Starting phenix.real_space_refine on Sun Mar 10 16:05:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wth_32786/03_2024/7wth_32786.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wth_32786/03_2024/7wth_32786.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wth_32786/03_2024/7wth_32786.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wth_32786/03_2024/7wth_32786.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wth_32786/03_2024/7wth_32786.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wth_32786/03_2024/7wth_32786.pdb" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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 16 5.16 5 C 2084 2.51 5 N 543 2.21 5 O 614 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E ASP 339": "OD1" <-> "OD2" Residue "E TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 420": "OD1" <-> "OD2" Residue "E PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 6": "OE1" <-> "OE2" Residue "H TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 3257 Number of models: 1 Model: "" Number of chains: 3 Chain: "E" Number of atoms: 1573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1573 Classifications: {'peptide': 197} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 184} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "L" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 772 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 99} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 912 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 111} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 2.34, per 1000 atoms: 0.72 Number of scatterers: 3257 At special positions: 0 Unit cell: (77.04, 77.04, 94.16, 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 16 16.00 O 614 8.00 N 543 7.00 C 2084 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.04 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.03 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 97 " 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: 1.14 Conformation dependent library (CDL) restraints added in 614.0 milliseconds 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 774 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 8 sheets defined 7.8% alpha, 21.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'E' and resid 337 through 342 removed outlier: 3.931A pdb=" N VAL E 341 " --> pdb=" O PRO E 337 " (cutoff:3.500A) Processing helix chain 'E' and resid 366 through 371 removed outlier: 3.672A pdb=" N TYR E 369 " --> pdb=" O SER E 366 " (cutoff:3.500A) Processing helix chain 'E' and resid 386 through 390 removed outlier: 3.966A pdb=" N LEU E 390 " --> pdb=" O LEU E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 403 through 410 removed outlier: 4.019A pdb=" N VAL E 407 " --> pdb=" O GLY E 404 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ARG E 408 " --> pdb=" O ASP E 405 " (cutoff:3.500A) Processing helix chain 'H' and resid 65 through 67 No H-bonds generated for 'chain 'H' and resid 65 through 67' Processing helix chain 'H' and resid 88 through 92 removed outlier: 3.593A pdb=" N THR H 92 " --> pdb=" O PRO H 89 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 356 through 358 removed outlier: 3.706A pdb=" N ALA E 397 " --> pdb=" O LYS E 356 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N VAL E 395 " --> pdb=" O ILE E 358 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 361 through 362 removed outlier: 7.179A pdb=" N CYS E 361 " --> pdb=" O CYS E 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'E' and resid 374 through 376 removed outlier: 3.772A pdb=" N THR E 376 " --> pdb=" O ALA E 435 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 452 through 454 removed outlier: 3.621A pdb=" N ARG E 493 " --> pdb=" O TYR E 453 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 19 through 23 removed outlier: 3.667A pdb=" N VAL L 20 " --> pdb=" O LEU L 75 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 44 through 50 removed outlier: 5.328A pdb=" N ALA L 45 " --> pdb=" O HIS L 41 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N HIS L 41 " --> pdb=" O ALA L 45 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS L 47 " --> pdb=" O GLN L 39 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N TRP L 37 " --> pdb=" O LEU L 49 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASP L 87 " --> pdb=" O HIS L 40 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 3 through 7 removed outlier: 4.404A pdb=" N THR H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.661A pdb=" N THR H 113 " --> pdb=" O TYR H 95 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N THR H 94 " --> pdb=" O GLN H 41 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ALA H 51 " --> pdb=" O TRP H 38 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ARG H 40 " --> pdb=" O TRP H 49 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N TRP H 49 " --> pdb=" O ARG H 40 " (cutoff:3.500A) 61 hydrogen bonds defined for protein. 141 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: 0.69 Time building geometry restraints manager: 1.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1027 1.35 - 1.47: 867 1.47 - 1.58: 1432 1.58 - 1.70: 0 1.70 - 1.82: 19 Bond restraints: 3345 Sorted by residual: bond pdb=" N ILE E 418 " pdb=" CA ILE E 418 " ideal model delta sigma weight residual 1.462 1.498 -0.036 1.17e-02 7.31e+03 9.28e+00 bond pdb=" N GLY E 447 " pdb=" CA GLY E 447 " ideal model delta sigma weight residual 1.447 1.478 -0.032 1.09e-02 8.42e+03 8.54e+00 bond pdb=" CA SER E 438 " pdb=" CB SER E 438 " ideal model delta sigma weight residual 1.528 1.490 0.038 1.34e-02 5.57e+03 8.07e+00 bond pdb=" N GLY E 416 " pdb=" CA GLY E 416 " ideal model delta sigma weight residual 1.447 1.475 -0.028 1.03e-02 9.43e+03 7.45e+00 bond pdb=" N ASN E 437 " pdb=" CA ASN E 437 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.22e-02 6.72e+03 6.75e+00 ... (remaining 3340 not shown) Histogram of bond angle deviations from ideal: 96.46 - 104.01: 57 104.01 - 111.55: 1429 111.55 - 119.09: 1188 119.09 - 126.63: 1828 126.63 - 134.18: 57 Bond angle restraints: 4559 Sorted by residual: angle pdb=" CA GLY E 447 " pdb=" C GLY E 447 " pdb=" O GLY E 447 " ideal model delta sigma weight residual 122.29 118.53 3.76 8.10e-01 1.52e+00 2.15e+01 angle pdb=" CA PRO H 9 " pdb=" CB PRO H 9 " pdb=" CG PRO H 9 " ideal model delta sigma weight residual 104.50 96.46 8.04 1.90e+00 2.77e-01 1.79e+01 angle pdb=" N PRO H 9 " pdb=" CD PRO H 9 " pdb=" CG PRO H 9 " ideal model delta sigma weight residual 103.20 97.15 6.05 1.50e+00 4.44e-01 1.62e+01 angle pdb=" N GLY E 404 " pdb=" CA GLY E 404 " pdb=" C GLY E 404 " ideal model delta sigma weight residual 111.02 118.30 -7.28 1.86e+00 2.89e-01 1.53e+01 angle pdb=" N ILE E 418 " pdb=" CA ILE E 418 " pdb=" C ILE E 418 " ideal model delta sigma weight residual 113.07 108.39 4.68 1.36e+00 5.41e-01 1.19e+01 ... (remaining 4554 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.35: 1742 15.35 - 30.70: 177 30.70 - 46.06: 34 46.06 - 61.41: 10 61.41 - 76.76: 5 Dihedral angle restraints: 1968 sinusoidal: 749 harmonic: 1219 Sorted by residual: dihedral pdb=" CB CYS E 336 " pdb=" SG CYS E 336 " pdb=" SG CYS E 361 " pdb=" CB CYS E 361 " ideal model delta sinusoidal sigma weight residual 93.00 18.13 74.87 1 1.00e+01 1.00e-02 7.09e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 97 " pdb=" CB CYS H 97 " ideal model delta sinusoidal sigma weight residual 93.00 147.18 -54.18 1 1.00e+01 1.00e-02 3.98e+01 dihedral pdb=" CA CYS E 432 " pdb=" C CYS E 432 " pdb=" N VAL E 433 " pdb=" CA VAL E 433 " ideal model delta harmonic sigma weight residual -180.00 -159.78 -20.22 0 5.00e+00 4.00e-02 1.64e+01 ... (remaining 1965 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 349 0.042 - 0.083: 96 0.083 - 0.125: 50 0.125 - 0.166: 4 0.166 - 0.208: 2 Chirality restraints: 501 Sorted by residual: chirality pdb=" CA VAL E 445 " pdb=" N VAL E 445 " pdb=" C VAL E 445 " pdb=" CB VAL E 445 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA SER E 446 " pdb=" N SER E 446 " pdb=" C SER E 446 " pdb=" CB SER E 446 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.77e-01 chirality pdb=" CA ILE H 39 " pdb=" N ILE H 39 " pdb=" C ILE H 39 " pdb=" CB ILE H 39 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.79e-01 ... (remaining 498 not shown) Planarity