Starting phenix.real_space_refine on Tue Sep 24 10:01:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ug4_42213/09_2024/8ug4_42213.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ug4_42213/09_2024/8ug4_42213.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ug4_42213/09_2024/8ug4_42213.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ug4_42213/09_2024/8ug4_42213.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ug4_42213/09_2024/8ug4_42213.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ug4_42213/09_2024/8ug4_42213.cif" } resolution = 3.02 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 52 5.16 5 C 5182 2.51 5 N 1270 2.21 5 O 1298 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 7802 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3901 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 486, 3891 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 8, 'TRANS': 477} Chain breaks: 3 Conformer: "B" Number of residues, atoms: 486, 3891 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 8, 'TRANS': 477} Chain breaks: 3 bond proxies already assigned to first conformer: 3975 Restraints were copied for chains: B Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AHIS A 567 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS A 567 " occ=0.50 residue: pdb=" N AHIS B 567 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS B 567 " occ=0.50 Time building chain proxies: 8.12, per 1000 atoms: 1.04 Number of scatterers: 7802 At special positions: 0 Unit cell: (100.43, 92.13, 90.47, 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 52 16.00 O 1298 8.00 N 1270 7.00 C 5182 6.00 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: 1.85 Conformation dependent library (CDL) restraints added in 1.9 seconds 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1828 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 2 sheets defined 77.8% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 57 through 86 Processing helix chain 'A' and resid 93 through 119 Processing helix chain 'A' and resid 122 through 136 Processing helix chain 'A' and resid 158 through 186 Processing helix chain 'A' and resid 190 through 213 removed outlier: 3.765A pdb=" N ILE A 194 " --> pdb=" O LYS A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 268 removed outlier: 3.890A pdb=" N ALA A 251 " --> pdb=" O ALA A 247 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS A 252 " --> pdb=" O LYS A 248 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA A 253 " --> pdb=" O GLN A 249 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N HIS A 254 " --> pdb=" O GLU A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 Processing helix chain 'A' and resid 314 through 340 removed outlier: 3.632A pdb=" N PHE A 318 " --> pdb=" O ASP A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 389 removed outlier: 3.589A pdb=" N PHE A 389 " --> pdb=" O MET A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 395 Processing helix chain 'A' and resid 395 through 425 Processing helix chain 'A' and resid 436 through 467 removed outlier: 4.273A pdb=" N GLU A 440 " --> pdb=" O GLU A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 499 Processing helix chain 'A' and resid 504 through 510 Processing helix chain 'A' and resid 513 through 535 Processing helix chain 'A' and resid 544 through 549 Processing helix chain 'A' and resid 563 through 579 Processing helix chain 'B' and resid 57 through 86 Processing helix chain 'B' and resid 93 through 119 Processing helix chain 'B' and resid 122 through 136 Processing helix chain 'B' and resid 158 through 186 Processing helix chain 'B' and resid 190 through 213 removed outlier: 3.765A pdb=" N ILE B 194 " --> pdb=" O LYS B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 268 removed outlier: 3.890A pdb=" N ALA B 251 " --> pdb=" O ALA B 247 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS B 252 " --> pdb=" O LYS B 248 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA B 253 " --> pdb=" O GLN B 249 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N HIS B 254 " --> pdb=" O GLU B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 312 Processing helix chain 'B' and resid 314 through 340 removed outlier: 3.632A pdb=" N PHE B 318 " --> pdb=" O ASP B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 389 removed outlier: 3.589A pdb=" N PHE B 389 " --> pdb=" O MET B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 395 Processing helix chain 'B' and resid 395 through 425 Processing helix chain 'B' and resid 436 through 467 removed outlier: 4.272A pdb=" N GLU B 440 " --> pdb=" O GLU B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 499 Processing helix chain 'B' and resid 504 through 510 Processing helix chain 'B' and resid 513 through 535 Processing helix chain 'B' and resid 544 through 549 Processing helix chain 'B' and resid 563 through 579 Processing sheet with id=AA1, first strand: chain 'A' and resid 428 through 429 Processing sheet with id=AA2, first strand: chain 'B' and resid 428 through 429 614 hydrogen bonds defined for protein. 