Starting phenix.real_space_refine on Sun Mar 10 18:18:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ouc_20202/03_2024/6ouc_20202.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ouc_20202/03_2024/6ouc_20202.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ouc_20202/03_2024/6ouc_20202.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ouc_20202/03_2024/6ouc_20202.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ouc_20202/03_2024/6ouc_20202.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ouc_20202/03_2024/6ouc_20202.pdb" } resolution = 2.8 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= -0.001 sd= 0.041 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 15 5.16 5 C 2421 2.51 5 N 642 2.21 5 O 820 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 409": "NH1" <-> "NH2" Residue "A ARG 495": "NH1" <-> "NH2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 3899 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 608, 3899 Unusual residues: {' ZN': 1} Classifications: {'peptide': 483, 'undetermined': 1, 'water': 124} Link IDs: {'PTRANS': 46, 'TRANS': 436, None: 125} Not linked: pdbres="GLY A 533 " pdbres=" ZN A 601 " Not linked: pdbres=" ZN A 601 " pdbres="HOH A 701 " Not linked: pdbres="HOH A 701 " pdbres="HOH A 702 " Not linked: pdbres="HOH A 702 " pdbres="HOH A 703 " Not linked: pdbres="HOH A 703 " pdbres="HOH A 704 " ... (remaining 120 not shown) Chain breaks: 1 Time building chain proxies: 2.55, per 1000 atoms: 0.65 Number of scatterers: 3899 At special positions: 0 Unit cell: (95.23, 95.23, 78.11, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 15 16.00 O 820 8.00 N 642 7.00 C 2421 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 - 3.50 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: 1.43 Conformation dependent library (CDL) restraints added in 803.0 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 601 " pdb="ZN ZN A 601 " - pdb=" ND1 HIS A 299 " pdb="ZN ZN A 601 " - pdb=" NE2 HIS A 293 " 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 900 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 9 sheets defined 6.2% alpha, 28.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 82 through 85 removed outlier: 3.522A pdb=" N LEU A 85 " --> pdb=" O GLY A 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 82 through 85' Processing helix chain 'A' and resid 86 through 93 Processing helix chain 'A' and resid 136 through 141 removed outlier: 3.628A pdb=" N THR A 139 " --> pdb=" O GLN A 136 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE A 141 " --> pdb=" O ILE A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 467 Processing sheet with id=AA1, first strand: chain 'A' and resid 57 through 58 Processing sheet with id=AA2, first strand: chain 'A' and resid 57 through 58 removed outlier: 4.053A pdb=" N SER A 199 " --> pdb=" O ALA A 110 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 80 removed outlier: 6.342A pdb=" N ALA A 180 " --> pdb=" O LEU A 76 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ASN A 78 " --> pdb=" O ILE A 178 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ILE A 178 " --> pdb=" O ASN A 78 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 167 through 168 Processing sheet with id=AA5, first strand: chain 'A' and resid 115 through 116 Processing sheet with id=AA6, first strand: chain 'A' and resid 450 through 453 removed outlier: 4.853A pdb=" N MET A 249 " --> pdb=" O VAL A 509 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 450 through 453 removed outlier: 4.743A pdb=" N MET A 499 " --> pdb=" O LEU A 434 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N PHE A 489 " --> pdb=" O TYR A 479 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N VAL A 474 " --> pdb=" O TRP A 522 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N TRP A 522 " --> pdb=" O VAL A 474 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LEU A 476 " --> pdb=" O ASP A 520 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 265 through 266 removed outlier: 4.565A pdb=" N ARG A 265 " --> pdb=" O GLN A 273 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 352 through 360 removed outlier: 7.700A pdb=" N ARG A 331 " --> pdb=" O LEU A 396 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N LEU A 396 " --> pdb=" O ARG A 331 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N PHE A 333 " --> pdb=" O VAL A 394 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ARG A 339 " --> pdb=" O PRO A 388 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N PHE A 286 " --> pdb=" O PHE A 391 " (cutoff:3.500A) 100 hydrogen bonds defined for protein. 