Starting phenix.real_space_refine on Thu Dec 7 18:04:50 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wef_32449/12_2023/7wef_32449.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wef_32449/12_2023/7wef_32449.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wef_32449/12_2023/7wef_32449.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wef_32449/12_2023/7wef_32449.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wef_32449/12_2023/7wef_32449.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wef_32449/12_2023/7wef_32449.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 15 5.16 5 C 2119 2.51 5 N 565 2.21 5 O 629 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 420": "OD1" <-> "OD2" Residue "E ASP 467": "OD1" <-> "OD2" Residue "L TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 3328 Number of models: 1 Model: "" Number of chains: 3 Chain: "C" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 902 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 114} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "E" Number of atoms: 1610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1610 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 12, 'TRANS': 188} Chain: "L" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 816 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 8, 'TRANS': 102} Time building chain proxies: 2.27, per 1000 atoms: 0.68 Number of scatterers: 3328 At special positions: 0 Unit cell: (79.18, 85.6, 86.67, 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 15 16.00 O 629 8.00 N 565 7.00 C 2119 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 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=2.04 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 L 22 " - pdb=" SG CYS L 89 " 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: 1.48 Conformation dependent library (CDL) restraints added in 609.7 milliseconds 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 782 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 8 sheets defined 7.2% alpha, 28.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'C' and resid 28 through 32 removed outlier: 3.672A pdb=" N HIS C 32 " --> pdb=" O PHE C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 90 removed outlier: 3.993A pdb=" N THR C 90 " --> pdb=" O SER C 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 343 Processing helix chain 'E' and resid 366 through 371 removed outlier: 3.776A pdb=" N ASN E 370 " --> pdb=" O SER E 366 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 411 removed outlier: 3.940A pdb=" N ARG E 408 " --> pdb=" O ASP E 405 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA E 411 " --> pdb=" O ARG E 408 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 3 through 5 removed outlier: 4.209A pdb=" N GLN C 3 " --> pdb=" O SER C 25 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N SER C 25 " --> pdb=" O GLN C 3 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N TYR C 79 " --> pdb=" O THR C 70 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 57 through 59 removed outlier: 6.346A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ILE C 50 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ILE C 34 " --> pdb=" O ILE C 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 354 through 358 removed outlier: 3.993A pdb=" N ASN E 354 " --> pdb=" O SER E 399 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER E 399 " --> pdb=" O ASN E 354 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL E 395 " --> pdb=" O ILE E 358 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AA5, first strand: chain 'E' and resid 473 through 474 removed outlier: 3.584A pdb=" N TYR E 473 " --> pdb=" O TYR E 489 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR E 489 " --> pdb=" O TYR E 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.041A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 9 through 12 removed outlier: 3.528A pdb=" N ALA L 91 " --> pdb=" O VAL L 102 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL L 102 " --> pdb=" O ALA L 91 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 18 through 23 removed outlier: 3.557A pdb=" N VAL L 18 " --> pdb=" O ILE L 76 " (cutoff:3.500A) 87 hydrogen bonds defined for protein. 