1820 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.32 Time building geometry restraints manager: 2.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1357 1.33 - 1.45: 2158 1.45 - 1.57: 4401 1.57 - 1.69: 0 1.69 - 1.81: 82 Bond restraints: 7998 Sorted by residual: bond pdb=" CA SER A 396 " pdb=" CB SER A 396 " ideal model delta sigma weight residual 1.531 1.481 0.049 1.59e-02 3.96e+03 9.65e+00 bond pdb=" CA SER B 396 " pdb=" CB SER B 396 " ideal model delta sigma weight residual 1.531 1.481 0.049 1.59e-02 3.96e+03 9.65e+00 bond pdb=" N ILE B 146 " pdb=" CA ILE B 146 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.12e-02 7.97e+03 9.61e+00 bond pdb=" N ILE A 146 " pdb=" CA ILE A 146 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.12e-02 7.97e+03 9.59e+00 bond pdb=" N VAL B 219 " pdb=" CA VAL B 219 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.89e+00 ... (remaining 7993 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.35: 10110 1.35 - 2.70: 551 2.70 - 4.05: 124 4.05 - 5.40: 25 5.40 - 6.75: 8 Bond angle restraints: 10818 Sorted by residual: angle pdb=" CA BHIS A 567 " pdb=" CB BHIS A 567 " pdb=" CG BHIS A 567 " ideal model delta sigma weight residual 113.80 107.05 6.75 1.00e+00 1.00e+00 4.56e+01 angle pdb=" CA BHIS B 567 " pdb=" CB BHIS B 567 " pdb=" CG BHIS B 567 " ideal model delta sigma weight residual 113.80 107.06 6.74 1.00e+00 1.00e+00 4.54e+01 angle pdb=" N LEU B 400 " pdb=" CA LEU B 400 " pdb=" C LEU B 400 " ideal model delta sigma weight residual 111.14 106.86 4.28 1.08e+00 8.57e-01 1.57e+01 angle pdb=" N VAL B 437 " pdb=" CA VAL B 437 " pdb=" C VAL B 437 " ideal model delta sigma weight residual 112.76 107.75 5.01 1.27e+00 6.20e-01 1.55e+01 angle pdb=" N LEU A 400 " pdb=" CA LEU A 400 " pdb=" C LEU A 400 " ideal model delta sigma weight residual 111.14 106.88 4.26 1.08e+00 8.57e-01 1.55e+01 ... (remaining 10813 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 4105 17.85 - 35.69: 435 35.69 - 53.53: 66 53.53 - 71.38: 12 71.38 - 89.22: 8 Dihedral angle restraints: 4626 sinusoidal: 1784 harmonic: 2842 Sorted by residual: dihedral pdb=" CD ARG A 133 " pdb=" NE ARG A 133 " pdb=" CZ ARG A 133 " pdb=" NH1 ARG A 133 " ideal model delta sinusoidal sigma weight residual 0.00 65.82 -65.82 1 1.00e+01 1.00e-02 5.67e+01 dihedral pdb=" CD ARG B 133 " pdb=" NE ARG B 133 " pdb=" CZ ARG B 133 " pdb=" NH1 ARG B 133 " ideal model delta sinusoidal sigma weight residual 0.00 65.78 -65.78 1 1.00e+01 1.00e-02 5.66e+01 dihedral pdb=" N LEU A 306 " pdb=" C LEU A 306 " pdb=" CA LEU A 306 " pdb=" CB LEU A 306 " ideal model delta harmonic sigma weight residual 122.80 113.75 9.05 0 2.50e+00 1.60e-01 1.31e+01 ... (remaining 4623 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1064 0.066 - 0.132: 141 0.132 - 0.198: 35 0.198 - 0.264: 8 0.264 - 0.331: 4 Chirality restraints: 1252 Sorted by residual: chirality pdb=" CA LEU A 306 " pdb=" N LEU A 306 " pdb=" C LEU A 306 " pdb=" CB LEU A 306 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.73e+00 chirality pdb=" CA LEU B 306 " pdb=" N LEU B 306 " pdb=" C LEU B 306 " pdb=" CB LEU B 306 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.70e+00 chirality pdb=" CA LEU B 400 " pdb=" N LEU B 400 " pdb=" C LEU B 400 " pdb=" CB LEU B 400 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.27 2.00e-01 2.50e+01 1.89e+00 ... (remaining 1249 not shown) Planarity restraints: 1294 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 133 " -1.003 9.50e-02 1.11e+02 4.49e-01 1.22e+02 pdb=" NE ARG A 133 " 0.060 2.00e-02 2.50e+03 pdb=" CZ ARG A 133 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG A 133 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 133 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 133 " -1.002 9.50e-02 1.11e+02 4.49e-01 1.22e+02 pdb=" NE ARG B 133 " 0.060 2.00e-02 2.50e+03 pdb=" CZ ARG B 133 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG B 133 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 133 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA BHIS B 567 " -0.024 2.00e-02 2.50e+03 4.85e-02 