258 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.09 Time building geometry restraints manager: 1.52 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: 969 1.33 - 1.45: 735 1.45 - 1.56: 2154 1.56 - 1.68: 0 1.68 - 1.80: 25 Bond restraints: 3883 Sorted by residual: bond pdb=" CA TYR A 214 " pdb=" C TYR A 214 " ideal model delta sigma weight residual 1.520 1.489 0.032 1.22e-02 6.72e+03 6.77e+00 bond pdb=" CA GLN A 170 " pdb=" C GLN A 170 " ideal model delta sigma weight residual 1.528 1.561 -0.033 1.33e-02 5.65e+03 6.30e+00 bond pdb=" N TRP A 378 " pdb=" CA TRP A 378 " ideal model delta sigma weight residual 1.459 1.430 0.029 1.24e-02 6.50e+03 5.52e+00 bond pdb=" CG LEU A 455 " pdb=" CD1 LEU A 455 " ideal model delta sigma weight residual 1.521 1.447 0.074 3.30e-02 9.18e+02 5.06e+00 bond pdb=" CA GLN A 170 " pdb=" CB GLN A 170 " ideal model delta sigma weight residual 1.527 1.498 0.029 1.44e-02 4.82e+03 3.96e+00 ... (remaining 3878 not shown) Histogram of bond angle deviations from ideal: 99.15 - 106.14: 186 106.14 - 113.13: 1971 113.13 - 120.12: 1399 120.12 - 127.11: 1698 127.11 - 134.09: 61 Bond angle restraints: 5315 Sorted by residual: angle pdb=" N GLY A 62 " pdb=" CA GLY A 62 " pdb=" C GLY A 62 " ideal model delta sigma weight residual 112.73 129.70 -16.97 1.20e+00 6.94e-01 2.00e+02 angle pdb=" N THR A 213 " pdb=" CA THR A 213 " pdb=" C THR A 213 " ideal model delta sigma weight residual 112.68 125.51 -12.83 1.33e+00 5.65e-01 9.31e+01 angle pdb=" N ASN A 297 " pdb=" CA ASN A 297 " pdb=" C ASN A 297 " ideal model delta sigma weight residual 111.28 101.34 9.94 1.09e+00 8.42e-01 8.32e+01 angle pdb=" N TYR A 301 " pdb=" CA TYR A 301 " pdb=" C TYR A 301 " ideal model delta sigma weight residual 111.02 121.74 -10.72 1.25e+00 6.40e-01 7.36e+01 angle pdb=" N LEU A 300 " pdb=" CA LEU A 300 " pdb=" C LEU A 300 " ideal model delta sigma weight residual 114.04 123.08 -9.04 1.24e+00 6.50e-01 5.31e+01 ... (remaining 5310 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.63: 2184 13.63 - 27.25: 101 27.25 - 40.87: 25 40.87 - 54.49: 3 54.49 - 68.11: 2 Dihedral angle restraints: 2315 sinusoidal: 917 harmonic: 1398 Sorted by residual: dihedral pdb=" C LEU A 300 " pdb=" N LEU A 300 " pdb=" CA LEU A 300 " pdb=" CB LEU A 300 " ideal model delta harmonic sigma weight residual -122.60 -138.63 16.03 0 2.50e+00 1.60e-01 4.11e+01 dihedral pdb=" CA ALA A 344 " pdb=" C ALA A 344 " pdb=" N ALA A 345 " pdb=" CA ALA A 345 " ideal model delta harmonic sigma weight residual -180.00 -150.63 -29.37 0 5.00e+00 4.00e-02 3.45e+01 dihedral pdb=" N LEU A 300 " pdb=" C LEU A 300 " pdb=" CA LEU A 300 " pdb=" CB LEU A 300 " ideal model delta harmonic sigma weight residual 122.80 137.25 -14.45 0 2.50e+00 1.60e-01 3.34e+01 ... (remaining 2312 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.161: 574 0.161 - 0.321: 11 0.321 - 0.482: 1 0.482 - 0.642: 1 0.642 - 0.802: 1 Chirality restraints: 588 Sorted by residual: chirality pdb=" CA LEU A 300 " pdb=" N LEU A 300 " pdb=" C LEU A 300 " pdb=" CB LEU A 300 " both_signs ideal model delta sigma weight residual False 2.51 1.71 0.80 2.00e-01 2.50e+01 1.61e+01 chirality pdb=" CA TYR A 301 " pdb=" N TYR A 301 " pdb=" C TYR A 301 " pdb=" CB TYR A 301 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.45e+00 chirality pdb=" CA THR A 213 " pdb=" N THR A 213 " pdb=" C THR A 213 " pdb=" CB THR A 213 " both_signs ideal model delta sigma weight residual False 2.53 2.09 0.43 2.00e-01 2.50e+01 4.66e+00 ... (remaining 585 not shown) Planarity restraints: 708 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 51 " 0.020 2.00e-02 2.50e+03 1.84e-02 8.44e+00 pdb=" CG TRP A 51 " -0.048 2.00e-02 2.50e+03 pdb=" CD1 TRP A 51 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP A 51 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP A 51 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 51 " -0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP A 51 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 51 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 51 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP A 51 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 405 " -0.010 2.00e-02 2.50e+03 1.45e-02 5.23e+00 pdb=" CG TRP A 405 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP A 405 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP A 405 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 405 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 405 " 0.007 2.00e-02 2.50e+03 pdb=" CE3 TRP A 405 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 405 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 405 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 405 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 49 " 0.038 5.00e-02 4.00e+02 5.68e-02 5.17e+00 pdb=" N PRO A 50 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO A 50 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 50 " 0.031 5.00e-02 4.00e+02 ... (remaining 705 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 158 2.68 - 3.24: 3304 3.24 - 3.79: 5839 3.79 - 4.35: 8181 4.35 - 4.90: 13624 Nonbonded interactions: 31106 Sorted by model distance: nonbonded pdb=" O PRO A 243 " pdb=" O HOH A 701 " model vdw 2.131 2.440 nonbonded pdb=" OE1 GLU A 84 " pdb=" O HOH A 702 " model vdw 2.140 2.440 nonbonded pdb=" O ALA A 496 " pdb=" O HOH A 703 " model vdw 2.163 2.440 nonbonded pdb=" O MET A 532 " pdb=" O HOH A 704 " model vdw 2.194 2.440 nonbonded pdb=" OD1 ASP A 211 " pdb=" N PHE A 212 " model vdw 2.197 2.520 ... (remaining 31101 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.100 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: 0.770 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.620 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 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:12.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 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 : 0.008 0.074 3883 Z= 0.532 Angle : 1.153 16.966 5315 Z= 0.699 Chirality : 0.081 0.802 588 Planarity : 0.010 0.057 708 Dihedral : 9.030 68.110 1415 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Cbeta Deviations : 0.22 % 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: -2.32 (0.31), residues: 479 helix: -3.43 (0.57), residues: 27 sheet: -0.80 (0.41), residues: 130 loop : -1.78 (0.27), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.006 TRP A 51 HIS 0.013 0.002 HIS A 494 PHE 0.035 0.004 PHE A 498 TYR 0.025 0.004 TYR A 410 ARG 0.015 0.002 ARG A 495 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 0.481 Fit side-chains REVERT: A 84 GLU cc_start: 0.7264 (mp0) cc_final: 0.7053 (mp0) REVERT: A 155 LEU cc_start: 0.8987 (mt) cc_final: 0.8739 (mt) REVERT: A 356 ASP cc_start: 0.8347 (m-30) cc_final: 0.8122 (m-30) REVERT: A 379 GLN cc_start: 0.7891 (mm-40) cc_final: 0.7605 (mm110) REVERT: A 443 LYS cc_start: 0.9112 (tttm) cc_final: 0.8850 (tttm) outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 1.0520 time to fit residues: 121.9696 Evaluate side-chains 100 residues out of total 416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 50.0000 chunk 45 optimal weight: 0.0010 chunk 25 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 30 optimal weight: 5.9990 chunk 24 optimal weight: 9.9990 chunk 47 optimal weight: 0.6980 chunk 18 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 54 optimal weight: 50.0000 overall best weight: 0.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN A 167 HIS A 189 ASN A 347 GLN A 386 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3883 Z= 0.155 Angle : 0.527 4.516 5315 Z= 0.277 Chirality : 0.045 0.127 588 Planarity : 0.006 0.038 708 Dihedral : 5.090 21.738 519 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.44 % Allowed : 8.17 % 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: -1.20 (0.34), residues: 479 helix: -1.67 (0.83), residues: 27 sheet: -0.28 (0.39), residues: 156 loop : -1.00 (0.31), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 51 HIS 0.005 0.001 HIS A 494 PHE 0.014 0.001 PHE A 64 TYR 0.011 0.001 TYR A 168 ARG 0.003 0.001 ARG A 241 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 97 time to evaluate : 