213 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: 1.59 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: 1066 1.35 - 1.47: 943 1.47 - 1.59: 1395 1.59 - 1.71: 0 1.71 - 1.84: 18 Bond restraints: 3422 Sorted by residual: bond pdb=" N LEU C 104 " pdb=" CA LEU C 104 " ideal model delta sigma weight residual 1.465 1.452 0.013 1.31e-02 5.83e+03 9.85e-01 bond pdb=" CB CYS E 379 " pdb=" SG CYS E 379 " ideal model delta sigma weight residual 1.808 1.837 -0.029 3.30e-02 9.18e+02 7.49e-01 bond pdb=" CA THR E 333 " pdb=" CB THR E 333 " ideal model delta sigma weight residual 1.530 1.544 -0.014 1.69e-02 3.50e+03 6.96e-01 bond pdb=" CA ILE L 76 " pdb=" CB ILE L 76 " ideal model delta sigma weight residual 1.540 1.529 0.011 1.36e-02 5.41e+03 6.45e-01 bond pdb=" CB TRP C 47 " pdb=" CG TRP C 47 " ideal model delta sigma weight residual 1.498 1.475 0.023 3.10e-02 1.04e+03 5.72e-01 ... (remaining 3417 not shown) Histogram of bond angle deviations from ideal: 100.10 - 106.88: 121 106.88 - 113.66: 1793 113.66 - 120.45: 1244 120.45 - 127.23: 1458 127.23 - 134.01: 46 Bond angle restraints: 4662 Sorted by residual: angle pdb=" C ARG C 64 " pdb=" N ASP C 65 " pdb=" CA ASP C 65 " ideal model delta sigma weight residual 121.54 126.02 -4.48 1.91e+00 2.74e-01 5.51e+00 angle pdb=" C ILE E 332 " pdb=" N THR E 333 " pdb=" CA THR E 333 " ideal model delta sigma weight residual 121.54 125.79 -4.25 1.91e+00 2.74e-01 4.95e+00 angle pdb=" CA PHE C 107 " pdb=" C PHE C 107 " pdb=" N ASP C 108 " ideal model delta sigma weight residual 115.29 117.80 -2.51 1.18e+00 7.18e-01 4.54e+00 angle pdb=" C MET C 69 " pdb=" CA MET C 69 " pdb=" CB MET C 69 " ideal model delta sigma weight residual 110.24 113.20 -2.96 1.46e+00 4.69e-01 4.10e+00 angle pdb=" CA PHE C 107 " pdb=" C PHE C 107 " pdb=" O PHE C 107 " ideal model delta sigma weight residual 122.36 119.97 2.39 1.21e+00 6.83e-01 3.91e+00 ... (remaining 4657 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.33: 1805 16.33 - 32.66: 148 32.66 - 48.99: 38 48.99 - 65.32: 4 65.32 - 81.65: 5 Dihedral angle restraints: 2000 sinusoidal: 763 harmonic: 1237 Sorted by residual: dihedral pdb=" CB CYS E 480 " pdb=" SG CYS E 480 " pdb=" SG CYS E 488 " pdb=" CB CYS E 488 " ideal model delta sinusoidal sigma weight residual 93.00 159.95 -66.95 1 1.00e+01 1.00e-02 5.84e+01 dihedral pdb=" CA ILE C 51 " pdb=" C ILE C 51 " pdb=" N ASN C 52 " pdb=" CA ASN C 52 " ideal model delta harmonic sigma weight residual 180.00 162.64 17.36 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CA ASP E 428 " pdb=" C ASP E 428 " pdb=" N PHE E 429 " pdb=" CA PHE E 429 " ideal model delta harmonic sigma weight residual -180.00 -163.76 -16.24 0 5.00e+00 4.00e-02 1.05e+01 ... (remaining 1997 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 278 0.030 - 0.060: 143 0.060 - 0.090: 51 0.090 - 0.120: 19 0.120 - 0.150: 5 Chirality restraints: 496 Sorted by residual: chirality pdb=" CA ILE C 51 " pdb=" N ILE C 51 " pdb=" C ILE C 51 " pdb=" CB ILE C 51 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.61e-01 chirality pdb=" CA ILE L 20 " pdb=" N ILE L 20 " pdb=" C ILE L 20 " pdb=" CB ILE L 20 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.58e-01 chirality pdb=" CA ILE E 434 " pdb=" N ILE E 434 " pdb=" C ILE E 434 " pdb=" CB ILE E 434 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.10e-01 ... (remaining 493 not shown) Planarity restraints: 604 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 47 " 0.012 2.00e-02 2.50e+03 1.66e-02 6.86e+00 pdb=" CG TRP C 47 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 TRP C 47 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP C 47 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP C 47 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TRP C 47 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP C 47 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 47 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 47 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP C 47 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP C 72 " -0.025 5.00e-02 4.00e+02 3.73e-02 2.22e+00 pdb=" N PRO C 73 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO C 73 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 73 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 108 " 0.023 5.00e-02 4.00e+02 3.42e-02 1.87e+00 pdb=" N PRO C 109 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO C 109 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 109 " 0.019 5.00e-02 4.00e+02 ... (remaining 601 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 592 2.77 - 3.30: 2922 3.30 - 3.84: 4973 3.84 - 4.37: 5725 4.37 - 4.90: 10342 Nonbonded interactions: 24554 Sorted by model distance: nonbonded pdb=" ND2 ASN E 439 " pdb=" OE1 GLN E 506 " model vdw 2.239 2.520 nonbonded pdb=" OG1 THR C 28 " pdb=" OG SER C 31 " model vdw 2.300 2.440 nonbonded pdb=" O THR C 28 " pdb=" OG SER C 31 " model vdw 2.309 2.440 nonbonded pdb=" O ASN L 53 " pdb=" NH1 ARG L 55 " model vdw 2.313 2.520 nonbonded pdb=" OH TYR E 369 " pdb=" O PRO E 384 " model vdw 2.326 2.440 ... (remaining 24549 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: 1.910 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: 9.120 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.850 Find NCS groups from input model: 0.080 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 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 : 0.003 0.029 3422 Z= 0.220 Angle : 0.624 5.176 4662 Z= 0.334 