Starting phenix.real_space_refine on Mon Jun 24 16:04:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wt9_32772/06_2024/7wt9_32772.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wt9_32772/06_2024/7wt9_32772.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/7wt9_32772/06_2024/7wt9_32772.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wt9_32772/06_2024/7wt9_32772.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wt9_32772/06_2024/7wt9_32772.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wt9_32772/06_2024/7wt9_32772.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 2117 2.51 5 N 564 2.21 5 O 646 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H GLU 6": "OE1" <-> "OE2" Residue "H ASP 61": "OD1" <-> "OD2" Residue "E TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 364": "OD1" <-> "OD2" Residue "E PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 471": "OE1" <-> "OE2" Residue "E GLU 516": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 3343 Number of models: 1 Model: "" Number of chains: 3 Chain: "H" Number of atoms: 900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 900 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 119} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1612 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 12, 'TRANS': 188} Chain: "A" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 831 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 100} Time building chain proxies: 3.67, per 1000 atoms: 1.10 Number of scatterers: 3343 At special positions: 0 Unit cell: (63.44, 80.08, 105.04, 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 646 8.00 N 564 7.00 C 2117 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 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=2.05 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.04 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 23 " - pdb=" SG CYS A 88 " 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: 1.19 Conformation dependent library (CDL) restraints added in 610.9 milliseconds 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 792 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 9 sheets defined 10.0% alpha, 18.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'H' and resid 61 through 64 removed outlier: 3.734A pdb=" N LYS H 64 " --> pdb=" O ASP H 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 61 through 64' Processing helix chain 'E' and resid 337 through 343 Processing helix chain 'E' and resid 365 through 372 removed outlier: 3.525A pdb=" N TYR E 369 " --> pdb=" O TYR E 365 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ALA E 372 " --> pdb=" O LEU E 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 387 removed outlier: 3.716A pdb=" N LEU E 387 " --> pdb=" O PRO E 384 " (cutoff:3.500A) Processing helix chain 'E' and resid 403 through 410 Processing helix chain 'E' and resid 417 through 422 Processing helix chain 'A' and resid 79 through 83 removed outlier: 4.116A pdb=" N ILE A 83 " --> pdb=" O PRO A 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 4 through 7 removed outlier: 3.562A pdb=" N SER H 7 " --> pdb=" O SER H 21 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER H 21 " --> pdb=" O SER H 7 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 12 removed outlier: 5.790A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 395 through 397 Processing sheet with id=AA4, first strand: chain 'E' and resid 400 through 402 removed outlier: 3.579A pdb=" N PHE E 400 " --> pdb=" O VAL E 510 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AA6, first strand: chain 'E' and resid 473 through 474 Processing sheet with id=AA7, first strand: chain 'A' and resid 10 through 11 Processing sheet with id=AA8, first strand: chain 'A' and resid 22 through 24 removed outlier: 3.510A pdb=" N THR A 72 " --> pdb=" O SER A 65 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR A 74 " --> pdb=" O SER A 63 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N SER A 63 " --> pdb=" O THR A 74 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 44 through 46 removed outlier: 3.515A pdb=" N GLN A 38 " --> pdb=" O THR A 85 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR A 85 " --> pdb=" O GLN A 38 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N THR A 97 " --> pdb=" O GLN A 90 " (cutoff:3.500A) 58 hydrogen bonds defined for protein. 