0.457 Fit side-chains REVERT: A 398 ASP cc_start: 0.8464 (OUTLIER) cc_final: 0.8197 (p0) REVERT: A 443 LYS cc_start: 0.9120 (tttm) cc_final: 0.8793 (tttm) outliers start: 6 outliers final: 0 residues processed: 97 average time/residue: 1.1518 time to fit residues: 115.5843 Evaluate side-chains 94 residues out of total 416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 93 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 30 optimal weight: 7.9990 chunk 16 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 54 optimal weight: 50.0000 chunk 58 optimal weight: 50.0000 chunk 48 optimal weight: 9.9990 chunk 18 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 53 optimal weight: 50.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 HIS A 386 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.051 3883 Z= 0.514 Angle : 0.709 7.730 5315 Z= 0.362 Chirality : 0.052 0.177 588 Planarity : 0.007 0.041 708 Dihedral : 5.487 21.066 519 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.12 % Allowed : 10.82 % Favored : 86.06 % 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: -1.27 (0.34), residues: 479 helix: -2.19 (0.72), residues: 33 sheet: -0.24 (0.41), residues: 144 loop : -0.98 (0.31), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 51 HIS 0.007 0.002 HIS A 299 PHE 0.016 0.002 PHE A 435 TYR 0.019 0.002 TYR A 214 ARG 0.006 0.001 ARG A 201 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 91 time to evaluate : 0.447 Fit side-chains REVERT: A 171 LYS cc_start: 0.8225 (tppt) cc_final: 0.7765 (mmmt) REVERT: A 211 ASP cc_start: 0.7838 (t0) cc_final: 0.7585 (t70) REVERT: A 398 ASP cc_start: 0.8494 (OUTLIER) cc_final: 0.8282 (p0) REVERT: A 443 LYS cc_start: 0.9163 (tttm) cc_final: 0.8894 (tttm) REVERT: A 525 GLN cc_start: 0.8252 (OUTLIER) cc_final: 0.7626 (pm20) outliers start: 13 outliers final: 8 residues processed: 96 average time/residue: 1.1162 time to fit residues: 110.9204 Evaluate side-chains 103 residues out of total 416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 93 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LYS Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 311 SER Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 397 ASN Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 525 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 41 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 chunk 36 optimal weight: 5.9990 chunk 54 optimal weight: 50.0000 chunk 57 optimal weight: 50.0000 chunk 51 optimal weight: 50.0000 chunk 15 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 32 optimal weight: 0.0060 overall best weight: 1.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 386 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3883 Z= 0.183 Angle : 0.523 5.974 5315 Z= 0.266 Chirality : 0.045 0.133 588 Planarity : 0.006 0.042 708 Dihedral : 4.775 20.569 519 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.64 % Allowed : 12.98 % Favored : 84.38 % 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: -0.82 (0.35), residues: 479 helix: -1.24 (0.85), residues: 33 sheet: -0.09 (0.40), residues: 154 loop : -0.68 (0.32), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 522 HIS 0.003 0.001 HIS A 494 PHE 0.012 0.001 PHE A 64 TYR 0.010 0.001 TYR A 168 ARG 0.002 0.000 ARG A 437 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 97 time to evaluate : 0.470 Fit side-chains revert: symmetry clash REVERT: A 211 ASP cc_start: 0.7868 (t0) cc_final: 0.7618 (t70) REVERT: A 238 SER cc_start: 0.9051 (m) cc_final: 0.8784 (p) REVERT: A 379 GLN cc_start: 0.7898 (mm-40) cc_final: 0.7629 (mm-40) REVERT: A 443 LYS cc_start: 0.9040 (tttm) cc_final: 0.8822 (tttm) outliers start: 11 outliers final: 5 residues processed: 101 average time/residue: 1.1364 time to fit residues: 118.9350 Evaluate side-chains 97 residues out of total 416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 92 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LYS Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 455 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 0 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 chunk 49 optimal weight: 50.0000 chunk 40 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 52 optimal weight: 50.0000 chunk 14 optimal