2.35e+01 pdb=" C BHIS B 567 " 0.084 2.00e-02 2.50e+03 pdb=" O BHIS B 567 " -0.031 2.00e-02 2.50e+03 pdb=" N SER B 568 " -0.029 2.00e-02 2.50e+03 ... (remaining 1291 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 875 2.75 - 3.28: 8130 3.28 - 3.82: 14096 3.82 - 4.36: 15823 4.36 - 4.90: 27639 Nonbonded interactions: 66563 Sorted by model distance: nonbonded pdb=" O PRO B 512 " pdb=" OH TYR B 580 " model vdw 2.207 3.040 nonbonded pdb=" O PRO A 512 " pdb=" OH TYR A 580 " model vdw 2.208 3.040 nonbonded pdb=" O ILE A 99 " pdb=" OG SER A 103 " model vdw 2.299 3.040 nonbonded pdb=" O ILE B 99 " pdb=" OG SER B 103 " model vdw 2.299 3.040 nonbonded pdb=" O ASP A 314 " pdb=" OG1 THR A 317 " model vdw 2.350 3.040 ... (remaining 66558 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 47 through 566 or resid 568 through 583)) selection = (chain 'B' and (resid 47 through 566 or resid 568 through 583)) } 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=0.50 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: 2.190 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: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 24.810 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 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 : 0.006 0.049 7998 Z= 0.364 Angle : 0.726 6.749 10818 Z= 0.505 Chirality : 0.055 0.331 1252 Planarity : 0.018 0.449 1294 Dihedral : 14.721 89.224 2798 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % 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: 1.83 (0.27), residues: 962 helix: 2.10 (0.18), residues: 724 sheet: None (None), residues: 0 loop : -1.70 (0.38), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 338 HIS 0.005 0.001 HIS B 578 PHE 0.018 0.001 PHE B 542 TYR 0.017 0.002 TYR B 101 ARG 0.002 0.000 ARG B 565 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 0.887 Fit side-chains REVERT: A 181 PHE cc_start: 0.7867 (t80) cc_final: 0.7575 (t80) REVERT: A 436 GLU cc_start: 0.6713 (tp30) cc_final: 0.6420 (tp30) REVERT: B 181 PHE cc_start: 0.7825 (t80) cc_final: 0.7568 (t80) REVERT: B 436 GLU cc_start: 0.6691 (tp30) cc_final: 0.6418 (tp30) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.2197 time to fit residues: 35.8211 Evaluate side-chains 101 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 40 optimal weight: 7.9990 chunk 24 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 75 optimal weight: 5.9990 chunk 29 optimal weight: 10.0000 chunk 45 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 87 optimal weight: 0.8980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 567 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.1099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 7998 Z= 0.237 Angle : 0.486 7.730 10818 Z= 0.273 Chirality : 0.040 0.231 1252 Planarity : 0.003 0.030 1294 Dihedral : 3.545 14.576 1058 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.71 % Allowed : 6.53 % Favored : 92.76 % 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: 2.49 (0.26), residues: 962 helix: 2.57 (0.18), residues: 722 sheet: None (None), residues: 0 loop : -1.39 (0.39), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 239 HIS 0.003 0.001 HIS A 209 PHE 0.012 0.001 PHE A 63 TYR 0.018 0.002 TYR A 101 ARG 0.002 0.000 ARG A 133 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 111 time to evaluate : 1.140 Fit side-chains REVERT: A 181 PHE cc_start: 0.7792 (t80) cc_final: 0.7581 (t80) REVERT: B 181 PHE cc_start: 0.7755 (t80) cc_final: 0.7555 (t80) REVERT: B 430 ARG cc_start: 0.8007 (ptt90) cc_final: 0.7688 (ptt180) outliers start: 6 outliers final: 4 residues processed: 113 average time/residue: 0.2178 time to fit residues: 33.2675 Evaluate side-chains 108 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 104 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 432 HIS Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 432 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 48 optimal weight: 10.0000 chunk 27 optimal weight: 7.9990 chunk 72 optimal weight: 0.9980 chunk 59 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 87 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 chunk 77 optimal weight: 0.0770 chunk 86 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 70 optimal weight: 0.9980 overall best weight: 0.7338 ------------------------------------------------------------------------------- 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: 0.8325 moved from start: 0.1342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 7998 Z= 0.155 Angle : 0.437 6.495 10818 Z= 0.247 Chirality : 0.037 0.176 1252 