Starting phenix.real_space_refine on Fri Apr 5 16:19:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zh6_14725/04_2024/7zh6_14725_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zh6_14725/04_2024/7zh6_14725.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zh6_14725/04_2024/7zh6_14725.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zh6_14725/04_2024/7zh6_14725.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zh6_14725/04_2024/7zh6_14725_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zh6_14725/04_2024/7zh6_14725_neut_updated.pdb" } resolution = 3.67 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= 0.001 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 2501 2.51 5 N 621 2.21 5 O 627 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 70": "OE1" <-> "OE2" Residue "A ARG 73": "NH1" <-> "NH2" Residue "A ARG 87": "NH1" <-> "NH2" Residue "A ARG 128": "NH1" <-> "NH2" Residue "A ARG 298": "NH1" <-> "NH2" Residue "A GLU 519": "OE1" <-> "OE2" Residue "A GLU 533": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 3771 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 479, 3771 Unusual residues: {'C0R': 1} Classifications: {'peptide': 478, 'undetermined': 1} Link IDs: {'PTRANS': 23, 'TRANS': 454, None: 1} Not linked: pdbres="LYS A 534 " pdbres="C0R A 601 " Chain breaks: 4 Time building chain proxies: 2.48, per 1000 atoms: 0.66 Number of scatterers: 3771 At special positions: 0 Unit cell: (101.64, 63.36, 79.2, 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 627 8.00 N 621 7.00 C 2501 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 51 " - pdb=" SG CYS A 127 " distance=2.03 Simple disulfide: pdb=" SG CYS A 90 " - pdb=" SG CYS A 148 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 1.73 Conformation dependent library (CDL) restraints added in 754.3 milliseconds 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 870 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 20 helices and 1 sheets defined 71.3% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 4 through 10 removed outlier: 3.691A pdb=" N LEU A 8 " --> pdb=" O PHE A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 16 through 42 removed outlier: 4.419A pdb=" N VAL A 39 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N VAL A 40 " --> pdb=" O PHE A 36 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N PHE A 41 " --> pdb=" O VAL A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 62 removed outlier: 3.789A pdb=" N ARG A 62 " --> pdb=" O ALA A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 73 Processing helix chain 'A' and resid 140 through 144 Processing helix chain 'A' and resid 148 through 178 removed outlier: 3.835A pdb=" N ALA A 151 " --> pdb=" O CYS A 148 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N TRP A 152 " --> pdb=" O VAL A 149 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N THR A 157 " --> pdb=" O LEU A 154 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR A 167 " --> pdb=" O GLY A 164 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR A 171 " --> pdb=" O GLY A 168 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLY A 173 " --> pdb=" O PHE A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 200 Processing helix chain 'A' and resid 205 through 233 Processing helix chain 'A' and resid 239 through 262 Proline residue: A 258 - end of helix removed outlier: 3.506A pdb=" N TYR A 262 " --> pdb=" O PRO A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 283 Proline residue: A 277 - end of helix removed outlier: 3.644A pdb=" N LEU A 280 " --> pdb=" O LEU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 295 No H-bonds generated for 'chain 'A' and resid 292 through 295' Processing helix chain 'A' and resid 302 through 310 Processing helix chain 'A' and resid 338 through 342 Processing helix chain 'A' and resid 345 through 371 Processing helix chain 'A' and resid 381 through 400 removed outlier: 3.749A pdb=" N GLU A 390 " --> pdb=" O SER A 386 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LEU A 391 " --> pdb=" O GLY A 387 " (cutoff:3.500A) Proline residue: A 392 - end of helix Processing helix chain 'A' and resid 406 through 425 removed outlier: 3.921A pdb=" N PHE A 410 " --> pdb=" O ARG A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 460 removed outlier: 3.658A pdb=" N LEU A 455 " --> pdb=" O GLU A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 494 Proline residue: A 485 - end of helix removed outlier: 3.946A pdb=" N VAL A 494 " --> pdb=" O ARG A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 516 removed outlier: 3.982A pdb=" N MET A 515 " --> pdb=" O GLY A 511 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N LEU A 516 " --> pdb=" O GLY A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 528 through 531 removed outlier: 3.659A pdb=" N ASP A 531 " --> pdb=" O THR A 528 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 528 through 531' Processing sheet with id= A, first strand: chain 'A' and resid 92 through 94 233 hydrogen bonds defined for protein. 