weight: 5.9990 chunk 19 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 34 optimal weight: 0.0470 overall best weight: 1.1684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 386 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3883 Z= 0.180 Angle : 0.515 5.383 5315 Z= 0.261 Chirality : 0.045 0.132 588 Planarity : 0.005 0.041 708 Dihedral : 4.581 20.059 519 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.16 % Allowed : 13.94 % Favored : 83.89 % 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: -0.62 (0.35), residues: 479 helix: -0.97 (0.87), residues: 33 sheet: 0.02 (0.41), residues: 154 loop : -0.53 (0.33), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 522 HIS 0.004 0.001 HIS A 299 PHE 0.012 0.001 PHE A 64 TYR 0.009 0.001 TYR A 168 ARG 0.002 0.000 ARG A 437 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 100 time to evaluate : 0.470 Fit side-chains REVERT: A 187 ARG cc_start: 0.7550 (mtm180) cc_final: 0.6863 (mtp85) REVERT: A 238 SER cc_start: 0.9054 (m) cc_final: 0.8784 (p) REVERT: A 379 GLN cc_start: 0.8019 (mm-40) cc_final: 0.7699 (mm-40) REVERT: A 398 ASP cc_start: 0.8111 (p0) cc_final: 0.7669 (p0) REVERT: A 443 LYS cc_start: 0.9015 (tttm) cc_final: 0.8799 (tttm) outliers start: 9 outliers final: 6 residues processed: 102 average time/residue: 1.1494 time to fit residues: 121.3484 Evaluate side-chains 100 residues out of total 416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 94 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LYS Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 455 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 14 optimal weight: 1.9990 chunk 58 optimal weight: 50.0000 chunk 48 optimal weight: 10.0000 chunk 26 optimal weight: 0.8980 chunk 4 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 30 optimal weight: 0.9990 chunk 55 optimal weight: 50.0000 chunk 6 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 386 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3883 Z= 0.222 Angle : 0.538 6.528 5315 Z= 0.270 Chirality : 0.045 0.135 588 Planarity : 0.005 0.041 708 Dihedral : 4.633 20.373 519 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.64 % Allowed : 14.18 % Favored : 83.17 % 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: -0.54 (0.35), residues: 479 helix: -0.88 (0.86), residues: 33 sheet: 0.06 (0.41), residues: 154 loop : -0.47 (0.33), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 522 HIS 0.004 0.001 HIS A 299 PHE 0.012 0.001 PHE A 64 TYR 0.011 0.001 TYR A 362 ARG 0.002 0.000 ARG A 437 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 94 time to evaluate : 0.476 Fit side-chains REVERT: A 187 ARG cc_start: 0.7522 (mtm180) cc_final: 0.7021 (mtp85) REVERT: A 211 ASP cc_start: 0.7879 (t0) cc_final: 0.7678 (t70) REVERT: A 238 SER cc_start: 0.9060 (m) cc_final: 0.8782 (p) REVERT: A 379 GLN cc_start: 0.7996 (mm-40) cc_final: 0.7669 (mm-40) REVERT: A 443 LYS cc_start: 0.9132 (tttm) cc_final: 0.8923 (tttm) outliers start: 11 outliers final: 9 residues processed: 98 average time/residue: 1.0791 time to fit residues: 109.4668 Evaluate side-chains 101 residues out of total 416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 92 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LYS Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 397 ASN Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 500 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 32 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 57 optimal weight: 50.0000 chunk 36 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 23 optimal weight: 5.9990 chunk 34 optimal weight: 0.6980 chunk 17 optimal weight: 7.9990 chunk 11 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 386 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3883 Z= 0.235 Angle : 0.544 6.513 5315 Z= 0.274 Chirality : 0.046 0.136 588 Planarity : 0.006 0.041 708 Dihedral : 4.653 19.817 519 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 3.12 % Allowed : 13.46 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.35), residues: 479 helix: -0.92 (0.86), residues: 33 sheet: 0.09 (0.41), residues: 154 loop : -0.43 (0.33), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 522 HIS 0.004 0.001 HIS A 299 PHE 0.012 0.001 PHE A 64 TYR 