Starting phenix.real_space_refine (version: 1.21rc1) on Mon Oct 2 22:22:14 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yho_33832/10_2023/7yho_33832_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yho_33832/10_2023/7yho_33832.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yho_33832/10_2023/7yho_33832.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yho_33832/10_2023/7yho_33832.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yho_33832/10_2023/7yho_33832_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yho_33832/10_2023/7yho_33832_updated.pdb" } resolution = 3.3 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: 6 Type Number sf(0) Gaussians Fe 4 7.16 5 P 49 5.49 5 S 23 5.16 5 C 2348 2.51 5 N 697 2.21 5 O 802 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 1300": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 3923 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2910 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 22, 'TRANS': 338} Chain breaks: 5 Chain: "B" Number of atoms: 539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 539 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "C" Number of atoms: 466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 466 Classifications: {'DNA': 23} Link IDs: {'rna3p': 22} Chain: "A" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1826 SG CYS A1045 53.403 54.606 40.943 1.00 78.34 S ATOM 1774 SG CYS A1038 50.038 53.672 46.312 1.00 73.18 S ATOM 1845 SG CYS A1048 55.115 57.801 46.484 1.00 81.69 S ATOM 1888 SG CYS A1054 55.624 51.262 45.560 1.00 83.08 S Time building chain proxies: 2.73, per 1000 atoms: 0.70 Number of scatterers: 3923 At special positions: 0 Unit cell: (73.03, 105.19, 89.11, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 4 26.01 S 23 16.00 P 49 15.00 O 802 8.00 N 697 7.00 C 2348 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.01 Conformation dependent library (CDL) restraints added in 410.6 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 A1401 " pdb="FE4 SF4 A1401 " - pdb=" SG CYS A1054 " pdb="FE3 SF4 A1401 " - pdb=" SG CYS A1048 " pdb="FE1 SF4 A1401 " - pdb=" SG CYS A1045 " pdb="FE2 SF4 A1401 " - pdb=" SG CYS A1038 " Number of angles added : 12 698 Ramachandran restraints generated. 349 Oldfield, 0 Emsley, 349 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 680 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 20 helices and 2 sheets defined 48.8% alpha, 5.0% beta 19 base pairs and 37 stacking pairs defined. Time for finding SS restraints: 1.73 Creating SS restraints... Processing helix chain 'A' and resid 561 through 583 removed outlier: 3.577A pdb=" N VAL A 568 " --> pdb=" O GLU A 564 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE A 569 " --> pdb=" O GLU A 565 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU A 582 " --> pdb=" O ALA A 578 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N VAL A 583 " --> pdb=" O ARG A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 605 Processing helix chain 'A' and resid 611 through 624 Processing helix chain 'A' and resid 885 through 890 Processing helix chain 'A' and resid 893 through 899 Processing helix chain 'A' and resid 906 through 922 Processing helix chain 'A' and resid 930 through 933 Processing helix chain 'A' and resid 937 through 946 Processing helix chain 'A' and resid 952 through 961 Processing helix chain 'A' and resid 972 through 980 Processing helix chain 'A' and resid 1007 through 1015 Proline residue: A1013 - end of helix Processing helix chain 'A' and resid 1020 through 1036 Processing helix chain 'A' and resid 1049 through 1051 No H-bonds generated for 'chain 'A' and resid 1049 through 1051' Processing helix chain 'A' and resid 1055 through 1060 Processing helix chain 'A' and resid 1213 through 1216 Processing helix chain 'A' and resid 1286 through 1290 Processing helix chain 'A' and resid 1296 through 1298 No H-bonds generated for 'chain 'A' and resid 1296 through 1298' Processing helix chain 'A' and resid 1310 through 1314 Processing helix chain 'A' and resid 1338 through 1341 No H-bonds generated for 'chain 'A' and resid 1338 through 1341' Processing helix chain 'A' and resid 1347 through 1356 Processing sheet with id= A, first strand: chain 'A' and resid 1204 through 1206 Processing sheet with id= B, first strand: chain 'A' and resid 1230 through 1232 104 hydrogen bonds defined for protein. 