Chirality : 0.043 0.150 496 Planarity : 0.004 0.037 604 Dihedral : 12.721 81.647 1200 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.41), residues: 426 helix: -3.97 (0.48), residues: 26 sheet: 0.64 (0.49), residues: 135 loop : -1.38 (0.37), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP C 47 HIS 0.002 0.001 HIS E 505 PHE 0.012 0.002 PHE E 374 TYR 0.015 0.001 TYR E 453 ARG 0.004 0.001 ARG E 509 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 0.422 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.1684 time to fit residues: 12.8189 Evaluate side-chains 55 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.403 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 36 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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: 0.7458 moved from start: 0.0991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3422 Z= 0.275 Angle : 0.618 5.397 4662 Z= 0.319 Chirality : 0.043 0.159 496 Planarity : 0.004 0.037 604 Dihedral : 4.793 17.839 474 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % Rotamer: Outliers : 1.96 % Allowed : 8.66 % Favored : 89.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.41), residues: 426 helix: -3.65 (0.60), residues: 27 sheet: 0.66 (0.49), residues: 135 loop : -1.43 (0.37), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP C 106 HIS 0.004 0.001 HIS E 505 PHE 0.014 0.002 PHE E 429 TYR 0.010 0.002 TYR E 453 ARG 0.003 0.000 ARG C 66 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 60 time to evaluate : 0.360 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 63 average time/residue: 0.1406 time to fit residues: 11.0674 Evaluate side-chains 62 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 56 time to evaluate : 0.392 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0354 time to fit residues: 0.9074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 21 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 32 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 chunk 10 optimal weight: 0.0870 chunk 39 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 31 optimal weight: 0.5980 overall best weight: 0.6158 ------------------------------------------------------------------------------- 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: 0.7440 moved from start: 0.1152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3422 Z= 0.204 Angle : 0.568 5.541 4662 Z= 0.291 Chirality : 0.042 0.161 496 Planarity : 0.004 0.037 604 Dihedral : 4.546 18.645 474 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 1.12 % Allowed : 13.41 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.41), residues: 426 helix: -2.77 (0.92), residues: 21 sheet: 0.84 (0.49), residues: 133 loop : -1.49 (0.36), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 106 HIS 0.002 0.001 HIS E 505 PHE 0.010 0.001 PHE C 63 TYR 0.009 0.001 TYR C 79 ARG 0.002 0.000 ARG C 66 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 59 time to evaluate : 0.334 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 61 average time/residue: 0.1639 time to fit residues: 12.3711 Evaluate side-chains 56 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 54 time to evaluate : 0.346 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0368 time to fit residues: 0.6189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 38 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 39 optimal weight: 0.6980 chunk 41 optimal weight: 0.0270 chunk 37 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 34 optimal weight: 6.9990 overall best weight: 0.6638 ------------------------------------------------------------------------------- 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: 0.7452 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3422 Z= 0.215 Angle : 0.567 5.554 4662 Z= 0.290 Chirality : 0.042 0.155 496 Planarity : 0.004 0.034 604 Dihedral : 4.556 19.463 474 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 1.96 % Allowed : 15.08 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.41), residues: 426 helix: -2.68 (0.98), residues: 21 sheet: 0.82 (0.48), residues: 133 loop : -1.54 (0.36), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 106 HIS 0.003 0.001 HIS E 505 PHE 0.010 0.001 PHE E 429 TYR 0.010 0.001 TYR C 94 ARG 0.002 0.000 ARG C 66 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 56 time to evaluate : 0.401 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 61 average time/residue: 0.1339 time to fit residues: 10.4210 Evaluate side-chains 58 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 53 time to evaluate : 0.336 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0360 time to fit residues: 0.8201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 23 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 21 optimal weight: 0.0570 chunk 37 optimal weight: 0.0770 chunk 