156 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: 0.79 Time building geometry restraints manager: 1.33 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: 1078 1.35 - 1.47: 865 1.47 - 1.59: 1460 1.59 - 1.70: 0 1.70 - 1.82: 20 Bond restraints: 3423 Sorted by residual: bond pdb=" N VAL E 445 " pdb=" CA VAL E 445 " ideal model delta sigma weight residual 1.461 1.494 -0.034 1.19e-02 7.06e+03 8.07e+00 bond pdb=" N LYS E 444 " pdb=" CA LYS E 444 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.23e-02 6.61e+03 7.60e+00 bond pdb=" C SER A 7 " pdb=" N PRO A 8 " ideal model delta sigma weight residual 1.334 1.393 -0.059 2.34e-02 1.83e+03 6.33e+00 bond pdb=" N SER E 446 " pdb=" CA SER E 446 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.23e-02 6.61e+03 5.19e+00 bond pdb=" N ASN E 448 " pdb=" CA ASN E 448 " ideal model delta sigma weight residual 1.460 1.486 -0.027 1.28e-02 6.10e+03 4.37e+00 ... (remaining 3418 not shown) Histogram of bond angle deviations from ideal: 99.91 - 106.71: 110 106.71 - 113.51: 1688 113.51 - 120.31: 1287 120.31 - 127.11: 1534 127.11 - 133.91: 35 Bond angle restraints: 4654 Sorted by residual: angle pdb=" C GLY A 68 " pdb=" N THR A 69 " pdb=" CA THR A 69 " ideal model delta sigma weight residual 123.91 131.91 -8.00 1.66e+00 3.63e-01 2.32e+01 angle pdb=" CA GLN E 409 " pdb=" CB GLN E 409 " pdb=" CG GLN E 409 " ideal model delta sigma weight residual 114.10 123.38 -9.28 2.00e+00 2.50e-01 2.15e+01 angle pdb=" CA LEU E 518 " pdb=" CB LEU E 518 " pdb=" CG LEU E 518 " ideal model delta sigma weight residual 116.30 132.20 -15.90 3.50e+00 8.16e-02 2.06e+01 angle pdb=" CB MET A 4 " pdb=" CG MET A 4 " pdb=" SD MET A 4 " ideal model delta sigma weight residual 112.70 124.79 -12.09 3.00e+00 1.11e-01 1.62e+01 angle pdb=" CB GLU E 340 " pdb=" CG GLU E 340 " pdb=" CD GLU E 340 " ideal model delta sigma weight residual 112.60 119.08 -6.48 1.70e+00 3.46e-01 1.46e+01 ... (remaining 4649 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.01: 1826 17.01 - 34.02: 162 34.02 - 51.04: 38 51.04 - 68.05: 4 68.05 - 85.06: 4 Dihedral angle restraints: 2034 sinusoidal: 787 harmonic: 1247 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 93.00 175.66 -82.66 1 1.00e+01 1.00e-02 8.37e+01 dihedral pdb=" CB CYS E 379 " pdb=" SG CYS E 379 " pdb=" SG CYS E 432 " pdb=" CB CYS E 432 " ideal model delta sinusoidal sigma weight residual -86.00 -13.69 -72.31 1 1.00e+01 1.00e-02 6.68e+01 dihedral pdb=" CA GLU H 98 " pdb=" C GLU H 98 " pdb=" N VAL H 99 " pdb=" CA VAL H 99 " ideal model delta harmonic sigma weight residual -180.00 -142.14 -37.86 0 5.00e+00 4.00e-02 5.73e+01 ... (remaining 2031 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 442 0.100 - 0.200: 58 0.200 - 0.300: 4 0.300 - 0.400: 1 0.400 - 0.500: 2 Chirality restraints: 507 Sorted by residual: chirality pdb=" CB THR H 114 " pdb=" CA THR H 114 " pdb=" OG1 THR H 114 " pdb=" CG2 THR H 114 " both_signs ideal model delta sigma weight residual False 2.55 2.05 0.50 2.00e-01 2.50e+01 6.24e+00 chirality pdb=" CB ILE E 402 " pdb=" CA ILE E 402 " pdb=" CG1 ILE E 402 " pdb=" CG2 ILE E 402 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.41 2.00e-01 2.50e+01 4.26e+00 chirality pdb=" CB VAL E 341 " pdb=" CA VAL E 341 " pdb=" CG1 VAL E 341 " pdb=" CG2 VAL E 341 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.41e+00 ... (remaining 504 not shown) Planarity restraints: 604 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 35 " -0.015 2.00e-02 2.50e+03 2.46e-02 1.52e+01 pdb=" CG TRP A 35 " 0.057 2.00e-02 2.50e+03 pdb=" CD1 TRP A 35 " -0.044 2.00e-02 2.50e+03 pdb=" CD2 TRP A 35 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 35 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 35 " 0.016 2.00e-02 2.50e+03 pdb=" CE3 TRP A 35 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 35 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 35 " -0.019 2.00e-02 2.50e+03 pdb=" CH2 TRP A 35 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 50 " 0.014 2.00e-02 2.50e+03 2.86e-02 8.16e+00 pdb=" C ASP A 50 " -0.049 2.00e-02 2.50e+03 pdb=" O ASP A 50 " 0.019 2.00e-02 2.50e+03 pdb=" N ALA A 51 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 351 " 0.014 2.00e-02 2.50e+03 1.93e-02 7.43e+00 pdb=" CG TYR E 351 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 TYR E 351 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR E 351 " 0.017 2.00e-02 2.50e+03 pdb=" CE1 TYR E 351 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR E 351 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR E 351 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR E 351 " -0.001 2.00e-02 2.50e+03 ... (remaining 601 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 974 2.82 - 3.34: 2792 3.34 - 3.86: 5460 3.86 - 4.38: 5736 4.38 - 4.90: 9882 Nonbonded interactions: 24844 Sorted by model distance: nonbonded pdb=" O TYR A 86 " pdb=" OG1 THR A 102 " model vdw 2.304 2.440 nonbonded pdb=" OG1 THR A 74 " pdb=" OD1 ASN A 76 " model vdw 2.318 2.440 nonbonded pdb=" OG SER H 56 " pdb=" OG1 THR E 415 " model vdw 2.339 2.440 nonbonded pdb=" OG1 THR E 376 " pdb=" NZ LYS E 378 " model vdw 2.358 2.520 nonbonded pdb=" O ALA A 25 " pdb=" OG1 THR A 69 " model vdw 2.392 2.440 ... (remaining 24839 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: 2.820 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: 9.210 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.210 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 3423 Z= 0.378 Angle : 1.266 15.900 4654 Z= 0.676 Chirality : 0.071 0.500 507 Planarity : 0.009 0.069 604 Dihedral : 13.288 85.060 1224 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer: Outliers : 0.27 % Allowed : 1.36 % Favored : 98.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.49 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.40 (0.35), residues: 424 helix: -3.94 (0.49), residues: 33 sheet: -2.31 (0.46), residues: 100 loop : -2.14 (0.32), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.006 TRP A 35 HIS 0.001 0.000 HIS E 505 PHE 0.045 0.003 PHE E 400 TYR 0.047 0.003 TYR E 351 ARG 0.005 0.001 ARG E 493 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 113 time to evaluate : 0.380 Fit side-chains REVERT: H 82 MET cc_start: 0.7811 (mpp) cc_final: 0.7220 (mpp) REVERT: H 106 MET cc_start: 0.6874 (ptm) cc_final: 0.6641 (ptm) REVERT: E 389 ASP cc_start: 0.8174 (m-30) cc_final: 0.7776 (p0) REVERT: E 460 ASN cc_start: 0.8024 (t0) cc_final: 0.7194 (p0) outliers start: 1 outliers final: 0 residues processed: 114 average time/residue: 0.1441 time to fit residues: 20.0437 Evaluate side-chains 85 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 21 optimal weight: 0.0670 chunk 32 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 20 optimal weight: 0.0970 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 overall best weight: 0.5516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 GLN ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3423 Z= 0.207 Angle : 0.625 10.059 4654 Z= 0.329 Chirality : 0.044 0.160 507 Planarity : 0.005 0.045 604 Dihedral : 5.626 28.320 475 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 15.