630 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: 0.98 Time building geometry restraints manager: 1.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 621 1.33 - 1.45: 1028 1.45 - 1.57: 2188 1.57 - 1.69: 0 1.69 - 1.81: 30 Bond restraints: 3867 Sorted by residual: bond pdb=" N THR A 297 " pdb=" CA THR A 297 " ideal model delta sigma weight residual 1.458 1.489 -0.032 1.00e-02 1.00e+04 9.98e+00 bond pdb=" N ASN A 335 " pdb=" CA ASN A 335 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.04e-02 9.25e+03 9.62e+00 bond pdb=" N ILE A 311 " pdb=" CA ILE A 311 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.25e-02 6.40e+03 9.10e+00 bond pdb=" N ILE A 264 " pdb=" CA ILE A 264 " ideal model delta sigma weight residual 1.461 1.498 -0.037 1.23e-02 6.61e+03 8.97e+00 bond pdb=" N VAL A 40 " pdb=" CA VAL A 40 " ideal model delta sigma weight residual 1.462 1.497 -0.035 1.18e-02 7.18e+03 8.83e+00 ... (remaining 3862 not shown) Histogram of bond angle deviations from ideal: 98.85 - 105.87: 93 105.87 - 112.90: 2048 112.90 - 119.92: 1382 119.92 - 126.95: 1694 126.95 - 133.97: 52 Bond angle restraints: 5269 Sorted by residual: angle pdb=" N ARG A 128 " pdb=" CA ARG A 128 " pdb=" C ARG A 128 " ideal model delta sigma weight residual 114.62 108.91 5.71 1.14e+00 7.69e-01 2.51e+01 angle pdb=" N PRO A 76 " pdb=" CA PRO A 76 " pdb=" C PRO A 76 " ideal model delta sigma weight residual 114.92 108.98 5.94 1.19e+00 7.06e-01 2.50e+01 angle pdb=" O GLU A 533 " pdb=" C GLU A 533 " pdb=" N LYS A 534 " ideal model delta sigma weight residual 122.03 126.35 -4.32 1.08e+00 8.57e-01 1.60e+01 angle pdb=" C GLU A 533 " pdb=" N LYS A 534 " pdb=" CA LYS A 534 " ideal model delta sigma weight residual 121.70 128.65 -6.95 1.80e+00 3.09e-01 1.49e+01 angle pdb=" N MET A 448 " pdb=" CA MET A 448 " pdb=" C MET A 448 " ideal model delta sigma weight residual 111.71 107.31 4.40 1.15e+00 7.56e-01 1.46e+01 ... (remaining 5264 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.07: 2011 18.07 - 36.14: 212 36.14 - 54.21: 47 54.21 - 72.28: 9 72.28 - 90.35: 7 Dihedral angle restraints: 2286 sinusoidal: 929 harmonic: 1357 Sorted by residual: dihedral pdb=" CB CYS A 90 " pdb=" SG CYS A 90 " pdb=" SG CYS A 148 " pdb=" CB CYS A 148 " ideal model delta sinusoidal sigma weight residual -86.00 -155.72 69.72 1 1.00e+01 1.00e-02 6.27e+01 dihedral pdb=" C ARG A 298 " pdb=" N ARG A 298 " pdb=" CA ARG A 298 " pdb=" CB ARG A 298 " ideal model delta harmonic sigma weight residual -122.60 -131.28 8.68 0 2.50e+00 1.60e-01 1.21e+01 dihedral pdb=" CB GLU A 519 " pdb=" CG GLU A 519 " pdb=" CD GLU A 519 " pdb=" OE1 GLU A 519 " ideal model delta sinusoidal sigma weight residual 0.00 -90.35 90.35 1 3.00e+01 1.11e-03 1.07e+01 ... (remaining 2283 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 429 0.046 - 0.092: 108 0.092 - 0.138: 57 0.138 - 0.184: 17 0.184 - 0.230: 6 Chirality restraints: 617 Sorted by residual: chirality pdb=" CA ARG A 298 " pdb=" N ARG A 298 " pdb=" C ARG A 298 " pdb=" CB ARG A 298 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CA VAL A 333 " pdb=" N VAL A 333 " pdb=" C VAL A 333 " pdb=" CB VAL A 333 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CA LEU A 186 " pdb=" N LEU A 186 " pdb=" C LEU A 186 " pdb=" CB LEU A 186 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.68e-01 ... (remaining 614 not shown) Planarity restraints: 647 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 C0R A 601 " -0.017 2.00e-02 2.50e+03 8.14e-02 8.29e+01 pdb=" C3 C0R A 601 " 0.100 2.00e-02 2.50e+03 pdb=" C4 C0R A 601 " -0.129 2.00e-02 2.50e+03 pdb=" C5 C0R A 601 " -0.027 2.00e-02 2.50e+03 pdb=" C6 C0R A 601 " 0.074 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 183 " -0.019 2.00e-02 2.50e+03 3.77e-02 1.42e+01 pdb=" C VAL A 183 " 0.065 2.00e-02 2.50e+03 pdb=" O VAL A 183 " -0.024 2.00e-02 2.50e+03 pdb=" N ILE A 184 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 262 " 0.012 2.00e-02 2.50e+03 2.43e-02 5.90e+00 pdb=" C TYR A 262 " -0.042 2.00e-02 2.50e+03 pdb=" O TYR A 262 " 0.016 2.00e-02 2.50e+03 pdb=" N PHE A 263 " 0.014 2.00e-02 2.50e+03 ... (remaining 