10 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 overall best weight: 0.5456 ------------------------------------------------------------------------------- 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: 0.7446 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3422 Z= 0.191 Angle : 0.553 5.582 4662 Z= 0.283 Chirality : 0.041 0.156 496 Planarity : 0.003 0.033 604 Dihedral : 4.445 20.358 474 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 1.96 % Allowed : 15.36 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.40), residues: 426 helix: -2.74 (0.98), residues: 21 sheet: 0.80 (0.48), residues: 134 loop : -1.54 (0.36), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 106 HIS 0.002 0.001 HIS E 505 PHE 0.011 0.001 PHE C 63 TYR 0.009 0.001 TYR C 79 ARG 0.001 0.000 ARG C 66 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 60 time to evaluate : 0.389 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 65 average time/residue: 0.1510 time to fit residues: 12.1821 Evaluate side-chains 59 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 54 time to evaluate : 0.377 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0345 time to fit residues: 0.8271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 24 optimal weight: 2.9990 chunk 10 optimal weight: 0.1980 chunk 41 optimal weight: 0.0020 chunk 34 optimal weight: 8.9990 chunk 19 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 40 optimal weight: 0.0000 chunk 4 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 overall best weight: 0.3392 ------------------------------------------------------------------------------- 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: 0.7414 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 3422 Z= 0.154 Angle : 0.526 5.554 4662 Z= 0.272 Chirality : 0.041 0.156 496 Planarity : 0.003 0.032 604 Dihedral : 4.203 19.307 474 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 0.56 % Allowed : 17.04 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.41), residues: 426 helix: -2.76 (0.97), residues: 21 sheet: 0.59 (0.47), residues: 141 loop : -1.40 (0.37), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 106 HIS 0.002 0.001 HIS C 35 PHE 0.010 0.001 PHE C 63 TYR 0.007 0.001 TYR E 423 ARG 0.002 0.000 ARG C 66 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 56 time to evaluate : 0.382 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 56 average time/residue: 0.1527 time to fit residues: 10.7368 Evaluate side-chains 56 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 55 time to evaluate : 0.307 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0276 time to fit residues: 0.4312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 30 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 19 optimal weight: 0.0770 chunk 16 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 12 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 26 optimal weight: 0.3980 overall best weight: 0.5538 ------------------------------------------------------------------------------- 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: 0.7446 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3422 Z= 0.191 Angle : 0.545 5.265 4662 Z= 0.281 Chirality : 0.041 0.152 496 Planarity : 0.004 0.031 604 Dihedral : 4.301 21.297 474 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 0.84 % Allowed : 17.60 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.41), residues: 426 helix: -2.77 (0.97), residues: 21 sheet: 0.40 (0.46), residues: 151 loop : -1.39 (0.38), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 106 HIS 0.002 0.001 HIS E 505 PHE 0.010 0.001 PHE C 107 TYR 0.009 0.001 TYR C 79 ARG 0.001 0.000 ARG C 66 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 55 time to evaluate : 0.376 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 56 average time/residue: 0.1420 time to fit residues: 10.0756 Evaluate side-chains 56 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 54 time to evaluate : 0.367 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0353 time to fit residues: 0.6434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 28 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 37 optimal weight: 0.0370 chunk 39 optimal weight: 4.9990 chunk 36 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 overall best weight: 0.6258 ------------------------------------------------------------------------------- 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: 0.7457 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3422 Z= 0.208 Angle : 0.552 5.259 4662 Z= 0.285 Chirality : 0.042 0.150 496 Planarity : 0.004 0.033 604 Dihedral : 4.344 22.854 474 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 1.68 % Allowed : 17.04 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.41), residues: 426 helix: -2.72 (0.99), residues: 21 sheet: 0.35 (0.46), residues: 151 loop : -1.40 (0.37), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 106 HIS 0.002 0.001 HIS E 505 PHE 0.010 0.001 PHE C 107 TYR 0.007 0.001 TYR E 423 ARG 0.002 0.000 ARG E 408 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 55 time to evaluate : 0.383 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 59 average time/residue: 0.1416 time to fit residues: 10.7420 Evaluate side-chains 58 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 55 time to evaluate : 0.394 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0513 time to fit residues: 0.7228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 11 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 38 optimal weight: 4.9990 chunk 25 optimal weight: 0.5980 chunk 40 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 28 optimal weight: 0.4980 chunk 42 optimal weight: 0.5980 chunk 39 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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: 0.7456 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 : 0.003 0.030 3422 Z= 0.203 Angle : 0.554 5.266 4662 Z= 0.286 Chirality : 0.042 0.150 496 Planarity : 0.004 0.035 604 Dihedral : 4.358 23.904 474 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 0.84 % Allowed : 18.16 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.41), residues: 426 helix: -2.75 (0.98), residues: 21 sheet: 0.34 (0.46), residues: 151 loop : -1.40 (0.37), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 106 HIS 0.002 0.001 HIS E 505 PHE 0.010 0.001 PHE C 107 TYR 0.009 0.001 TYR C 79 ARG 0.001 0.000 ARG C 66 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 58 time to evaluate : 0.367 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 58 average time/residue: 0.1472 time to fit residues: 10.6585 Evaluate side-chains 59 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 57 time to evaluate : 0.352 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0437 time to fit residues: 0.6075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 34 optimal weight: 0.5980 chunk 3 optimal weight: 0.6980 chunk 26 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 chunk 27 optimal weight: 0.0050 chunk 36 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 overall best weight: 0.4994 ------------------------------------------------------------------------------- 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: 0.7446 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3422 Z= 0.188 Angle : 0.548 5.337 4662 Z= 0.283 Chirality : 0.041 0.151 496 Planarity : 0.004 0.035 604 Dihedral : 4.299 23.887 474 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 0.56 % Allowed : 18.72 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.41), residues: 426 helix: -2.72 (0.99), residues: 21 sheet: 0.38 (0.47), residues: 151 loop : -1.37 (0.37), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C 106 HIS 0.002 0.001 HIS E 505 PHE 0.008 0.001 PHE C 107 TYR 0.007 0.001 TYR E 423 ARG 0.001 0.000 ARG E 493 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 59 time to evaluate : 0.373 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 59 average time/residue: 0.1511 time to fit residues: 11.1476 Evaluate side-chains 60 residues out of total 362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 58 time to evaluate : 0.368 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0434 time to fit residues: 0.6297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 35 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 6 optimal weight: 0.0870 chunk 29 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 27 optimal weight: 0.3980 chunk 26 optimal weight: 1.9990 chunk 16 optimal weight: 0.0000 overall best weight: 0.3362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.152669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.133953 restraints weight = 4645.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.135840 restraints weight = 3377.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.137562 restraints weight = 2681.768| |-----------------------------------------------------------------------------| r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 3422 Z= 0.166 Angle : 0.544 5.732 4662 Z= 0.281 Chirality : 0.041 0.154 496 Planarity : 0.004 0.038 604 Dihedral : 4.163 22.673 474 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 0.00 % Allowed : 18.99 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.41), residues: 426 helix: -2.52 (0.91), residues: 27 sheet: 0.62 (0.48), residues: 141 loop : -1.40 (0.37), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP C 106 HIS 0.002 0.001 HIS C 35 PHE 0.007 0.001 PHE E 400 TYR 0.010 0.001 TYR C 79 ARG 0.001 0.000 ARG C 66 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1285.28 seconds wall clock time: 23 minutes 56.38 seconds (1436.38 seconds total)