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 0.27 % Allowed : 3.80 % Favored : 95.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -2.99 (0.36), residues: 424 helix: -2.86 (0.74), residues: 33 sheet: -1.94 (0.43), residues: 125 loop : -1.93 (0.34), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 35 HIS 0.003 0.001 HIS E 519 PHE 0.023 0.002 PHE A 71 TYR 0.024 0.002 TYR E 380 ARG 0.003 0.000 ARG H 97 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 88 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 389 ASP cc_start: 0.8321 (m-30) cc_final: 0.7906 (p0) REVERT: A 3 GLN cc_start: 0.8067 (mp10) cc_final: 0.7853 (mp10) REVERT: A 53 ASN cc_start: 0.7563 (m110) cc_final: 0.7230 (m110) outliers start: 1 outliers final: 0 residues processed: 88 average time/residue: 0.1669 time to fit residues: 17.6393 Evaluate side-chains 65 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 chunk 38 optimal weight: 0.4980 chunk 41 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 30 optimal weight: 0.3980 chunk 28 optimal weight: 0.5980 chunk 19 optimal weight: 0.2980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.2998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3423 Z= 0.190 Angle : 0.590 8.454 4654 Z= 0.306 Chirality : 0.044 0.148 507 Planarity : 0.005 0.044 604 Dihedral : 5.312 27.238 475 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -2.80 (0.37), residues: 424 helix: -2.63 (0.72), residues: 33 sheet: -1.90 (0.42), residues: 125 loop : -1.76 (0.35), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 35 HIS 0.001 0.000 HIS E 505 PHE 0.021 0.002 PHE E 392 TYR 0.021 0.001 TYR E 380 ARG 0.004 0.001 ARG E 355 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 378 LYS cc_start: 0.6302 (mttp) cc_final: 0.5924 (mttp) REVERT: E 389 ASP cc_start: 0.8348 (m-30) cc_final: 0.7941 (p0) REVERT: E 418 ILE cc_start: 0.8646 (mp) cc_final: 0.8412 (mp) REVERT: A 4 MET cc_start: 0.7434 (tpt) cc_final: 0.7209 (tpp) REVERT: A 50 ASP cc_start: 0.9026 (t0) cc_final: 0.8800 (t0) REVERT: A 53 ASN cc_start: 0.7604 (m110) cc_final: 0.7165 (m110) REVERT: A 71 PHE cc_start: 0.9087 (m-80) cc_final: 0.8362 (m-10) outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.1631 time to fit residues: 18.4714 Evaluate side-chains 70 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 0.9980 chunk 18 optimal weight: 0.1980 chunk 25 optimal weight: 0.5980 chunk 38 optimal weight: 4.9990 chunk 40 optimal weight: 0.0980 chunk 20 optimal weight: 0.0170 chunk 36 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 overall best weight: 0.3818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.3265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3423 Z= 0.166 Angle : 0.597 9.982 4654 Z= 0.308 Chirality : 0.044 0.145 507 Planarity : 0.004 0.045 604 Dihedral : 5.169 27.706 475 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 15.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -2.69 (0.37), residues: 424 helix: -2.31 (0.77), residues: 33 sheet: -1.76 (0.43), residues: 122 loop : -1.77 (0.36), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP H 36 HIS 0.000 0.000 HIS E 505 PHE 0.017 0.002 PHE E 392 TYR 0.022 0.001 TYR E 380 ARG 0.002 0.000 ARG H 97 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 33 TYR cc_start: 0.6545 (m-10) cc_final: 0.6260 (m-10) REVERT: H 34 MET cc_start: 0.6203 (mmp) cc_final: 0.5753 (mmm) REVERT: H 78 LEU cc_start: 0.8218 (tp) cc_final: 0.7971 (tp) REVERT: E 378 LYS cc_start: 0.6313 (mttp) cc_final: 0.5999 (mttp) REVERT: E 389 ASP cc_start: 0.8384 (m-30) cc_final: 0.7937 (p0) REVERT: E 418 ILE cc_start: 0.8583 (mp) cc_final: 0.8330 (mp) REVERT: A 50 ASP cc_start: 0.9033 (t0) cc_final: 0.8782 (t0) REVERT: A 71 PHE cc_start: 0.9048 (m-80) cc_final: 0.8353 (m-10) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.1718 time to fit residues: 17.7688 Evaluate side-chains 68 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 chunk 36 optimal weight: 0.2980 chunk 10 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.3804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3423 Z= 0.255 Angle : 0.648 9.078 4654 Z= 0.335 Chirality : 0.045 0.154 507 Planarity : 0.005 0.044 604 Dihedral : 5.483 29.308 475 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 19.