - 0.121: 56 0.121 - 0.162: 14 0.162 - 0.202: 3 Chirality restraints: 738 Sorted by residual: chirality pdb=" CA PRO L 95 " pdb=" N PRO L 95 " pdb=" C PRO L 95 " pdb=" CB PRO L 95 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CA ILE M 51 " pdb=" N ILE M 51 " pdb=" C ILE M 51 " pdb=" CB ILE M 51 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 8.11e-01 chirality pdb=" CA CYS A 480 " pdb=" N CYS A 480 " pdb=" C CYS A 480 " pdb=" CB CYS A 480 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.68e-01 ... (remaining 735 not shown) Planarity restraints: 883 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA L 94 " -0.089 5.00e-02 4.00e+02 1.36e-01 2.96e+01 pdb=" N PRO L 95 " 0.235 5.00e-02 4.00e+02 pdb=" CA PRO L 95 " -0.076 5.00e-02 4.00e+02 pdb=" CD PRO L 95 " -0.071 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG L 65 " 0.120 9.50e-02 1.11e+02 5.45e-02 2.48e+00 pdb=" NE ARG L 65 " -0.012 2.00e-02 2.50e+03 pdb=" CZ ARG L 65 " 0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG L 65 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG L 65 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU N 80 " -0.026 5.00e-02 4.00e+02 3.93e-02 2.48e+00 pdb=" N PRO N 81 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO N 81 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO N 81 " -0.022 5.00e-02 4.00e+02 ... (remaining 880 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 56 2.61 - 3.18: 4302 3.18 - 3.75: 7412 3.75 - 4.33: 10832 4.33 - 4.90: 18369 Nonbonded interactions: 40971 Sorted by model distance: nonbonded pdb=" OG1 THR M 28 " pdb=" O CYS M 101 " model vdw 2.034 3.040 nonbonded pdb=" O ASN A 439 " pdb=" OG SER A 443 " model vdw 2.173 3.040 nonbonded pdb=" NH2 ARG A 346 " pdb=" OD2 ASP H 54 " model vdw 2.248 3.120 nonbonded pdb=" OD1 ASP A 442 " pdb=" OH TYR A 451 " model vdw 2.252 3.040 nonbonded pdb=" OD2 ASP M 73 " pdb=" OG1 THR M 76 " model vdw 2.290 3.040 ... (remaining 40966 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 14.560 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 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 : 0.005 0.049 5060 Z= 0.326 Angle : 0.712 9.008 6873 Z= 0.394 Chirality : 0.047 0.202 738 Planarity : 0.007 0.136 883 Dihedral : 13.537 87.335 1804 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.36 % Favored : 91.32 % Rotamer: Outliers : 0.75 % Allowed : 0.75 % Favored : 98.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.45 % 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: -0.96 (0.33), residues: 622 helix: -3.09 (0.74), residues: 27 sheet: -0.21 (0.33), residues: 253 loop : -0.69 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP M 36 HIS 0.006 0.004 HIS M 100 PHE 0.018 0.002 PHE H 24 TYR 0.015 0.002 TYR L 91 ARG 0.014 0.001 ARG L 65 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 101 time to evaluate : 0.436 Fit side-chains revert: symmetry clash REVERT: L 90 GLN cc_start: 0.9069 (OUTLIER) cc_final: 0.8752 (pp30) REVERT: N 101 GLN cc_start: 0.7980 (OUTLIER) cc_final: 0.7772 (pp30) outliers start: 4 outliers final: 0 residues processed: 104 average time/residue: 0.2323 time to fit residues: 28.8804 Evaluate side-chains 88 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 86 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain N residue 101 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 51 optimal weight: 0.0040 chunk 46 optimal weight: 8.9990 chunk 25 optimal weight: 5.9990 chunk 15 optimal weight: 0.6980 chunk 31 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 overall best weight: 1.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 90 GLN M 100 HIS N 101 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 5060 Z= 0.326 Angle : 0.660 8.631 6873 Z= 0.349 Chirality : 0.046 0.157 738 Planarity : 0.005 0.040 883 Dihedral : 6.223 44.368 709 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.56 % Favored : 92.28 % Rotamer: Outliers : 2.24 % Allowed : 9.70 % Favored : 88.