Starting phenix.real_space_refine on Mon Sep 23 13:58:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wth_32786/09_2024/7wth_32786.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wth_32786/09_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_32786/09_2024/7wth_32786.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wth_32786/09_2024/7wth_32786.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wth_32786/09_2024/7wth_32786.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wth_32786/09_2024/7wth_32786.cif" } 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. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 3.53, per 1000 atoms: 1.08 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.73 Conformation dependent library (CDL) restraints added in 388.0 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: 0.33 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: 0.80 Time building geometry restraints manager: 0.88 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: 0.00 - 1.74: 4362 1.74 - 3.48: 165 3.48 - 5.23: 25 5.23 - 6.97: 4 6.97 - 8.71: 3 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 3.040 nonbonded pdb=" OG1 THR H 3 " pdb=" OG SER H 25 " model vdw 2.291 3.040 nonbonded pdb=" NZ LYS H 45 " pdb=" O ALA H 46 " model vdw 2.311 3.120 nonbonded pdb=" N GLU H 6 " pdb=" OE1 GLU H 6 " model vdw 2.334 3.120 nonbonded pdb=" NZ LYS H 5 " pdb=" O GLU H 6 " model vdw 2.409 3.120 ... (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 Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 3.400 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: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.610 Find NCS groups from input model: 0.040 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: 0.010 Load rotamer database and sin/cos tables:3.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.430 ------------------------------------------------------------------------------- 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 : 0.403 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: 0.1431 time to fit residues: 14.8743 Evaluate side-chains 57 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 0.374 ------------------------------------------------------------------------------- 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: 0.6980 chunk 30 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 36 optimal weight: 0.1980 chunk 11 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 439 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 3345 Z= 0.271 Angle : 0.681 7.078 4559 Z= 0.359 Chirality : 0.046 0.139 501 Planarity : 0.005 0.051 584 Dihedral : 5.159 23.212 462 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.60 % Favored : 89.40 % 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: -2.24 (0.41), residues: 415 helix: -4.77 (0.50), residues: 20 sheet: 0.17 (0.55), residues: 105 loop : -2.04 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 436 HIS 0.005 0.001 HIS H 100 PHE 0.016 0.002 PHE E 464 TYR 0.012 0.002 TYR H 61 ARG 0.002 0.000 ARG H 40 *********************** 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 75 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 0.335 Fit side-chains REVERT: L 51 TYR cc_start: 0.6776 (p90) cc_final: 0.6517 (p90) REVERT: H 18 LEU cc_start: 0.6484 (mm) cc_final: 0.6171 (mm) REVERT: H 45 LYS cc_start: 0.8736 (ttpp) cc_final: 0.8499 (mptt) outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.1658 time to fit residues: 14.9524 Evaluate side-chains 52 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.380 ------------------------------------------------------------------------------- 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: 0.3980 chunk 24 optimal weight: 0.3980 chunk 10 optimal weight: 0.7980 chunk 36 optimal weight: 0.4980 chunk 39 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 35 optimal weight: 0.7980 chunk 27 optimal weight: 0.0970 chunk 18 optimal weight: 0.6980 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 439 ASN H 99 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3345 Z= 0.200 Angle : 0.619 5.022 4559 Z= 0.324 Chirality : 0.046 0.208 501 Planarity : 0.005 0.052 584 Dihedral : 5.063 23.628 462 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.92 % Favored : 91.08 % 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: -2.22 (0.40), residues: 415 helix: -4.84 (0.42), residues: 20 sheet: 0.14 (0.54), residues: 104 loop : -1.99 (0.35), residues: 291 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 0.016 0.002 PHE L 102 TYR 0.015 0.001 TYR H 61 ARG 0.005 0.000 ARG H 60 *********************** 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 74 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 0.385 Fit side-chains revert: symmetry clash REVERT: E 340 GLU cc_start: 0.7167 (mm-30) cc_final: 0.6685 (mm-30) REVERT: L 51 TYR cc_start: 0.6744 (p90) cc_final: 0.6422 (p90) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.1464 time to fit residues: 13.3643 Evaluate side-chains 54 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.373 ------------------------------------------------------------------------------- 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: 0.7980 chunk 17 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 19 optimal weight: 0.2980 chunk 34 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 chunk 21 optimal weight: 4.9990 chunk 0 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 422 ASN H 99 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3345 Z= 0.248 Angle : 0.664 6.173 4559 Z= 0.347 Chirality : 0.046 0.148 501 Planarity : 0.005 0.058 584 Dihedral : 5.345 25.865 462 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.60 % Favored : 89.40 % Rotamer: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % 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: -2.36 (0.40), residues: 415 helix: -5.22 (0.25), residues: 14 sheet: 0.04 (0.55), residues: 104 loop : -2.15 (0.34), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 436 HIS 0.005 0.001 HIS H 100 PHE 0.017 0.002 PHE L 102 TYR 0.013 0.002 TYR L 38 ARG 0.003 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 71 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 0.286 Fit side-chains revert: symmetry clash REVERT: E 340 GLU cc_start: 0.7230 (mm-30) cc_final: 0.6800 (mm-30) REVERT: L 51 TYR cc_start: 0.7027 (p90) cc_final: 0.6812 (p90) outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.1553 time to fit residues: 13.3411 Evaluate side-chains 54 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.287 ------------------------------------------------------------------------------- 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: 0.5980 chunk 15 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 26 optimal weight: 0.5980 chunk 0 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 9 optimal weight: 0.1980 chunk 13 optimal weight: 0.4980 chunk 7 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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: 0.7179 moved from start: 0.3098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3345 Z= 0.229 Angle : 0.655 7.124 4559 Z= 0.340 Chirality : 0.046 0.152 501 Planarity : 0.005 0.057 584 Dihedral : 5.289 23.592 462 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.12 % Favored : 89.88 % Rotamer: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % 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: -2.34 (0.39), residues: 415 helix: -5.14 (0.30), residues: 14 sheet: -0.07 (0.53), residues: 104 loop : -2.09 (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 0.012 0.002 TYR H 95 ARG 0.003 0.000 ARG H 40 *********************** 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 83 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 359 SER cc_start: 0.8139 (p) cc_final: 0.7861 (p) REVERT: H 29 LEU cc_start: 0.8139 (mm) cc_final: 0.7390 (mp) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.1519 time to fit residues: 15.4405 Evaluate side-chains 60 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 0.389 ------------------------------------------------------------------------------- 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: 0.9990 chunk 38 optimal weight: 3.9990 chunk 32 optimal weight: 0.5980 chunk 17 optimal weight: 0.4980 chunk 3 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 chunk 20 optimal weight: 0.0980 chunk 37 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 28 optimal weight: 0.0000 overall best weight: 0.3584 ------------------------------------------------------------------------------- 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: 0.7144 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3345 Z= 0.191 Angle : 0.629 6.066 4559 Z= 0.326 Chirality : 0.045 0.151 501 Planarity : 0.005 0.054 584 Dihedral : 5.242 25.739 462 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.92 % Favored : 91.08 % Rotamer: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % 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: -2.20 (0.40), residues: 415 helix: -4.17 (0.86), residues: 14 sheet: -0.02 (0.54), residues: 104 loop : -2.02 (0.34), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 55 HIS 0.003 0.001 HIS H 100 PHE 0.012 0.002 PHE L 102 TYR 0.010 0.001 TYR H 61 ARG 0.003 0.000 ARG H 60 *********************** 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 74 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 29 LEU cc_start: 0.8102 (mm) cc_final: 0.7382 (mp) REVERT: H 45 LYS cc_start: 0.8702 (ttpp) cc_final: 0.8353 (mptt) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.1628 time to fit residues: 15.1553 Evaluate side-chains 57 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 0.500 ------------------------------------------------------------------------------- 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: 0.2980 chunk 32 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 24 optimal weight: 0.0060 chunk 23 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 15 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 moved from start: 0.3325 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= 0.235 Angle : 0.665 5.814 4559 Z= 0.346 Chirality : 0.046 0.147 501 Planarity : 0.005 0.057 584 Dihedral : 5.469 26.243 462 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.36 % Favored : 89.64 % Rotamer: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % 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: -2.33 (0.40), residues: 415 helix: -3.74 (1.12), residues: 14 sheet: -0.05 (0.53), residues: 104 loop : -2.17 (0.34), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 436 HIS 0.004 0.001 HIS H 100 PHE 0.014 0.002 PHE E 490 TYR 0.015 0.001 TYR E 489 ARG 0.003 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 74 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 29 LEU cc_start: 0.8108 (mm) cc_final: 0.7404 (mp) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.1478 time to fit residues: 13.4875 Evaluate side-chains 57 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 0.362 ------------------------------------------------------------------------------- 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: 0.7980 chunk 30 optimal weight: 0.5980 chunk 35 optimal weight: 0.7980 chunk 36 optimal weight: 0.1980 chunk 33 optimal weight: 0.0970 chunk 21 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 chunk 28 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 moved from start: 0.3523 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= 