644 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.27: 8 2.27 - 2.92: 1687 2.92 - 3.58: 6092 3.58 - 4.24: 8151 4.24 - 4.90: 13820 Nonbonded interactions: 29758 Sorted by model distance: nonbonded pdb=" CD1 ILE A 523 " pdb=" OE1 GLU A 533 " model vdw 1.607 3.460 nonbonded pdb=" OG1 THR A 28 " pdb=" OH TYR A 185 " model vdw 2.143 2.440 nonbonded pdb=" CE2 PHE A 4 " pdb=" NE ARG A 293 " model vdw 2.154 3.420 nonbonded pdb=" O PHE A 468 " pdb=" OG SER A 471 " model vdw 2.230 2.440 nonbonded pdb=" OE2 GLU A 232 " pdb=" NH1 ARG A 466 " model vdw 2.235 2.520 ... (remaining 29753 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 2.270 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: 8.540 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 15.270 Find NCS groups from input model: 0.110 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:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 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 0.062 3867 Z= 0.370 Angle : 0.900 9.731 5269 Z= 0.586 Chirality : 0.057 0.230 617 Planarity : 0.005 0.081 647 Dihedral : 15.908 90.348 1410 Min Nonbonded Distance : 1.607 Molprobity Statistics. All-atom Clashscore : 26.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 1.26 % Allowed : 28.46 % Favored : 70.28 % 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: 0.99 (0.40), residues: 468 helix: 1.81 (0.28), residues: 353 sheet: None (None), residues: 0 loop : -3.22 (0.46), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 358 HIS 0.001 0.000 HIS A 137 PHE 0.016 0.001 PHE A 41 TYR 0.008 0.001 TYR A 174 ARG 0.002 0.000 ARG A 89 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 103 time to evaluate : 0.426 Fit side-chains outliers start: 5 outliers final: 0 residues processed: 105 average time/residue: 0.1341 time to fit residues: 17.9149 Evaluate side-chains 89 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 39 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 19 optimal weight: 0.3980 chunk 12 optimal weight: 0.5980 chunk 24 optimal weight: 0.0670 chunk 36 optimal weight: 0.9980 chunk 14 optimal weight: 0.5980 chunk 22 optimal weight: 0.2980 chunk 27 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 23 optimal weight: 0.3980 overall best weight: 0.3518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 GLN A 18 GLN A 150 ASN A 414 ASN A 467 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 3867 Z= 0.192 Angle : 0.643 8.401 5269 Z= 0.314 Chirality : 0.041 0.185 617 Planarity : 0.005 0.050 647 Dihedral : 4.509 36.664 579 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 5.29 % Allowed : 25.19 % Favored : 69.52 % 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: 1.21 (0.40), residues: 468 helix: 1.94 (0.28), residues: 357 sheet: None (None), residues: 0 loop : -3.24 (0.46), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 358 HIS 0.001 0.000 HIS A 137 PHE 0.011 0.001 PHE A 213 TYR 0.009 0.001 TYR A 461 ARG 0.002 0.000 ARG A 298 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 98 time to evaluate : 0.420 Fit side-chains REVERT: A 93 TYR cc_start: 0.6270 (m-80) cc_final: 0.5972 (m-10) outliers start: 21 outliers final: 12 residues processed: 109 average time/residue: 0.1128 time to fit residues: 16.3055 Evaluate side-chains 104 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 92 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 520 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 13 optimal weight: 0.4980 chunk 35 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 34 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 ASN ** A 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3867 Z= 0.220 Angle : 0.641 8.373 5269 Z= 0.314 Chirality : 0.041 0.158 617 Planarity : 0.004 0.036 647 Dihedral : 4.356 30.752 579 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 6.05 % Allowed : 24.94 % Favored : 69.02 % 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: 1.25 (0.40), residues: 468 helix: 2.01 (0.28), residues: 356 sheet: None (None), residues: 0 loop : -3.36 (0.46), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 131 HIS 0.001 0.000 HIS A 137 PHE 0.013 0.002 PHE A 41 TYR 0.012 0.002 TYR A 174 ARG 0.002 0.000 ARG A 309 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 100 time to evaluate : 0.434 Fit side-chains REVERT: A 124 LEU cc_start: 0.8141 (tt) cc_final: 0.7455 (mp) outliers start: 24 outliers final: 20 residues processed: 113 average time/residue: 0.1131 time to fit residues: 17.0382 Evaluate side-chains 113 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 93 