0.011 0.001 TYR A 214 ARG 0.002 0.000 ARG A 201 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 93 time to evaluate : 0.407 Fit side-chains REVERT: A 103 MET cc_start: 0.8634 (mtp) cc_final: 0.8350 (mmm) REVERT: A 114 PHE cc_start: 0.7714 (m-80) cc_final: 0.7455 (m-80) REVERT: A 187 ARG cc_start: 0.7508 (mtm180) cc_final: 0.7006 (mtp85) REVERT: A 379 GLN cc_start: 0.8032 (mm-40) cc_final: 0.7696 (mm-40) REVERT: A 398 ASP cc_start: 0.7976 (p0) cc_final: 0.7725 (p0) REVERT: A 443 LYS cc_start: 0.9148 (tttm) cc_final: 0.8912 (tttm) REVERT: A 525 GLN cc_start: 0.8131 (OUTLIER) cc_final: 0.7517 (pm20) outliers start: 13 outliers final: 9 residues processed: 99 average time/residue: 1.1126 time to fit residues: 113.9052 Evaluate side-chains 102 residues out of total 416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 92 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LYS Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 397 ASN Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 525 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 28 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 52 optimal weight: 50.0000 chunk 55 optimal weight: 50.0000 chunk 50 optimal weight: 50.0000 chunk 53 optimal weight: 50.0000 chunk 32 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 chunk 42 optimal weight: 0.1980 chunk 16 optimal weight: 1.9990 overall best weight: 2.2388 ------------------------------------------------------------------------------- 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: 0.8658 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 3883 Z= 0.300 Angle : 0.581 6.414 5315 Z= 0.292 Chirality : 0.047 0.138 588 Planarity : 0.006 0.041 708 Dihedral : 4.782 18.834 519 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.88 % Allowed : 13.70 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.35), residues: 479 helix: -1.09 (0.84), residues: 33 sheet: 0.09 (0.42), residues: 152 loop : -0.48 (0.32), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 522 HIS 0.004 0.001 HIS A 299 PHE 0.012 0.002 PHE A 64 TYR 0.013 0.001 TYR A 214 ARG 0.003 0.001 ARG A 437 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 90 time to evaluate : 0.474 Fit side-chains REVERT: A 103 MET cc_start: 0.8614 (mtp) cc_final: 0.8318 (mmm) REVERT: A 114 PHE cc_start: 0.7775 (m-80) cc_final: 0.7535 (m-80) REVERT: A 171 LYS cc_start: 0.8147 (tppt) cc_final: 0.7737 (mmmt) REVERT: A 187 ARG cc_start: 0.7520 (mtm180) cc_final: 0.6982 (mtp85) REVERT: A 294 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8340 (mp) REVERT: A 379 GLN cc_start: 0.8003 (mm-40) cc_final: 0.7671 (mm-40) REVERT: A 398 ASP cc_start: 0.8099 (p0) cc_final: 0.7795 (p0) REVERT: A 443 LYS cc_start: 0.9187 (tttm) cc_final: 0.8967 (tttm) REVERT: A 525 GLN cc_start: 0.8216 (OUTLIER) cc_final: 0.7620 (pm20) outliers start: 12 outliers final: 8 residues processed: 95 average time/residue: 1.0890 time to fit residues: 107.1722 Evaluate side-chains 101 residues out of total 416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 91 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LYS Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 525 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 0.7980 chunk 50 optimal weight: 50.0000 chunk 53 optimal weight: 50.0000 chunk 35 optimal weight: 1.9990 chunk 56 optimal weight: 50.0000 chunk 34 optimal weight: 1.9990 chunk 27 optimal weight: 6.9990 chunk 39 optimal weight: 0.9990 chunk 59 optimal weight: 50.0000 chunk 55 optimal weight: 50.0000 chunk 47 optimal weight: 4.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- 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: 0.8657 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3883 Z= 0.291 Angle : 0.576 5.995 5315 Z= 0.290 Chirality : 0.047 0.142 588 Planarity : 0.006 0.041 708 Dihedral : 4.776 19.164 519 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.40 % Allowed : 14.18 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.35), residues: 479 helix: -1.06 (0.85), residues: 33 sheet: 0.10 (0.42), residues: 152 loop : -0.48 (0.32), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 522 HIS 0.004 0.001 HIS A 299 PHE 0.012 0.002 PHE A 64 TYR 0.012 0.001 TYR A 214 ARG 0.003 0.001 ARG A 437 