restraints: 584 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA E 419 " -0.012 2.00e-02 2.50e+03 2.44e-02 5.97e+00 pdb=" C ALA E 419 " 0.042 2.00e-02 2.50e+03 pdb=" O ALA E 419 " -0.016 2.00e-02 2.50e+03 pdb=" N ASP E 420 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS E 440 " 0.009 2.00e-02 2.50e+03 1.73e-02 2.99e+00 pdb=" C LYS E 440 " -0.030 2.00e-02 2.50e+03 pdb=" O LYS E 440 " 0.011 2.00e-02 2.50e+03 pdb=" N LEU E 441 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE L 98 " -0.028 5.00e-02 4.00e+02 4.20e-02 2.82e+00 pdb=" N PRO L 99 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO L 99 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO L 99 " -0.023 5.00e-02 4.00e+02 ... (remaining 581 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 153 2.71 - 3.26: 3186 3.26 - 3.81: 4694 3.81 - 4.35: 5739 4.35 - 4.90: 9754 Nonbonded interactions: 23526 Sorted by model distance: nonbonded pdb=" OD2 ASP H 74 " pdb=" OG SER H 76 " model vdw 2.169 2.440 nonbonded pdb=" OG1 THR H 3 " pdb=" OG SER H 25 " model vdw 2.291 2.440 nonbonded pdb=" NZ LYS H 45 " pdb=" O ALA H 46 " model vdw 2.311 2.520 nonbonded pdb=" N GLU H 6 " pdb=" OE1 GLU H 6 " model vdw 2.334 2.520 nonbonded pdb=" NZ LYS H 5 " pdb=" O GLU H 6 " model vdw 2.409 2.520 ... (remaining 23521 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: 2.330 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: 9.140 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 13.700 Find NCS groups from input model: 0.090 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7016 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 : 0.004 0.061 3345 Z= 0.256 Angle : 0.778 8.712 4559 Z= 0.455 Chirality : 0.048 0.208 501 Planarity : 0.005 0.042 584 Dihedral : 12.973 76.758 1176 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Rotamer: Outliers : 0.85 % Allowed : 0.57 % Favored : 98.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.40), residues: 415 helix: -4.34 (0.65), residues: 26 sheet: 0.36 (0.54), residues: 104 loop : -1.85 (0.35), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 49 HIS 0.001 0.000 HIS L 41 PHE 0.008 0.001 PHE H 106 TYR 0.021 0.001 TYR H 61 ARG 0.003 0.000 ARG H 60 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 84 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 359 SER cc_start: 0.8534 (p) cc_final: 0.8255 (p) REVERT: H 29 LEU cc_start: 0.7854 (mm) cc_final: 0.7439 (mm) outliers start: 3 outliers final: 0 residues processed: 85 average time/residue: 0.1503 time to fit residues: 15.6484 Evaluate side-chains 57 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 20 optimal weight: 0.0570 chunk 31 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 19 optimal weight: 0.0010 chunk 23 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 overall best weight: 0.5304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 439 ASN L 71 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3345 Z= 0.241 Angle : 0.649 5.735 4559 Z= 0.340 Chirality : 0.045 0.133 501 Planarity : 0.005 0.048 584 Dihedral : 4.920 22.517 462 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.40 % Favored : 90.60 % Rotamer: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.14 (0.41), residues: 415 helix: -4.77 (0.48), residues: 20 sheet: 0.22 (0.55), residues: 104 loop : -1.94 (0.35), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 436 HIS 0.005 0.001 HIS H 100 PHE 0.015 0.002 PHE L 102 TYR 0.012 0.001 TYR H 61 ARG 0.001 0.000 ARG H 60 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 0.373 Fit side-chains REVERT: E 359 SER cc_start: 0.8364 (p) cc_final: 0.8051 (p) REVERT: H 18 LEU cc_start: 0.6502 (mm) cc_final: 0.6179 (mm) REVERT: H 45 LYS cc_start: 0.8696 (ttpp) cc_final: 0.8491 (mptt) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.1447 time to fit residues: 14.2007 Evaluate side-chains 51 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 0.9990 chunk 24 optimal weight: 0.0970 chunk 10 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 39 optimal weight: 0.2980 chunk 32 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 439 ASN L 71 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3345 