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 266 ASN Chi-restraints excluded: chain A residue 267 TRP Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 520 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 4 optimal weight: 6.9990 chunk 20 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 45 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 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 247 GLN ** A 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 3867 Z= 0.226 Angle : 0.634 9.075 5269 Z= 0.313 Chirality : 0.040 0.158 617 Planarity : 0.004 0.037 647 Dihedral : 4.548 34.272 579 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 6.80 % Allowed : 25.94 % Favored : 67.25 % 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: 1.14 (0.40), residues: 468 helix: 2.03 (0.28), residues: 353 sheet: None (None), residues: 0 loop : -3.60 (0.45), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 131 HIS 0.001 0.000 HIS A 137 PHE 0.013 0.002 PHE A 34 TYR 0.022 0.002 TYR A 284 ARG 0.002 0.000 ARG A 309 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 94 time to evaluate : 0.436 Fit side-chains REVERT: A 93 TYR cc_start: 0.6979 (m-10) cc_final: 0.6579 (m-10) REVERT: A 124 LEU cc_start: 0.8522 (tt) cc_final: 0.7834 (mp) outliers start: 27 outliers final: 25 residues processed: 108 average time/residue: 0.1075 time to fit residues: 15.5171 Evaluate side-chains 115 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 90 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 152 TRP Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 266 ASN Chi-restraints excluded: chain A residue 267 TRP Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 520 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 33 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 38 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 11 optimal weight: 0.0870 chunk 15 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 GLN ** A 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 3867 Z= 0.206 Angle : 0.615 9.051 5269 Z= 0.302 Chirality : 0.039 0.160 617 Planarity : 0.004 0.039 647 Dihedral : 4.453 32.877 579 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 7.81 % Allowed : 27.46 % Favored : 64.74 % 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: 1.19 (0.40), residues: 468 helix: 2.03 (0.28), residues: 353 sheet: None (None), residues: 0 loop : -3.45 (0.46), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 358 HIS 0.001 0.000 HIS A 137 PHE 0.012 0.001 PHE A 213 TYR 0.008 0.001 TYR A 461 ARG 0.001 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 100 time to evaluate : 0.433 Fit side-chains REVERT: A 93 TYR cc_start: 0.6829 (m-10) cc_final: 0.6152 (m-10) REVERT: A 124 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.7659 (mt) REVERT: A 131 TRP cc_start: 0.8041 (m100) cc_final: 0.7456 (m100) REVERT: A 237 LYS cc_start: 0.8883 (tppt) cc_final: 0.8643 (tppp) outliers start: 31 outliers final: 24 residues processed: 119 average time/residue: 0.1267 time to fit residues: 19.3904 Evaluate side-chains 122 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 97 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 152 TRP Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 226 CYS Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 266 ASN Chi-restraints excluded: chain A residue 267 TRP Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 520 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 11 optimal weight: 0.8980 chunk 45 optimal weight: 5.9990 chunk 37 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 43 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 33 optimal weight: 0.3980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 ASN A 247 GLN A 335 ASN A 414 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3867 Z= 0.204 Angle : 0.622 9.167 5269 Z= 0.305 Chirality : 0.040 0.159 617 Planarity : 0.004 0.040 647 Dihedral : 4.436 33.561 579 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 7.81 % Allowed : 27.71 % Favored : 64.