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 91 time to evaluate : 0.452 Fit side-chains REVERT: A 103 MET cc_start: 0.8597 (mtp) cc_final: 0.8328 (mmm) REVERT: A 114 PHE cc_start: 0.7804 (m-80) cc_final: 0.7539 (m-80) REVERT: A 171 LYS cc_start: 0.8160 (tppt) cc_final: 0.7749 (mmmt) REVERT: A 187 ARG cc_start: 0.7512 (mtm180) cc_final: 0.7189 (mtp85) REVERT: A 294 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8337 (mp) REVERT: A 379 GLN cc_start: 0.7994 (mm-40) cc_final: 0.7588 (mm110) REVERT: A 398 ASP cc_start: 0.8160 (p0) cc_final: 0.7941 (p0) REVERT: A 443 LYS cc_start: 0.9184 (tttm) cc_final: 0.8971 (tttm) REVERT: A 525 GLN cc_start: 0.8215 (OUTLIER) cc_final: 0.7622 (pm20) outliers start: 10 outliers final: 8 residues processed: 96 average time/residue: 1.1298 time to fit residues: 112.1816 Evaluate side-chains 99 residues out of total 416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 89 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LYS Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 525 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 4 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 50 optimal weight: 50.0000 chunk 14 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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: 0.8659 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 3883 Z= 0.297 Angle : 0.587 6.061 5315 Z= 0.295 Chirality : 0.048 0.305 588 Planarity : 0.006 0.041 708 Dihedral : 4.788 18.885 519 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.40 % Allowed : 14.66 % Favored : 82.93 % 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: -0.55 (0.35), residues: 479 helix: -1.09 (0.84), residues: 33 sheet: 0.11 (0.42), residues: 152 loop : -0.49 (0.32), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 522 HIS 0.004 0.001 HIS A 299 PHE 0.012 0.002 PHE A 64 TYR 0.013 0.001 TYR A 214 ARG 0.003 0.001 ARG A 437 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 958 Ramachandran restraints generated. 479 Oldfield, 0 Emsley, 479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 88 time to evaluate : 0.447 Fit side-chains REVERT: A 103 MET cc_start: 0.8601 (mtp) cc_final: 0.8370 (mmm) REVERT: A 114 PHE cc_start: 0.7839 (m-80) cc_final: 0.7558 (m-80) REVERT: A 171 LYS cc_start: 0.8190 (tppt) cc_final: 0.7808 (mmmt) REVERT: A 187 ARG cc_start: 0.7507 (mtm180) cc_final: 0.7187 (mtp85) REVERT: A 294 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8340 (mp) REVERT: A 379 GLN cc_start: 0.7977 (mm-40) cc_final: 0.7573 (mm110) REVERT: A 443 LYS cc_start: 0.9195 (tttm) cc_final: 0.8991 (tttm) REVERT: A 525 GLN cc_start: 0.8217 (OUTLIER) cc_final: 0.7625 (pm20) outliers start: 10 outliers final: 8 residues processed: 93 average time/residue: 1.1521 time to fit residues: 110.7533 Evaluate side-chains 97 residues out of total 416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 87 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LYS Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 525 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 10.0000 chunk 6 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 2 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 chunk 54 optimal weight: 50.0000 chunk 32 optimal weight: 6.9990 chunk 40 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.3099 r_free = 0.3099 target = 0.107585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.091944 restraints weight = 4868.085| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 1.58 r_work: 0.2848 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3883 Z= 0.168 Angle : 0.522 5.702 5315 Z= 0.262 Chirality : 0.046 0.295 588 Planarity : 0.005 0.042 708 Dihedral : 4.455 19.684 519 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.16 % Allowed : 14.90 % Favored : 82.93 % 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: -0.36 (0.36), residues: 479 helix: -0.74 (0.89), residues: 33 sheet: 0.17 (0.42), residues: 154 loop : -0.34 (0.33), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 522 HIS 0.003 0.001 HIS A 299 PHE 0.011 0.001 PHE A 64 TYR 0.008 0.001 TYR A 168 ARG 0.003 0.000 ARG A 69 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2225.57 seconds wall clock time: 40 minutes 4.62 seconds (2404.62 seconds total)