Planarity : 0.003 0.032 1294 Dihedral : 3.352 12.930 1058 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.07 % Allowed : 8.55 % Favored : 90.38 % 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: 2.86 (0.26), residues: 962 helix: 2.83 (0.18), residues: 722 sheet: None (None), residues: 0 loop : -1.19 (0.38), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 239 HIS 0.002 0.001 HIS A 232 PHE 0.010 0.001 PHE A 542 TYR 0.015 0.001 TYR A 101 ARG 0.004 0.000 ARG A 430 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 109 time to evaluate : 0.879 Fit side-chains REVERT: A 430 ARG cc_start: 0.7978 (ptt90) cc_final: 0.7555 (ptt180) REVERT: B 430 ARG cc_start: 0.7989 (ptt90) cc_final: 0.7700 (ptt180) outliers start: 9 outliers final: 5 residues processed: 113 average time/residue: 0.1901 time to fit residues: 29.5710 Evaluate side-chains 106 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 101 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 432 HIS Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 432 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 45 optimal weight: 8.9990 chunk 9 optimal weight: 0.0470 chunk 41 optimal weight: 6.9990 chunk 58 optimal weight: 4.9990 chunk 87 optimal weight: 0.7980 chunk 92 optimal weight: 8.9990 chunk 83 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 overall best weight: 1.3282 ------------------------------------------------------------------------------- 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: 0.8358 moved from start: 0.1501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 7998 Z= 0.209 Angle : 0.443 4.384 10818 Z= 0.252 Chirality : 0.038 0.160 1252 Planarity : 0.003 0.033 1294 Dihedral : 3.438 14.062 1058 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.07 % Allowed : 9.38 % Favored : 89.55 % 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: 2.76 (0.26), residues: 962 helix: 2.74 (0.18), residues: 722 sheet: None (None), residues: 0 loop : -1.17 (0.38), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 239 HIS 0.003 0.001 HIS B 209 PHE 0.012 0.001 PHE A 63 TYR 0.018 0.001 TYR A 101 ARG 0.003 0.000 ARG A 430 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 104 time to evaluate : 0.805 Fit side-chains REVERT: A 430 ARG cc_start: 0.8051 (ptt90) cc_final: 0.7589 (ptt180) REVERT: B 430 ARG cc_start: 0.8054 (ptt90) cc_final: 0.7706 (ptt180) outliers start: 9 outliers final: 4 residues processed: 109 average time/residue: 0.2137 time to fit residues: 32.2978 Evaluate side-chains 106 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 102 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 539 SER Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 539 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 69 optimal weight: 9.9990 chunk 38 optimal weight: 2.9990 chunk 79 optimal weight: 6.9990 chunk 64 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 chunk 47 optimal weight: 5.9990 chunk 83 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 261 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 7998 Z= 0.301 Angle : 0.490 4.821 10818 Z= 0.277 Chirality : 0.040 0.151 1252 Planarity : 0.003 0.035 1294 Dihedral : 3.614 15.097 1058 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.31 % Allowed : 9.62 % Favored : 89.07 % 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: 2.44 (0.26), residues: 962 helix: 2.45 (0.18), residues: 726 sheet: None (None), residues: 0 loop : -1.15 (0.38), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 239 HIS 0.004 0.001 HIS A 209 PHE 0.013 0.001 PHE A 63 TYR 0.020 0.002 TYR A 453 ARG 0.003 0.000 ARG A 430 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 103 time to evaluate : 0.801 Fit side-chains REVERT: B 260 LYS cc_start: 0.7138 (mmtt) cc_final: 0.6786 (mmmt) REVERT: B 261 GLN cc_start: 0.7158 (mm-40) cc_final: 0.6953 (mm-40) outliers start: 11 outliers final: 8 residues processed: 109 average time/residue: 0.2259 time to fit residues: 33.8968 Evaluate side-chains 109 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 101 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 539 SER Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 539 SER Chi-restraints excluded: chain B residue 554 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 54 optimal weight: 4.9990 chunk 22 optimal weight: 6.9990 chunk 92 optimal weight: 8.9990 chunk 77 optimal weight: 10.0000 chunk 43 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 30 optimal weight: 7.9990 chunk 48 optimal weight: 3.9990 chunk 89 optimal weight: 0.