Z= 0.216 Angle : 0.621 5.000 4559 Z= 0.326 Chirality : 0.045 0.134 501 Planarity : 0.005 0.051 584 Dihedral : 5.134 23.963 462 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.12 % Favored : 89.88 % Rotamer: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.25 (0.40), residues: 415 helix: -4.88 (0.41), residues: 20 sheet: 0.12 (0.54), residues: 104 loop : -2.00 (0.35), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 436 HIS 0.004 0.001 HIS H 100 PHE 0.010 0.002 PHE E 486 TYR 0.015 0.001 TYR H 61 ARG 0.002 0.000 ARG E 457 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 0.356 Fit side-chains REVERT: E 339 ASP cc_start: 0.7611 (p0) cc_final: 0.7347 (p0) REVERT: E 340 GLU cc_start: 0.7110 (mm-30) cc_final: 0.6460 (mm-30) REVERT: E 359 SER cc_start: 0.8394 (p) cc_final: 0.8130 (p) outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.1353 time to fit residues: 11.8184 Evaluate side-chains 49 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 24 optimal weight: 0.0770 chunk 36 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 chunk 21 optimal weight: 0.0270 chunk 0 optimal weight: 0.9990 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 71 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 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 : 0.003 0.027 3345 Z= 0.197 Angle : 0.609 5.335 4559 Z= 0.316 Chirality : 0.044 0.133 501 Planarity : 0.005 0.048 584 Dihedral : 5.098 24.395 462 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.40 % Favored : 90.60 % Rotamer: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.40), residues: 415 helix: -5.21 (0.26), residues: 14 sheet: 0.12 (0.56), residues: 104 loop : -2.06 (0.34), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 436 HIS 0.003 0.001 HIS H 100 PHE 0.014 0.002 PHE L 102 TYR 0.013 0.001 TYR H 61 ARG 0.001 0.000 ARG H 60 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 0.397 Fit side-chains revert: symmetry clash REVERT: E 340 GLU cc_start: 0.7045 (mm-30) cc_final: 0.6680 (mm-30) REVERT: H 6 GLU cc_start: 0.6969 (mp0) cc_final: 0.6495 (mm-30) REVERT: H 18 LEU cc_start: 0.6292 (mm) cc_final: 0.6067 (mm) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.1363 time to fit residues: 13.2607 Evaluate side-chains 54 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 26 optimal weight: 6.9990 chunk 0 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 9 optimal weight: 0.3980 chunk 13 optimal weight: 0.0370 chunk 7 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 71 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3345 Z= 0.222 Angle : 0.634 6.010 4559 Z= 0.330 Chirality : 0.045 0.134 501 Planarity : 0.005 0.049 584 Dihedral : 5.216 23.920 462 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.57 % Favored : 88.43 % Rotamer: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.40), residues: 415 helix: -5.22 (0.25), residues: 14 sheet: 0.02 (0.55), residues: 104 loop : -2.07 (0.34), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 109 HIS 0.003 0.001 HIS H 100 PHE 0.008 0.001 PHE E 486 TYR 0.012 0.002 TYR H 61 ARG 0.002 0.000 ARG E 355 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 0.294 Fit side-chains revert: symmetry clash REVERT: E 340 GLU cc_start: 0.7198 (mm-30) cc_final: 0.6853 (mm-30) REVERT: E 359 SER cc_start: 0.8403 (p) cc_final: 0.8146 (p) REVERT: H 18 LEU cc_start: 0.6220 (mm) cc_final: 0.5960 (mm) REVERT: H 29 LEU cc_start: 0.8073 (mm) cc_final: 0.7341 (mp) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.1480 time to fit residues: 13.1989 Evaluate side-chains 56 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 0.5980 chunk 38 optimal weight: 3.9990 chunk 32 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 chunk 3 optimal weight: 0.0470 chunk 12 optimal weight: 0.5980 chunk 20 optimal weight: 0.0270 chunk 37 optimal weight: 0.6980 chunk 4 optimal weight: 0.2980 chunk 22 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 overall best weight: 0.3136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 71 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7134 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3345 Z= 0.176 Angle : 0.608 7.142 4559 Z= 