300 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 48 hydrogen bonds 96 hydrogen bond angles 0 basepair planarities 19 basepair parallelities 37 stacking parallelities Total time for adding SS restraints: 1.35 Time building geometry restraints manager: 2.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.41: 1676 1.41 - 1.63: 2406 1.63 - 1.84: 30 1.84 - 2.06: 0 2.06 - 2.28: 12 Bond restraints: 4124 Sorted by residual: bond pdb=" CA LEU A1026 " pdb=" C LEU A1026 " ideal model delta sigma weight residual 1.523 1.432 0.092 1.30e-02 5.92e+03 4.97e+01 bond pdb=" CA HIS A1027 " pdb=" C HIS A1027 " ideal model delta sigma weight residual 1.522 1.443 0.079 1.39e-02 5.18e+03 3.25e+01 bond pdb=" C THR A1022 " pdb=" O THR A1022 " ideal model delta sigma weight residual 1.236 1.186 0.050 1.15e-02 7.56e+03 1.90e+01 bond pdb=" N TYR A1028 " pdb=" CA TYR A1028 " ideal model delta sigma weight residual 1.459 1.407 0.053 1.21e-02 6.83e+03 1.89e+01 bond pdb=" CA HIS A1027 " pdb=" CB HIS A1027 " ideal model delta sigma weight residual 1.530 1.457 0.073 1.68e-02 3.54e+03 1.87e+01 ... (remaining 4119 not shown) Histogram of bond angle deviations from ideal: 73.67 - 85.73: 12 85.73 - 97.79: 0 97.79 - 109.86: 1019 109.86 - 121.92: 3919 121.92 - 133.98: 846 Bond angle restraints: 5796 Sorted by residual: angle pdb=" N TYR A1028 " pdb=" CA TYR A1028 " pdb=" C TYR A1028 " ideal model delta sigma weight residual 111.28 98.69 12.59 1.09e+00 8.42e-01 1.34e+02 angle pdb=" N HIS A1027 " pdb=" CA HIS A1027 " pdb=" C HIS A1027 " ideal model delta sigma weight residual 112.89 123.53 -10.64 1.24e+00 6.50e-01 7.36e+01 angle pdb=" N ILE A1031 " pdb=" CA ILE A1031 " pdb=" C ILE A1031 " ideal model delta sigma weight residual 110.62 103.40 7.22 1.02e+00 9.61e-01 5.00e+01 angle pdb=" N LEU A1026 " pdb=" CA LEU A1026 " pdb=" C LEU A1026 " ideal model delta sigma weight residual 111.28 103.77 7.51 1.09e+00 8.42e-01 4.74e+01 angle pdb=" CB HIS A1027 " pdb=" CG HIS A1027 " pdb=" CD2 HIS A1027 " ideal model delta sigma weight residual 131.20 123.55 7.65 1.30e+00 5.92e-01 3.46e+01 ... (remaining 5791 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.70: 1999 35.70 - 71.39: 263 71.39 - 107.09: 2 107.09 - 142.79: 0 142.79 - 178.48: 1 Dihedral angle restraints: 2265 sinusoidal: 1220 harmonic: 1045 Sorted by residual: dihedral pdb=" C HIS A1027 " pdb=" N HIS A1027 " pdb=" CA HIS A1027 " pdb=" CB HIS A1027 " ideal model delta harmonic sigma weight residual -122.60 -143.67 21.07 0 2.50e+00 1.60e-01 7.11e+01 dihedral pdb=" N HIS A1027 " pdb=" C HIS A1027 " pdb=" CA HIS A1027 " pdb=" CB HIS A1027 " ideal model delta harmonic sigma weight residual 122.80 143.77 -20.97 0 2.50e+00 1.60e-01 7.04e+01 dihedral pdb=" C4' DT C 17 " pdb=" C3' DT C 17 " pdb=" O3' DT C 17 " pdb=" P DT C 18 " ideal model delta sinusoidal sigma weight residual 220.00 41.52 178.48 1 3.50e+01 8.16e-04 1.57e+01 ... (remaining 2262 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.231: 634 0.231 - 0.462: 0 0.462 - 0.693: 2 0.693 - 0.924: 0 0.924 - 1.155: 1 Chirality restraints: 637 Sorted by residual: chirality pdb=" CA HIS A1027 " pdb=" N HIS A1027 " pdb=" C HIS A1027 " pdb=" CB HIS A1027 " both_signs ideal model delta sigma weight residual False 2.51 1.36 1.15 2.00e-01 2.50e+01 3.33e+01 chirality pdb=" P DG B 6 " pdb=" OP1 DG B 6 " pdb=" OP2 DG B 6 " pdb=" O5' DG B 6 " both_signs ideal model delta