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 7998 Z= 0.294 Angle : 0.482 4.641 10818 Z= 0.272 Chirality : 0.040 0.143 1252 Planarity : 0.003 0.035 1294 Dihedral : 3.644 15.703 1058 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.43 % Allowed : 10.21 % Favored : 88.36 % 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: 2.38 (0.26), residues: 962 helix: 2.38 (0.18), residues: 726 sheet: None (None), residues: 0 loop : -1.08 (0.38), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 338 HIS 0.004 0.001 HIS A 209 PHE 0.013 0.001 PHE A 63 TYR 0.020 0.002 TYR B 453 ARG 0.004 0.000 ARG A 133 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 96 time to evaluate : 0.924 Fit side-chains REVERT: A 260 LYS cc_start: 0.7099 (mmtt) cc_final: 0.6763 (mmmt) REVERT: A 261 GLN cc_start: 0.7152 (mm-40) cc_final: 0.6938 (mm-40) REVERT: B 260 LYS cc_start: 0.7133 (mmtt) cc_final: 0.6800 (mmmt) REVERT: B 430 ARG cc_start: 0.8123 (ptt90) cc_final: 0.7722 (ptt180) outliers start: 12 outliers final: 7 residues processed: 101 average time/residue: 0.2113 time to fit residues: 29.2936 Evaluate side-chains 100 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 93 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 539 SER Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 539 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 10 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 67 optimal weight: 0.8980 chunk 78 optimal weight: 7.9990 chunk 51 optimal weight: 0.9990 chunk 92 optimal weight: 0.7980 chunk 57 optimal weight: 6.9990 chunk 56 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 36 optimal weight: 4.9990 chunk 55 optimal weight: 0.7980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 HIS B 311 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 7998 Z= 0.167 Angle : 0.421 4.536 10818 Z= 0.240 Chirality : 0.037 0.125 1252 Planarity : 0.003 0.035 1294 Dihedral : 3.414 15.494 1058 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.71 % Allowed : 11.40 % Favored : 87.89 % 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: 2.83 (0.26), residues: 962 helix: 2.74 (0.18), residues: 722 sheet: None (None), residues: 0 loop : -0.97 (0.38), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 338 HIS 0.002 0.000 HIS B 209 PHE 0.010 0.001 PHE A 63 TYR 0.015 0.001 TYR A 101 ARG 0.004 0.000 ARG A 430 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 96 time to evaluate : 0.818 Fit side-chains REVERT: A 260 LYS cc_start: 0.7063 (mmtt) cc_final: 0.6793 (mmmt) REVERT: B 260 LYS cc_start: 0.7125 (mmtt) cc_final: 0.6812 (mmmt) REVERT: B 430 ARG cc_start: 0.8063 (ptt90) cc_final: 0.7726 (ptt180) outliers start: 6 outliers final: 4 residues processed: 98 average time/residue: 0.2109 time to fit residues: 27.8860 Evaluate side-chains 98 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 94 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 266 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 27 optimal weight: 7.9990 chunk 18 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 8 optimal weight: 10.0000 chunk 72 optimal weight: 0.7980 chunk 84 optimal weight: 0.5980 chunk 88 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN B 261 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 7998 Z= 0.161 Angle : 0.416 5.050 10818 Z= 0.236 Chirality : 0.037 0.122 1252 Planarity : 0.003 0.035 1294 Dihedral : 3.367 16.052 1058 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.71 % Allowed : 11.05 % Favored : 88.24 % 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: 2.93 (0.26), residues: 962 helix: 2.82 (0.18), residues: 722 sheet: None (None), residues: 0 loop : -0.97 (0.38), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 338 HIS 0.002 0.000 HIS A 232 PHE 0.011 0.001 PHE A 389 TYR 0.015 0.001 TYR A 101 ARG 0.004 0.000 ARG A 430 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 95 time to evaluate : 0.922 Fit side-chains REVERT: A 260 LYS cc_start: 0.7064 (mmtt) cc_final: 0.6807 (mmmt) REVERT: B 261 GLN cc_start: 0.7132 (mm-40) cc_final: 0.6889 (mm-40) REVERT: B 430 ARG cc_start: 0.8076 (ptt90) cc_final: 0.7715 (ptt180) outliers start: 6 outliers final: 4 residues processed: 97 average time/residue: 0.2146 time to fit residues: 28.1128 Evaluate side-chains 98 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 94 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 337 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 0.7980 chunk 88 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 37 optimal weight: 0.0970 chunk 67 optimal weight: 0.6980 chunk 26 optimal weight: 20.0000 chunk 77 optimal weight: 8.9990 chunk 81 optimal weight: 0.8980 chunk 85 optimal weight: 0.5980 chunk 56 optimal weight: 10.0000 chunk 91 optimal weight: 3.