0.313 Chirality : 0.045 0.187 501 Planarity : 0.005 0.046 584 Dihedral : 5.073 25.107 462 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.92 % Favored : 91.08 % Rotamer: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.40), residues: 415 helix: -5.21 (0.25), residues: 14 sheet: 0.03 (0.55), residues: 104 loop : -1.98 (0.34), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 55 HIS 0.002 0.000 HIS H 100 PHE 0.013 0.002 PHE L 102 TYR 0.011 0.001 TYR H 61 ARG 0.002 0.000 ARG H 40 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 0.371 Fit side-chains revert: symmetry clash REVERT: E 359 SER cc_start: 0.8416 (p) cc_final: 0.8149 (p) REVERT: L 51 TYR cc_start: 0.6624 (p90) cc_final: 0.6370 (p90) REVERT: H 29 LEU cc_start: 0.8126 (mm) cc_final: 0.7368 (mp) REVERT: H 45 LYS cc_start: 0.8168 (ptpp) cc_final: 0.7951 (ttpt) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.1276 time to fit residues: 11.8515 Evaluate side-chains 52 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 23 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 15 optimal weight: 0.0870 chunk 11 optimal weight: 0.7980 chunk 7 optimal weight: 0.0370 chunk 26 optimal weight: 0.0670 chunk 19 optimal weight: 2.9990 overall best weight: 0.2974 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 409 GLN L 71 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7134 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3345 Z= 0.169 Angle : 0.587 5.372 4559 Z= 0.304 Chirality : 0.045 0.140 501 Planarity : 0.005 0.049 584 Dihedral : 4.909 24.447 462 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.64 % Favored : 90.36 % Rotamer: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % 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: -2.17 (0.40), residues: 415 helix: -5.12 (0.22), residues: 20 sheet: 0.10 (0.55), residues: 104 loop : -1.89 (0.35), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 37 HIS 0.002 0.000 HIS H 100 PHE 0.007 0.001 PHE E 392 TYR 0.011 0.001 TYR H 61 ARG 0.002 0.000 ARG H 40 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 0.387 Fit side-chains revert: symmetry clash REVERT: E 359 SER cc_start: 0.8422 (p) cc_final: 0.8154 (p) REVERT: H 18 LEU cc_start: 0.6228 (mm) cc_final: 0.5364 (mm) REVERT: H 29 LEU cc_start: 0.8068 (mm) cc_final: 0.7427 (mp) REVERT: H 87 MET cc_start: 0.3964 (tpt) cc_final: 0.3353 (mmm) outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.1299 time to fit residues: 12.3365 Evaluate side-chains 53 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 0.0980 chunk 30 optimal weight: 0.6980 chunk 35 optimal weight: 0.0470 chunk 36 optimal weight: 0.7980 chunk 33 optimal weight: 0.3980 chunk 21 optimal weight: 0.0980 chunk 15 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 overall best weight: 0.2678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 71 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7117 moved from start: 0.3254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3345 Z= 0.166 Angle : 0.602 5.696 4559 Z= 0.310 Chirality : 0.046 0.164 501 Planarity : 0.005 0.043 584 Dihedral : 5.038 26.117 462 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.67 % Favored : 91.33 % Rotamer: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % 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: -2.22 (0.40), residues: 415 helix: -5.10 (0.22), residues: 20 sheet: 0.08 (0.55), residues: 104 loop : -1.93 (0.34), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 37 HIS 0.002 0.001 HIS H 100 PHE 0.019 0.001 PHE E 490 TYR 0.016 0.001 TYR L 51 ARG 0.001 0.000 ARG H 60 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 0.371 Fit side-chains revert: symmetry clash REVERT: H 29 LEU cc_start: 0.8075 (mm) cc_final: 0.7434 (mp) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.1488 time to fit residues: 14.3909 Evaluate side-chains 54 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 39 optimal weight: 0.0980 chunk 36 optimal weight: 0.0060 chunk 31 optimal weight: 0.7980 chunk 3 optimal weight: 0.0770 chunk 24 optimal weight: 0.5980 chunk 19 optimal weight: 0.0670 chunk 25 optimal weight: 0.5980 overall best weight: 0.1692 