sigma weight residual True 2.35 -2.86 -0.51 2.00e-01 2.50e+01 6.51e+00 chirality pdb=" P DG B 3 " pdb=" OP1 DG B 3 " pdb=" OP2 DG B 3 " pdb=" O5' DG B 3 " both_signs ideal model delta sigma weight residual True 2.35 -2.82 -0.47 2.00e-01 2.50e+01 5.56e+00 ... (remaining 634 not shown) Planarity restraints: 561 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR A1028 " -0.011 2.00e-02 2.50e+03 2.11e-02 4.44e+00 pdb=" C TYR A1028 " 0.036 2.00e-02 2.50e+03 pdb=" O TYR A1028 " -0.014 2.00e-02 2.50e+03 pdb=" N GLN A1029 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A1294 " 0.027 5.00e-02 4.00e+02 4.02e-02 2.59e+00 pdb=" N PRO A1295 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO A1295 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A1295 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A1023 " 0.007 2.00e-02 2.50e+03 1.38e-02 1.92e+00 pdb=" C LEU A1023 " -0.024 2.00e-02 2.50e+03 pdb=" O LEU A1023 " 0.009 2.00e-02 2.50e+03 pdb=" N TYR A1024 " 0.008 2.00e-02 2.50e+03 ... (remaining 558 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 951 2.80 - 3.32: 3530 3.32 - 3.85: 7111 3.85 - 4.37: 7849 4.37 - 4.90: 12194 Nonbonded interactions: 31635 Sorted by model distance: nonbonded pdb=" NH1 ARG A 566 " pdb=" O PRO A1013 " model vdw 2.273 2.520 nonbonded pdb=" O GLN A 607 " pdb=" NH2 ARG A 903 " model vdw 2.286 2.520 nonbonded pdb=" N HIS A1310 " pdb=" O PHE A1364 " model vdw 2.338 2.520 nonbonded pdb=" NH1 ARG A 572 " pdb=" O GLY A 982 " model vdw 2.374 2.520 nonbonded pdb=" O MET A 580 " pdb=" N GLN A 584 " model vdw 2.376 2.520 ... (remaining 31630 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 12.460 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 17.280 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7114 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 : 0.005 0.092 4124 Z= 0.311 Angle : 0.744 12.594 5796 Z= 0.488 Chirality : 0.067 1.155 637 Planarity : 0.004 0.040 561 Dihedral : 23.402 178.481 1585 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 8.78 % Allowed : 12.85 % Favored : 78.37 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.45), residues: 349 helix: 1.33 (0.40), residues: 178 sheet: 1.75 (1.40), residues: 12 loop : -1.04 (0.49), residues: 159 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 698 Ramachandran restraints generated. 349 Oldfield, 0 Emsley, 349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 698 Ramachandran restraints generated. 349 Oldfield, 0 Emsley, 349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 79 time to evaluate : 0.369 Fit side-chains revert: symmetry clash outliers start: 28 outliers final: 12 residues processed: 95 average time/residue: 0.1795 time to fit residues: 20.5223 Evaluate side-chains 69 residues out of total 319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 57 time to evaluate : 0.370 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0473 time to fit residues: 1.4074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 12 optimal weight: 0.3980 chunk 19 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 607 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7229 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 4124 Z= 0.294 Angle : 0.641 7.503 5796 Z= 0.361 Chirality : 0.042 0.206 637 Planarity : 0.005 0.045 561 Dihedral : 27.275 179.685 874 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.51 % Allowed : 21.00 % Favored : 76.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.45), residues: 349 helix: 1.16 (0.40), residues: 162 sheet: 1.38 (1.39), residues: 12 loop : -1.07 (0.49), residues: 175 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 698 Ramachandran restraints generated. 349 Oldfield, 0 Emsley, 349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 698 Ramachandran restraints generated. 