0.216 Angle : 0.660 6.898 4559 Z= 0.341 Chirality : 0.046 0.158 501 Planarity : 0.005 0.052 584 Dihedral : 5.344 25.047 462 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 8.30 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: -2.26 (0.40), residues: 415 helix: -3.75 (1.12), residues: 14 sheet: -0.00 (0.54), residues: 104 loop : -2.11 (0.34), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 436 HIS 0.002 0.001 HIS H 100 PHE 0.013 0.002 PHE E 490 TYR 0.010 0.001 TYR L 93 ARG 0.003 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 76 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 29 LEU cc_start: 0.8221 (mm) cc_final: 0.7450 (mp) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.1411 time to fit residues: 13.2807 Evaluate side-chains 55 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.371 ------------------------------------------------------------------------------- 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: 0.9990 chunk 23 optimal weight: 0.4980 chunk 18 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 36 optimal weight: 0.0060 chunk 31 optimal weight: 0.9980 chunk 3 optimal weight: 0.0000 chunk 24 optimal weight: 2.9990 chunk 19 optimal weight: 0.0170 chunk 25 optimal weight: 1.9990 overall best weight: 0.2238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 moved from start: 0.3483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3345 Z= 0.172 Angle : 0.640 6.401 4559 Z= 0.331 Chirality : 0.047 0.220 501 Planarity : 0.005 0.049 584 Dihedral : 5.108 25.729 462 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 8.30 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: -2.15 (0.40), residues: 415 helix: -3.49 (1.28), residues: 14 sheet: 0.09 (0.54), residues: 104 loop : -2.05 (0.34), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 55 HIS 0.002 0.001 HIS H 100 PHE 0.010 0.001 PHE E 490 TYR 0.010 0.001 TYR H 61 ARG 0.003 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 76 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.539 Fit side-chains revert: symmetry clash REVERT: H 5 LYS cc_start: 0.8045 (tptp) cc_final: 0.7704 (tptp) REVERT: H 29 LEU cc_start: 0.8154 (mm) cc_final: 0.7462 (mp) REVERT: H 45 LYS cc_start: 0.8667 (ttpp) cc_final: 0.8374 (mptt) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.1398 time to fit residues: 13.2161 Evaluate side-chains 57 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 0.350 ------------------------------------------------------------------------------- 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: 0.0970 chunk 9 optimal weight: 0.7980 chunk 29 optimal weight: 0.0980 chunk 4 optimal weight: 0.3980 chunk 8 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 13 optimal weight: 0.4980 chunk 32 optimal weight: 0.9980 chunk 5 optimal weight: 0.0570 chunk 27 optimal weight: 0.9990 chunk 1 optimal weight: 0.5980 overall best weight: 0.2296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 99 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7112 moved from start: 0.3583 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= 0.171 Angle : 0.640 6.332 4559 Z= 0.328 Chirality : 0.046 0.169 501 Planarity : 0.005 0.051 584 Dihedral : 5.024 25.322 462 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % 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: -2.07 (0.40), residues: 415 helix: -3.55 (1.24), residues: 14 sheet: 0.27 (0.56), residues: 104 loop : -2.05 (0.33), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 55 HIS 0.002 0.001 HIS H 100 PHE 0.010 0.001 PHE E 490 TYR 0.011 0.001 TYR H 61 ARG 0.003 0.000 ARG H 60 ********************** 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 71 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 0.371 Fit side-chains revert: symmetry clash REVERT: H 5 LYS cc_start: 0.7941 (tptp) cc_final: 0.7666 (tptp) REVERT: H 29 LEU cc_start: 0.8086 (mm) cc_final: 0.7443 (mp) outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.1441 time to fit residues: 12.6800 Evaluate side-chains 56 residues out of total 359 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.473 ------------------------------------------------------------------------------- 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: 0.9990 chunk 36 optimal weight: 0.0670 chunk 21 optimal weight: 0.1980 chunk 27 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 23 optimal weight: 0.2980 chunk 15 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 409 GLN ** 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 = 0.3558 r_free = 0.3558 target = 0.106991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.088538 restraints weight = 8090.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.090552 restraints weight = 5372.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.091917 restraints weight = 4013.567| |-----------------------------------------------------------------------------| r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7120 moved from start: 0.3803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3345 Z= 0.222 Angle : 0.660 6.235 4559 Z= 0.342 Chirality : 0.047 0.150 501 Planarity : 0.005 0.056 584 Dihedral : 5.304 26.407 462 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.84 % Favored : 89.16 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % 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: -2.21 (0.40), residues: 415 helix: -3.73 (1.12), residues: 14 sheet: 0.19 (0.55), residues: 104 loop : -2.14 (0.33), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 353 HIS 0.003 0.001 HIS H 100 PHE 0.010 0.002 PHE E 400 TYR 0.018 0.001 TYR L 51 ARG 0.003 0.000 ARG H 40 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1303.38 seconds wall clock time: 23 minutes 40.41 seconds (1420.41 seconds total)