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.45 % 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: -1.14 (0.33), residues: 622 helix: -3.00 (0.83), residues: 27 sheet: -0.21 (0.33), residues: 254 loop : -0.95 (0.33), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 36 HIS 0.004 0.002 HIS M 100 PHE 0.015 0.002 PHE N 99 TYR 0.015 0.002 TYR L 91 ARG 0.007 0.001 ARG L 65 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 94 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 408 ARG cc_start: 0.8520 (mtm110) cc_final: 0.8286 (ptp-110) REVERT: M 27 PHE cc_start: 0.8209 (OUTLIER) cc_final: 0.7330 (m-80) REVERT: M 73 ASP cc_start: 0.7360 (t0) cc_final: 0.7023 (t0) REVERT: M 80 TYR cc_start: 0.8275 (m-80) cc_final: 0.7968 (m-10) REVERT: N 104 LYS cc_start: 0.7641 (tmmt) cc_final: 0.7384 (ttpp) outliers start: 12 outliers final: 5 residues processed: 100 average time/residue: 0.2584 time to fit residues: 30.9498 Evaluate side-chains 91 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 85 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 417 ASN Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain M residue 27 PHE Chi-restraints excluded: chain N residue 20 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 30 optimal weight: 0.0040 chunk 17 optimal weight: 2.9990 chunk 46 optimal weight: 7.9990 chunk 37 optimal weight: 0.7980 chunk 15 optimal weight: 5.9990 chunk 55 optimal weight: 0.0970 chunk 59 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 18 optimal weight: 0.9980 chunk 44 optimal weight: 5.9990 chunk 54 optimal weight: 0.6980 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 37 GLN L 38 GLN M 39 GLN N 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 5060 Z= 0.183 Angle : 0.577 6.262 6873 Z= 0.305 Chirality : 0.045 0.213 738 Planarity : 0.004 0.043 883 Dihedral : 5.353 37.074 703 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.40 % Favored : 92.44 % Rotamer: Outliers : 2.05 % Allowed : 10.07 % Favored : 87.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.45 % 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: -0.86 (0.33), residues: 622 helix: -2.97 (1.01), residues: 20 sheet: 0.09 (0.34), residues: 248 loop : -0.90 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 436 HIS 0.000 0.000 HIS M 100 PHE 0.011 0.001 PHE H 24 TYR 0.018 0.001 TYR M 107 ARG 0.008 0.001 ARG L 65 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 97 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 378 LYS cc_start: 0.8759 (ttmm) cc_final: 0.8546 (ptmm) REVERT: A 408 ARG cc_start: 0.8492 (OUTLIER) cc_final: 0.8196 (ptp-110) REVERT: H 54 ASP cc_start: 0.8349 (OUTLIER) cc_final: 0.7871 (t70) REVERT: M 73 ASP cc_start: 0.7429 (t0) cc_final: 0.7185 (t0) REVERT: M 80 TYR cc_start: 0.8178 (m-80) cc_final: 0.7872 (m-10) REVERT: N 104 LYS cc_start: 0.7620 (tmmt) cc_final: 0.7303 (ttpp) REVERT: N 106 GLU cc_start: 0.6763 (tm-30) cc_final: 0.6028 (tm-30) outliers start: 11 outliers final: 3 residues processed: 102 average time/residue: 0.2529 time to fit residues: 31.3680 Evaluate side-chains 86 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 81 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 417 ASN Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain L residue 20 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 41 optimal weight: 10.0000 chunk 28 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 52 optimal weight: 0.0050 chunk 15 optimal weight: 4.9990 chunk 49 optimal weight: 0.7980 overall best weight: 0.6594 ------------------------------------------------------------------------------- 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: 0.8280 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 5060 Z= 0.197 Angle : 0.582 6.755 6873 Z= 0.306 Chirality : 0.045 0.176 738 Planarity : 0.004 0.044 883 Dihedral : 5.129 25.454 703 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.75 % Favored : 93.09 % Rotamer: Outliers : 2.05 % Allowed : 12.31 % Favored : 85.63 % 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: -0.74 (0.34), residues: 622 helix: -2.41 (1.53), residues: 12 sheet: 0.02 (0.33), residues: 251 loop : -0.76 (0.32), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP N 36 HIS 0.000 0.000 HIS M 100 PHE 0.010 0.001 PHE H 24 TYR 0.013 0.001 TYR M 107 ARG 0.009 0.001 ARG L 65 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 86 time to evaluate : 0.681 Fit side-chains revert: symmetry clash REVERT: A 406 GLU cc_start: 0.8498 (mt-10) cc_final: 0.8289 (mt-10) REVERT: A 408 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.8186 (ptp-110) REVERT: H 54 ASP cc_start: 0.8430 (OUTLIER) cc_final: 