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 71 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7084 moved from start: 0.3271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3345 Z= 0.149 Angle : 0.584 5.373 4559 Z= 0.299 Chirality : 0.045 0.140 501 Planarity : 0.005 0.045 584 Dihedral : 4.818 24.239 462 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.41), residues: 415 helix: -5.08 (0.22), residues: 20 sheet: 0.21 (0.55), residues: 104 loop : -1.87 (0.35), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 37 HIS 0.001 0.000 HIS H 100 PHE 0.014 0.001 PHE E 490 TYR 0.015 0.001 TYR L 51 ARG 0.002 0.000 ARG H 60 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 0.393 Fit side-chains revert: symmetry clash REVERT: E 359 SER cc_start: 0.8410 (p) cc_final: 0.8151 (p) REVERT: E 516 GLU cc_start: 0.7283 (tp30) cc_final: 0.7040 (tp30) REVERT: H 18 LEU cc_start: 0.6114 (mm) cc_final: 0.5465 (mm) REVERT: H 29 LEU cc_start: 0.8088 (mm) cc_final: 0.7424 (mp) REVERT: H 87 MET cc_start: 0.3553 (tpt) cc_final: 0.3135 (mmm) outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.1149 time to fit residues: 11.1459 Evaluate side-chains 57 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 0.0570 chunk 9 optimal weight: 0.2980 chunk 29 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 8 optimal weight: 0.1980 chunk 31 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 5 optimal weight: 5.9990 chunk 27 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 overall best weight: 0.4098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 71 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 moved from start: 0.3481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3345 Z= 0.198 Angle : 0.619 5.353 4559 Z= 0.320 Chirality : 0.047 0.166 501 Planarity : 0.005 0.049 584 Dihedral : 5.031 25.507 462 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.36 % Favored : 89.64 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.41), residues: 415 helix: -5.11 (0.21), residues: 20 sheet: 0.27 (0.55), residues: 104 loop : -1.92 (0.35), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 109 HIS 0.002 0.001 HIS H 100 PHE 0.013 0.002 PHE E 490 TYR 0.016 0.001 TYR L 51 ARG 0.002 0.000 ARG E 355 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 0.354 Fit side-chains REVERT: E 340 GLU cc_start: 0.6809 (mm-30) cc_final: 0.6423 (mm-30) REVERT: H 18 LEU cc_start: 0.6121 (mm) cc_final: 0.5448 (mm) REVERT: H 29 LEU cc_start: 0.8092 (mm) cc_final: 0.7420 (mp) REVERT: H 87 MET cc_start: 0.3658 (tpt) cc_final: 0.3203 (mmm) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.1230 time to fit residues: 10.2382 Evaluate side-chains 51 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 1.9990 chunk 36 optimal weight: 0.0770 chunk 21 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 1 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 24 optimal weight: 0.3980 chunk 23 optimal weight: 0.5980 chunk 15 optimal weight: 4.9990 chunk 14 optimal weight: 0.7980 chunk 39 optimal weight: 0.1980 overall best weight: 0.3938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.107855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.089806 restraints weight = 8147.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.091696 restraints weight = 5561.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.093038 restraints weight = 4226.131| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7120 moved from start: 0.3569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3345 Z= 0.193 Angle : 0.620 5.656 4559 Z= 0.318 Chirality : 0.046 0.181 501 Planarity : 0.005 0.049 584 Dihedral : 5.050 24.817 462 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.12 % Favored : 89.88 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.41), residues: 415 helix: -5.10 (0.22), residues: 20 sheet: 0.21 (0.55), residues: 104 loop : -1.92 (0.35), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 38 HIS 0.002 0.001 HIS H 100 PHE 0.012 0.002 PHE E 490 TYR 0.016 0.001 TYR L 51 ARG 0.001 0.000 ARG L 63 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1359.97 seconds wall clock time: 25 minutes 15.08 seconds (1515.08 seconds total)