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.40), residues: 468 helix: 1.92 (0.28), residues: 355 sheet: None (None), residues: 0 loop : -3.30 (0.49), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 358 HIS 0.001 0.000 HIS A 137 PHE 0.013 0.001 PHE A 41 TYR 0.022 0.001 TYR A 284 ARG 0.001 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 98 time to evaluate : 0.413 Fit side-chains REVERT: A 128 ARG cc_start: 0.6554 (tpm170) cc_final: 0.6117 (tpm170) REVERT: A 131 TRP cc_start: 0.7938 (m100) cc_final: 0.7443 (m100) REVERT: A 290 GLU cc_start: 0.6660 (OUTLIER) cc_final: 0.6157 (mt-10) outliers start: 31 outliers final: 24 residues processed: 118 average time/residue: 0.1319 time to fit residues: 19.6601 Evaluate side-chains 119 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 94 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 152 TRP Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 226 CYS Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 266 ASN Chi-restraints excluded: chain A residue 267 TRP Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 520 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 25 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 45 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 13 optimal weight: 0.7980 chunk 8 optimal weight: 0.1980 chunk 30 optimal weight: 0.5980 chunk 22 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 3867 Z= 0.206 Angle : 0.630 9.409 5269 Z= 0.309 Chirality : 0.040 0.162 617 Planarity : 0.004 0.043 647 Dihedral : 4.439 33.276 579 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 7.05 % Allowed : 29.22 % Favored : 63.73 % 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: 1.13 (0.40), residues: 468 helix: 1.86 (0.28), residues: 356 sheet: None (None), residues: 0 loop : -3.13 (0.51), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 358 HIS 0.001 0.000 HIS A 137 PHE 0.016 0.001 PHE A 281 TYR 0.009 0.001 TYR A 174 ARG 0.001 0.000 ARG A 239 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 99 time to evaluate : 0.434 Fit side-chains REVERT: A 128 ARG cc_start: 0.6632 (tpm170) cc_final: 0.6164 (tpm170) REVERT: A 131 TRP cc_start: 0.7987 (m100) cc_final: 0.7510 (m100) REVERT: A 290 GLU cc_start: 0.6675 (OUTLIER) cc_final: 0.6146 (mt-10) REVERT: A 527 GLU cc_start: 0.7761 (mm-30) cc_final: 0.7077 (tp30) outliers start: 28 outliers final: 23 residues processed: 117 average time/residue: 0.1297 time to fit residues: 19.4948 Evaluate side-chains 117 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 93 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 93 TYR Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 152 TRP Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 226 CYS Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 266 ASN Chi-restraints excluded: chain A residue 267 TRP Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 520 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 4 optimal weight: 2.9990 chunk 35 optimal weight: 0.3980 chunk 41 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 chunk 25 optimal weight: 0.0010 chunk 18 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 GLN A 414 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 3867 Z= 0.207 Angle : 0.644 9.458 5269 Z= 0.314 Chirality : 0.040 0.161 617 Planarity : 0.004 0.045 647 Dihedral : 4.402 33.473 579 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 7.05 % Allowed : 29.22 % Favored : 63.73 % 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: 1.07 (0.40), residues: 468 helix: 1.81 (0.28), residues: 356 sheet: None (None), residues: 0 loop : -3.12 (0.51), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 358 HIS 0.001 0.000 HIS A 137 PHE 0.014 0.001 PHE A 41 TYR 0.007 0.001 TYR A 174 ARG 0.002 0.000 ARG A 239 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 97 time to evaluate : 0.379 Fit side-chains REVERT: A 34 PHE cc_start: 0.7004 (m-80) cc_final: 0.6764 (m-80) REVERT: A 131 TRP cc_start: 0.8018 (m100) cc_final: 0.7547 (m100) REVERT: A 290 GLU cc_start: 0.6683 (OUTLIER) cc_final: 0.6099 (mt-10) REVERT: A 527 GLU cc_start: 0.7787 (mm-30) cc_final: 0.7047 (tp30) REVERT: A 530 ASP cc_start: 0.7758 (t0) cc_final: 0.7291 (t0) outliers start: 28 outliers final: 25 residues processed: 114 average time/residue: 0.1345 time to fit residues: 19.5404 Evaluate side-chains 118 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 92 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 152 TRP Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 226 CYS Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 266 ASN Chi-restraints excluded: chain A residue 267 TRP Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 520 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 39 optimal weight: 0.6980 chunk 42 optimal weight: 0.3980 chunk 27 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 chunk 21 optimal weight: 0.5980 chunk 31 optimal weight: 0.5980 chunk 46 optimal weight: 0.3980 chunk 43 optimal weight: 1.9990 chunk 37 optimal weight: 0.4980 chunk 3 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 