0.7932 (t70) REVERT: M 27 PHE cc_start: 0.7685 (OUTLIER) cc_final: 0.6928 (m-80) REVERT: M 73 ASP cc_start: 0.7634 (t0) cc_final: 0.7398 (t0) REVERT: M 80 TYR cc_start: 0.8191 (m-80) cc_final: 0.7911 (m-10) REVERT: N 104 LYS cc_start: 0.7665 (tmmt) cc_final: 0.7395 (ttpp) outliers start: 11 outliers final: 5 residues processed: 90 average time/residue: 0.2631 time to fit residues: 28.5259 Evaluate side-chains 88 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 80 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 417 ASN Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain M residue 27 PHE Chi-restraints excluded: chain M residue 105 THR Chi-restraints excluded: chain N residue 79 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 43 optimal weight: 0.0980 chunk 24 optimal weight: 5.9990 chunk 50 optimal weight: 6.9990 chunk 40 optimal weight: 7.9990 chunk 30 optimal weight: 0.1980 chunk 52 optimal weight: 7.9990 chunk 14 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN L 38 GLN M 39 GLN N 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 5060 Z= 0.364 Angle : 0.652 7.676 6873 Z= 0.344 Chirality : 0.046 0.171 738 Planarity : 0.005 0.044 883 Dihedral : 5.494 24.454 703 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.36 % Favored : 91.48 % Rotamer: Outliers : 3.36 % Allowed : 12.50 % Favored : 84.14 % 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: -1.02 (0.33), residues: 622 helix: -3.05 (0.76), residues: 27 sheet: -0.20 (0.33), residues: 261 loop : -0.79 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP M 50 HIS 0.001 0.000 HIS M 100 PHE 0.009 0.002 PHE H 24 TYR 0.020 0.002 TYR L 91 ARG 0.010 0.001 ARG L 65 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 86 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 408 ARG cc_start: 0.8603 (OUTLIER) cc_final: 0.8261 (ptp-110) REVERT: A 420 ASP cc_start: 0.8291 (m-30) cc_final: 0.8079 (m-30) REVERT: M 19 ARG cc_start: 0.8633 (OUTLIER) cc_final: 0.8375 (mmm160) REVERT: M 27 PHE cc_start: 0.8281 (OUTLIER) cc_final: 0.7210 (m-80) outliers start: 18 outliers final: 10 residues processed: 93 average time/residue: 0.2743 time to fit residues: 30.3411 Evaluate side-chains 92 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 79 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 417 ASN Chi-restraints excluded: chain A residue 474 GLN Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 24 PHE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain M residue 19 ARG Chi-restraints excluded: chain M residue 27 PHE Chi-restraints excluded: chain N residue 13 LEU Chi-restraints excluded: chain N residue 75 THR Chi-restraints excluded: chain N residue 79 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 11 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 14 optimal weight: 4.9990 chunk 59 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 30 optimal weight: 5.9990 chunk 56 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5060 Z= 0.217 Angle : 0.610 6.666 6873 Z= 0.322 Chirality : 0.045 0.164 738 Planarity : 0.005 0.043 883 Dihedral : 5.226 24.535 703 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.91 % Favored : 92.93 % Rotamer: Outliers : 3.17 % Allowed : 13.81 % Favored : 83.02 % 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: -0.90 (0.33), residues: 622 helix: -3.07 (0.77), residues: 26 sheet: -0.13 (0.33), residues: 258 loop : -0.69 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP M 47 HIS 0.001 0.000 HIS M 100 PHE 0.010 0.001 PHE H 24 TYR 0.020 0.001 TYR M 107 ARG 0.011 0.001 ARG L 65 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 408 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.8221 (ptp-110) REVERT: A 420 ASP cc_start: 0.8272 (m-30) cc_final: 0.8060 (m-30) REVERT: A 468 ILE cc_start: 0.9427 (pt) cc_final: 0.9093 (mt) REVERT: H 54 ASP cc_start: 0.8459 (OUTLIER) cc_final: 0.7990 (t70) REVERT: M 27 PHE cc_start: 0.7977 (OUTLIER) cc_final: 0.7088 (m-80) outliers start: 17 outliers final: 10 residues processed: 91 average time/residue: 0.2340 time to fit residues: 25.7862 Evaluate side-chains 93 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 80 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 417 ASN Chi-restraints excluded: chain A residue 474 GLN Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain M residue 27 PHE Chi-restraints excluded: chain N residue 13 LEU Chi-restraints excluded: chain N residue 61 ASP Chi-restraints excluded: chain N residue 75 THR Chi-restraints excluded: chain N residue 79 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 0.0470 chunk 43 optimal weight: 2.9990 chunk 49 optimal weight: 0.0970 chunk 32 optimal weight: 0.7980 chunk 58 optimal weight: 8.9990 chunk 36 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 overall best weight: 0.5276 ------------------------------------------------------------------------------- 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: 0.8282 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5060 Z= 0.183 Angle : 0.592 6.283 6873 Z= 0.310 Chirality : 0.044 0.151 738 Planarity : 0.005 0.049 883 Dihedral : 5.028 25.452 703 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.56 % Favored : 92.28 % Rotamer: Outliers : 2.61 % Allowed : 15.30 % Favored : 82.09 % 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: -0.76 (0.34), residues: 622 helix: -3.05 (0.77), residues: 26 sheet: -0.09 (0.34), residues: 251 loop : -0.55 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 83 HIS 0.001 0.000 HIS M 100 PHE 0.011 0.001 PHE H 24 TYR 0.018 0.001 TYR M 107 ARG 0.013 0.001 ARG L 65 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 408 ARG cc_start: 0.8546 (mtm110) cc_final: 0.8219 (ptp-110) REVERT: A 420 ASP cc_start: 0.8260 (m-30) cc_final: 0.8030 (m-30) REVERT: A 468 ILE cc_start: 0.9408 (pt) cc_final: 0.9090 (mt) REVERT: H 54 ASP cc_start: 0.8435 (OUTLIER) cc_final: 0.7961 (t70) REVERT: M 27 PHE cc_start: 0.7685 (OUTLIER) cc_final: 0.6903 (m-80) outliers start: 14 outliers final: 9 residues processed: 90 average time/residue: 0.2299 time to fit residues: 25.2718 Evaluate side-chains 93 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 82 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 417 ASN Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain M residue 27 PHE Chi-restraints excluded: chain N residue 13 LEU Chi-restraints excluded: chain N residue 21 LEU Chi-restraints excluded: chain N residue 75 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 11 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 5 optimal weight: 0.4980 chunk 46 optimal weight: 0.9980 chunk 53 optimal weight: 0.5980 chunk 56 optimal weight: 0.1980 chunk 51 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5060 Z= 0.196 Angle : 0.601 6.265 6873 Z= 0.315 Chirality : 0.044 0.143 738 Planarity : 0.005 0.054 883 Dihedral : 4.989 24.948 703 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.91 % Favored : 92.93 % Rotamer: Outliers : 2.80 % Allowed : 16.04 % Favored : 81.16 % 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: -0.72 (0.34), residues: 622 helix: -3.11 (0.78), residues: 26 sheet: -0.09 (0.34), residues: 260 loop : -0.49 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP M 47 HIS 0.000 0.000 HIS M 100 PHE 0.011 0.001 PHE H 24 TYR 0.017 0.001 TYR M 80 ARG 0.013 0.001 ARG L 65 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 406 GLU cc_start: 0.8420 (mt-10) cc_final: 0.7988 (mt-10) REVERT: A 408 ARG cc_start: 0.8546 (OUTLIER) cc_final: 0.8209 (ptp-110) REVERT: A 420 ASP cc_start: 0.8237 (m-30) cc_final: 0.7997 (m-30) REVERT: A 468 ILE cc_start: 0.9404 (pt) cc_final: 0.9103 (mt) REVERT: H 54 ASP cc_start: 0.8431 (OUTLIER) cc_final: 0.7956 (t70) REVERT: M 80 TYR cc_start: 0.7778 (m-10) cc_final: 0.7538 (m-10) outliers start: 15 outliers final: 10 residues processed: 86 average time/residue: 0.2405 time to fit residues: 25.2666 Evaluate side-chains 90 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 417 ASN Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain N residue 13 LEU Chi-restraints excluded: chain N residue 21 LEU Chi-restraints excluded: chain N residue 61 ASP Chi-restraints excluded: chain N residue 75 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 23 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 57 optimal weight: 7.9990 chunk 27 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN L 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 5060 Z= 0.353 Angle : 0.670 6.984 6873 Z= 0.353 Chirality : 0.046 0.150 738 Planarity : 0.005 0.055 883 Dihedral : 5.351 24.844 703 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.52 % Favored : 91.32 % Rotamer: Outliers : 2.99 % Allowed : 16.60 % Favored : 80.41 % 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: -0.97 (0.33), residues: 622 helix: -3.16 (0.75), residues: 27 sheet: -0.26 (0.33), residues: 251 loop : -0.65 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 36 HIS 0.002 0.001 HIS M 100 PHE 0.009 0.002 PHE N 34 TYR 0.021 0.002 TYR L 91 ARG 0.013 0.001 ARG L 65 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 81 time to evaluate : 0.811 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 408 ARG cc_start: 0.8568 (OUTLIER) cc_final: 0.8210 (ptp-110) REVERT: M 27 PHE cc_start: 0.8215 (OUTLIER) cc_final: 0.7134 (m-80) REVERT: N 17 GLU cc_start: 0.7500 (pt0) cc_final: 0.7106 (pt0) outliers start: 16 outliers final: 11 residues processed: 88 average time/residue: 0.2716 time to fit residues: 28.7441 Evaluate side-chains 90 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 417 ASN Chi-restraints excluded: chain A residue 474 GLN Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 24 PHE Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain M residue 27 PHE Chi-restraints excluded: chain N residue 61 ASP Chi-restraints excluded: chain N residue 75 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 55 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 14 optimal weight: 4.9990 chunk 44 optimal weight: 0.0870 chunk 7 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 overall best weight: 0.6958 ------------------------------------------------------------------------------- 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: 0.8307 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5060 Z= 0.206 Angle : 0.623 6.357 6873 Z= 0.329 Chirality : 0.045 0.151 738 Planarity : 0.005 0.058 883 Dihedral : 5.126 25.621 703 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.91 % Favored : 92.93 % Rotamer: Outliers : 2.05 % Allowed : 17.54 % Favored : 80.41 % 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: -0.72 (0.34), residues: 622 helix: -2.86 (0.81), residues: 26 sheet: -0.05 (0.33), residues: 264 loop : -0.55 (0.34), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 47 HIS 0.001 0.001 HIS M 100 PHE 0.009 0.001 PHE H 24 TYR 0.019 0.001 TYR M 80 ARG 0.015 0.001 ARG L 65 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1244 Ramachandran restraints generated. 622 Oldfield, 0 Emsley, 622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 408 ARG cc_start: 0.8538 (OUTLIER) cc_final: 0.8196 (ptp-110) REVERT: A 468 ILE cc_start: 0.9400 (pt) cc_final: 0.9085 (mt) REVERT: M 27 PHE cc_start: 0.7855 (OUTLIER) cc_final: 0.6988 (m-80) outliers start: 11 outliers final: 9 residues processed: 86 average time/residue: 0.2340 time to fit residues: 24.3631 Evaluate side-chains 93 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 82 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 417 ASN Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain M residue 27 PHE Chi-restraints excluded: chain N residue 61 ASP Chi-restraints excluded: chain N residue 75 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 48 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 42 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 41 optimal weight: 8.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.3271 r_free = 0.3271 target = 0.070787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.059286 restraints weight = 13916.076| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 2.68 r_work: 0.2906 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5060 Z= 0.231 Angle : 0.643 8.285 6873 Z= 0.335 Chirality : 0.045 0.201 738 Planarity : 0.005 0.059 883 Dihedral : 5.098 25.367 703 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.40 % Favored : 92.44 % Rotamer: Outliers : 2.05 % Allowed : 17.91 % Favored : 80.04 % 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: -0.70 (0.34), residues: 622 helix: -2.60 (0.89), residues: 26 sheet: -0.05 (0.34), residues: 253 loop : -0.54 (0.34), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP M 47 HIS 0.000 0.000 HIS M 100 PHE 0.011 0.001 PHE A 377 TYR 0.019 0.001 TYR M 107 ARG 0.015 0.001 ARG L 65 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1649.75 seconds wall clock time: 30 minutes 54.41 seconds (1854.41 seconds total)