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.43 % Favored : 90.57 % Rotamer: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -2.74 (0.38), residues: 424 helix: -2.39 (0.77), residues: 33 sheet: -2.03 (0.43), residues: 123 loop : -1.65 (0.37), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP E 353 HIS 0.000 0.000 HIS E 505 PHE 0.025 0.002 PHE E 392 TYR 0.021 0.002 TYR E 380 ARG 0.005 0.001 ARG E 457 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 20 LEU cc_start: 0.9453 (mt) cc_final: 0.9167 (mp) REVERT: H 78 LEU cc_start: 0.8262 (tp) cc_final: 0.8029 (tp) REVERT: H 103 ASN cc_start: 0.7627 (t0) cc_final: 0.7381 (t0) REVERT: E 418 ILE cc_start: 0.8612 (mp) cc_final: 0.8349 (mp) REVERT: E 516 GLU cc_start: 0.7129 (pm20) cc_final: 0.6864 (pm20) REVERT: A 50 ASP cc_start: 0.9130 (t0) cc_final: 0.8701 (t0) REVERT: A 53 ASN cc_start: 0.7904 (m110) cc_final: 0.7570 (m-40) REVERT: A 71 PHE cc_start: 0.9083 (m-80) cc_final: 0.8405 (m-10) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.1790 time to fit residues: 18.6970 Evaluate side-chains 67 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 3 optimal weight: 0.5980 chunk 13 optimal weight: 0.8980 chunk 21 optimal weight: 0.0670 chunk 39 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 chunk 23 optimal weight: 0.6980 chunk 29 optimal weight: 0.7980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.3849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3423 Z= 0.199 Angle : 0.618 8.640 4654 Z= 0.313 Chirality : 0.045 0.148 507 Planarity : 0.005 0.041 604 Dihedral : 5.230 28.391 475 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 17.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -2.66 (0.38), residues: 424 helix: -2.28 (0.79), residues: 34 sheet: -1.79 (0.42), residues: 130 loop : -1.69 (0.37), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 353 HIS 0.000 0.000 HIS E 505 PHE 0.017 0.002 PHE A 71 TYR 0.020 0.002 TYR E 380 ARG 0.004 0.000 ARG H 97 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 20 LEU cc_start: 0.9421 (mt) cc_final: 0.9146 (mp) REVERT: E 417 ASN cc_start: 0.6851 (p0) cc_final: 0.6345 (p0) REVERT: E 418 ILE cc_start: 0.8694 (mp) cc_final: 0.8219 (mp) REVERT: A 3 GLN cc_start: 0.8238 (mp10) cc_final: 0.7987 (mp10) REVERT: A 50 ASP cc_start: 0.9191 (t0) cc_final: 0.8894 (t0) REVERT: A 53 ASN cc_start: 0.7939 (m110) cc_final: 0.7664 (m-40) REVERT: A 71 PHE cc_start: 0.9061 (m-80) cc_final: 0.8484 (m-10) outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.1569 time to fit residues: 17.2605 Evaluate side-chains 73 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 25 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 18 optimal weight: 0.3980 chunk 16 optimal weight: 0.2980 chunk 12 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 27 optimal weight: 0.2980 chunk 20 optimal weight: 0.8980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.4018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3423 Z= 0.189 Angle : 0.620 10.532 4654 Z= 0.314 Chirality : 0.045 0.172 507 Planarity : 0.004 0.039 604 Dihedral : 5.156 28.334 475 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 18.