GLN A 414 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.2931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 3867 Z= 0.203 Angle : 0.636 9.514 5269 Z= 0.311 Chirality : 0.040 0.167 617 Planarity : 0.004 0.047 647 Dihedral : 4.367 33.683 579 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 7.56 % Allowed : 29.47 % Favored : 62.97 % 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: 1.12 (0.40), residues: 468 helix: 1.85 (0.28), residues: 356 sheet: None (None), residues: 0 loop : -3.10 (0.51), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 358 HIS 0.001 0.000 HIS A 137 PHE 0.013 0.001 PHE A 41 TYR 0.007 0.001 TYR A 174 ARG 0.002 0.000 ARG A 239 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 97 time to evaluate : 0.433 Fit side-chains REVERT: A 131 TRP cc_start: 0.7936 (m100) cc_final: 0.7567 (m100) REVERT: A 290 GLU cc_start: 0.6599 (OUTLIER) cc_final: 0.6041 (mt-10) REVERT: A 527 GLU cc_start: 0.7728 (mm-30) cc_final: 0.7039 (tp30) REVERT: A 530 ASP cc_start: 0.7735 (t0) cc_final: 0.7268 (t0) outliers start: 30 outliers final: 26 residues processed: 117 average time/residue: 0.1123 time to fit residues: 17.2452 Evaluate side-chains 122 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 95 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 226 CYS Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 266 ASN Chi-restraints excluded: chain A residue 267 TRP Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 520 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 22 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 34 optimal weight: 0.4980 chunk 5 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 HIS A 247 GLN A 414 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 3867 Z= 0.224 Angle : 0.670 9.978 5269 Z= 0.329 Chirality : 0.041 0.162 617 Planarity : 0.004 0.048 647 Dihedral : 4.421 33.340 579 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 6.80 % Allowed : 29.72 % Favored : 63.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.40), residues: 468 helix: 1.80 (0.28), residues: 356 sheet: None (None), residues: 0 loop : -3.20 (0.50), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 152 HIS 0.001 0.000 HIS A 137 PHE 0.020 0.002 PHE A 22 TYR 0.008 0.001 TYR A 174 ARG 0.002 0.000 ARG A 239 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 94 time to evaluate : 0.417 Fit side-chains REVERT: A 34 PHE cc_start: 0.7158 (m-80) cc_final: 0.6943 (m-80) REVERT: A 131 TRP cc_start: 0.8030 (m100) cc_final: 0.7597 (m100) REVERT: A 290 GLU cc_start: 0.6667 (OUTLIER) cc_final: 0.6098 (mt-10) REVERT: A 527 GLU cc_start: 0.7814 (mm-30) cc_final: 0.7115 (tp30) REVERT: A 530 ASP cc_start: 0.7757 (t0) cc_final: 0.7246 (t0) outliers start: 27 outliers final: 25 residues processed: 110 average time/residue: 0.1186 time to fit residues: 17.0732 Evaluate side-chains 119 residues out of total 397 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 93 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 152 TRP Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 226 CYS Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 266 ASN Chi-restraints excluded: chain A residue 267 TRP Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 520 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 6 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 28 optimal weight: 0.0010 chunk 27 optimal weight: 4.9990 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.162187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.142118 restraints weight = 6985.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.146618 restraints weight = 3650.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.149715 restraints weight = 2246.116| |-----------------------------------------------------------------------------| r_work (final): 0.3868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 3867 Z= 0.220 Angle : 0.657 9.709 5269 Z= 0.324 Chirality : 0.041 0.163 617 Planarity : 0.004 0.046 647 Dihedral : 4.428 33.605 579 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 6.80 % Allowed : 29.97 % Favored : 63.22 % 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: 1.06 (0.40), residues: 468 helix: 1.83 (0.28), residues: 356 sheet: None (None), residues: 0 loop : -3.21 (0.49), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 152 HIS 0.001 0.000 HIS A 137 PHE 0.017 0.001 PHE A 22 TYR 0.008 0.001 TYR A 174 ARG 0.002 0.000 ARG A 239 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1226.34 seconds wall clock time: 22 minutes 44.53 seconds (1364.53 seconds total)