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- 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: 0.8321 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 7998 Z= 0.144 Angle : 0.414 5.917 10818 Z= 0.233 Chirality : 0.036 0.119 1252 Planarity : 0.003 0.035 1294 Dihedral : 3.319 16.506 1058 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.71 % Allowed : 11.28 % Favored : 88.00 % 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: 3.07 (0.26), residues: 962 helix: 2.91 (0.18), residues: 724 sheet: None (None), residues: 0 loop : -0.93 (0.38), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 338 HIS 0.002 0.000 HIS A 232 PHE 0.009 0.001 PHE A 493 TYR 0.015 0.001 TYR A 101 ARG 0.004 0.000 ARG A 430 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 98 time to evaluate : 0.958 Fit side-chains REVERT: A 260 LYS cc_start: 0.6994 (mmtt) cc_final: 0.6738 (mmmt) REVERT: A 261 GLN cc_start: 0.7416 (mm-40) cc_final: 0.6973 (mm-40) REVERT: B 430 ARG cc_start: 0.8046 (ptt90) cc_final: 0.7706 (ptt180) outliers start: 6 outliers final: 3 residues processed: 101 average time/residue: 0.2255 time to fit residues: 30.6389 Evaluate side-chains 98 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 95 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 432 HIS Chi-restraints excluded: chain B residue 266 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 63 optimal weight: 0.6980 chunk 95 optimal weight: 0.9980 chunk 88 optimal weight: 4.9990 chunk 76 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 chunk 60 optimal weight: 0.9980 chunk 81 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 261 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7998 Z= 0.167 Angle : 0.429 7.449 10818 Z= 0.241 Chirality : 0.037 0.143 1252 Planarity : 0.003 0.035 1294 Dihedral : 3.338 17.450 1058 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.36 % Allowed : 12.11 % Favored : 87.53 % 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: 3.05 (0.26), residues: 962 helix: 2.91 (0.18), residues: 724 sheet: None (None), residues: 0 loop : -0.96 (0.38), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 422 HIS 0.002 0.000 HIS A 232 PHE 0.010 0.001 PHE A 493 TYR 0.016 0.001 TYR A 101 ARG 0.004 0.000 ARG A 430 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 93 time to evaluate : 0.857 Fit side-chains REVERT: A 260 LYS cc_start: 0.7079 (mmtt) cc_final: 0.6808 (mmmt) REVERT: B 261 GLN cc_start: 0.7152 (mm-40) cc_final: 0.6915 (mm-40) REVERT: B 430 ARG cc_start: 0.8055 (ptt90) cc_final: 0.7703 (ptt180) outliers start: 3 outliers final: 2 residues processed: 94 average time/residue: 0.2150 time to fit residues: 27.4342 Evaluate side-chains 95 residues out of total 838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 93 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain B residue 337 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 23 optimal weight: 0.9990 chunk 70 optimal weight: 5.9990 chunk 11 optimal weight: 0.6980 chunk 21 optimal weight: 0.2980 chunk 76 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 78 optimal weight: 4.9990 chunk 9 optimal weight: 8.9990 chunk 14 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 = 0.3683 r_free = 0.3683 target = 0.139505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.099256 restraints weight = 25574.840| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 3.63 r_work: 0.2874 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2756 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2756 r_free = 0.2756 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2755 r_free = 0.2755 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2755 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7998 Z= 0.178 Angle : 0.433 7.204 10818 Z= 0.244 Chirality : 0.037 0.125 1252 Planarity : 0.003 0.035 1294 Dihedral : 3.369 17.336 1058 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.36 % Allowed : 12.11 % Favored : 87.53 % 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: 3.01 (0.26), residues: 962 helix: 2.87 (0.18), residues: 724 sheet: None (None), residues: 0 loop : -0.96 (0.38), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 422 HIS 0.002 0.001 HIS A 209 PHE 0.010 0.001 PHE A 63 TYR 0.016 0.001 TYR A 101 ARG 0.004 0.000 ARG A 430 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1775.95 seconds wall clock time: 32 minutes 32.93 seconds (1952.93 seconds total)