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.96 % Favored : 91.04 % Rotamer: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -2.58 (0.39), residues: 424 helix: -2.28 (0.79), residues: 34 sheet: -1.70 (0.44), residues: 127 loop : -1.65 (0.37), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.003 TRP H 36 HIS 0.001 0.000 HIS E 519 PHE 0.015 0.002 PHE A 71 TYR 0.013 0.001 TYR E 380 ARG 0.005 0.000 ARG H 97 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 33 TYR cc_start: 0.7376 (m-10) cc_final: 0.7139 (m-10) REVERT: H 78 LEU cc_start: 0.8428 (tp) cc_final: 0.8105 (tp) REVERT: H 85 LEU cc_start: 0.8638 (mt) cc_final: 0.8023 (mt) REVERT: E 417 ASN cc_start: 0.6803 (p0) cc_final: 0.6440 (p0) REVERT: E 418 ILE cc_start: 0.8756 (mp) cc_final: 0.8251 (mp) REVERT: A 3 GLN cc_start: 0.8233 (mp10) cc_final: 0.7991 (mp10) REVERT: A 50 ASP cc_start: 0.9096 (t0) cc_final: 0.8679 (t0) REVERT: A 71 PHE cc_start: 0.9080 (m-80) cc_final: 0.8510 (m-10) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.1538 time to fit residues: 16.4670 Evaluate side-chains 72 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 36 optimal weight: 0.0570 chunk 38 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 11 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 103 ASN ** A 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 53 ASN ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.4392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3423 Z= 0.236 Angle : 0.662 10.163 4654 Z= 0.338 Chirality : 0.046 0.161 507 Planarity : 0.005 0.042 604 Dihedral : 5.279 28.027 475 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 20.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.38 % Favored : 89.62 % Rotamer: Outliers : 0.27 % Allowed : 2.72 % Favored : 97.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -2.70 (0.39), residues: 424 helix: -2.43 (0.77), residues: 34 sheet: -1.90 (0.44), residues: 130 loop : -1.65 (0.38), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP H 36 HIS 0.001 0.000 HIS E 505 PHE 0.019 0.002 PHE A 71 TYR 0.020 0.002 TYR H 58 ARG 0.004 0.001 ARG E 457 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 87 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 33 TYR cc_start: 0.7730 (m-10) cc_final: 0.7282 (m-10) REVERT: H 78 LEU cc_start: 0.8440 (tp) cc_final: 0.8156 (tp) REVERT: H 85 LEU cc_start: 0.8968 (mt) cc_final: 0.8465 (mt) REVERT: E 393 THR cc_start: 0.8577 (t) cc_final: 0.8331 (m) REVERT: E 417 ASN cc_start: 0.6912 (p0) cc_final: 0.6518 (p0) REVERT: E 418 ILE cc_start: 0.8617 (mp) cc_final: 0.8133 (mp) REVERT: E 516 GLU cc_start: 0.7131 (pm20) cc_final: 0.6761 (pm20) REVERT: A 3 GLN cc_start: 0.8132 (mp10) cc_final: 0.7895 (mp10) REVERT: A 50 ASP cc_start: 0.9108 (t0) cc_final: 0.8773 (t0) REVERT: A 71 PHE cc_start: 0.9131 (m-80) cc_final: 0.8565 (m-10) outliers start: 1 outliers final: 1 residues processed: 87 average time/residue: 0.1780 time to fit residues: 18.5693 Evaluate side-chains 70 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 69 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.9990 chunk 37 optimal weight: 0.0030 chunk 24 optimal weight: 0.3980 chunk 39 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 53 ASN ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.4457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3423 Z= 0.215 Angle : 0.690 10.014 4654 Z= 0.349 Chirality : 0.046 0.150 507 Planarity : 0.004 0.042 604 Dihedral : 5.210 27.724 475 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 18.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.20 % Favored : 90.80 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -2.70 (0.39), residues: 424 helix: -2.53 (0.74), residues: 35 sheet: -1.84 (0.44), residues: 127 loop : -1.67 (0.38), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP H 36 HIS 0.001 0.000 HIS E 505 PHE 0.018 0.002 PHE A 71 TYR 0.012 0.002 TYR E 473 ARG 0.003 0.000 ARG E 457 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 46 GLU cc_start: 0.8767 (tp30) cc_final: 0.8331 (mp0) REVERT: H 78 LEU cc_start: 0.8278 (tp) cc_final: 0.8010 (tp) REVERT: H 85 LEU cc_start: 0.8977 (mt) cc_final: 0.8512 (mt) REVERT: E 417 ASN cc_start: 0.6700 (p0) cc_final: 0.6267 (p0) REVERT: E 418 ILE cc_start: 0.8501 (mp) cc_final: 0.7939 (mp) REVERT: A 3 GLN cc_start: 0.8129 (mp10) cc_final: 0.7901 (mp10) REVERT: A 4 MET cc_start: 0.7249 (tpp) cc_final: 0.6996 (tpt) REVERT: A 27 GLN cc_start: 0.8634 (tm-30) cc_final: 0.8425 (tm-30) REVERT: A 50 ASP cc_start: 0.9109 (t0) cc_final: 0.8806 (t0) REVERT: A 53 ASN cc_start: 0.8086 (m110) cc_final: 0.7753 (m-40) REVERT: A 71 PHE cc_start: 0.9112 (m-80) cc_final: 0.8544 (m-10) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.1585 time to fit residues: 16.3550 Evaluate side-chains 68 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 0.9980 chunk 26 optimal weight: 0.0570 chunk 35 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 4 optimal weight: 0.0970 chunk 9 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 overall best weight: 0.5296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.4546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3423 Z= 0.216 Angle : 0.692 9.964 4654 Z= 0.348 Chirality : 0.046 0.150 507 Planarity : 0.005 0.058 604 Dihedral : 5.264 27.614 475 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 21.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.14 % Favored : 89.86 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -2.70 (0.39), residues: 424 helix: -2.44 (0.75), residues: 34 sheet: -1.94 (0.44), residues: 129 loop : -1.63 (0.38), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP H 36 HIS 0.000 0.000 HIS E 505 PHE 0.019 0.002 PHE E 464 TYR 0.028 0.002 TYR E 351 ARG 0.012 0.001 ARG A 61 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 78 LEU cc_start: 0.8244 (tp) cc_final: 0.7961 (tp) REVERT: H 85 LEU cc_start: 0.8980 (mt) cc_final: 0.8552 (mt) REVERT: E 393 THR cc_start: 0.8584 (t) cc_final: 0.8383 (m) REVERT: E 417 ASN cc_start: 0.6791 (p0) cc_final: 0.6416 (p0) REVERT: E 418 ILE cc_start: 0.8540 (mp) cc_final: 0.7992 (mp) REVERT: A 3 GLN cc_start: 0.8124 (mp10) cc_final: 0.7902 (mp10) REVERT: A 27 GLN cc_start: 0.8632 (tm-30) cc_final: 0.8405 (tm-30) REVERT: A 50 ASP cc_start: 0.9140 (t0) cc_final: 0.8834 (t0) REVERT: A 53 ASN cc_start: 0.8207 (m110) cc_final: 0.7626 (m-40) REVERT: A 71 PHE cc_start: 0.9157 (m-80) cc_final: 0.8610 (m-10) outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.1540 time to fit residues: 16.5562 Evaluate side-chains 70 residues out of total 370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 0.2980 chunk 1 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 28 optimal weight: 0.2980 chunk 26 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 370 ASN ** A 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.093229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.078666 restraints weight = 11986.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.080526 restraints weight = 7574.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.081847 restraints weight = 5418.872| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.4929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 3423 Z= 0.304 Angle : 0.740 9.862 4654 Z= 0.380 Chirality : 0.048 0.152 507 Planarity : 0.005 0.062 604 Dihedral : 5.596 28.393 475 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 25.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.03 % Favored : 87.97 % Rotamer: Outliers : 0.27 % Allowed : 0.54 % Favored : 99.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.83 (0.40), residues: 424 helix: -2.65 (0.73), residues: 34 sheet: -2.02 (0.45), residues: 129 loop : -1.70 (0.38), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP H 36 HIS 0.001 0.000 HIS E 505 PHE 0.024 0.003 PHE A 71 TYR 0.015 0.002 TYR E 396 ARG 0.011 0.001 ARG A 61 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1386.89 seconds wall clock time: 25 minutes 10.96 seconds (1510.96 seconds total)