349 Oldfield, 0 Emsley, 349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 59 time to evaluate : 0.327 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 65 average time/residue: 0.1542 time to fit residues: 12.4633 Evaluate side-chains 61 residues out of total 319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 55 time to evaluate : 0.334 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0404 time to fit residues: 0.8454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 0.5980 chunk 24 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 29 optimal weight: 0.1980 chunk 35 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 18 optimal weight: 0.2980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4124 Z= 0.189 Angle : 0.559 6.158 5796 Z= 0.318 Chirality : 0.037 0.186 637 Planarity : 0.004 0.041 561 Dihedral : 27.123 178.396 874 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 3.45 % Allowed : 23.82 % Favored : 72.73 % 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: -0.17 (0.45), residues: 349 helix: 0.79 (0.40), residues: 183 sheet: 0.57 (1.17), residues: 17 loop : -1.34 (0.49), residues: 149 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 698 Ramachandran restraints generated. 349 Oldfield, 0 Emsley, 349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 698 Ramachandran restraints generated. 349 Oldfield, 0 Emsley, 349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 59 time to evaluate : 0.354 Fit side-chains outliers start: 11 outliers final: 7 residues processed: 67 average time/residue: 0.1620 time to fit residues: 13.5793 Evaluate side-chains 62 residues out of total 319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 55 time to evaluate : 0.330 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0486 time to fit residues: 1.0457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 36 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 32 optimal weight: 0.0020 chunk 21 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 overall best weight: 0.7590 ------------------------------------------------------------------------------- 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: 0.7213 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4124 Z= 0.221 Angle : 0.578 5.269 5796 Z= 0.325 Chirality : 0.038 0.190 637 Planarity : 0.004 0.040 561 Dihedral : 27.104 178.948 874 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.82 % Allowed : 26.33 % Favored : 70.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.46), residues: 349 helix: 0.91 (0.40), residues: 181 sheet: -0.44 (0.92), residues: 26 loop : -1.41 (0.52), residues: 142 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 698 Ramachandran restraints generated. 349 Oldfield, 0 Emsley, 349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 698 Ramachandran restraints generated. 349 Oldfield, 0 Emsley, 349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 54 time to evaluate : 0.350 Fit side-chains outliers start: 9 outliers final: 4 residues processed: 60 average time/residue: 0.1692 time to fit residues: 12.6740 Evaluate side-chains 56 residues out of total 319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 52 time to evaluate : 0.374 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1558 time to fit residues: 1.2333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 0.8980 chunk 15 optimal weight: 0.0870 chunk 32 optimal weight: 0.9980 chunk 26 optimal weight: 0.0980 chunk 0 optimal weight: 4.9990 chunk 19 optimal weight: 0.4980 chunk 34 optimal weight: 0.8980 chunk 9 optimal weight: 0.2980 chunk 13 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 22 optimal weight: 0.2980 overall best weight: 0.2558 ------------------------------------------------------------------------------- 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: 0.7141 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4124 Z= 0.164 Angle : 0.554 5.701 5796 Z= 0.313 Chirality : 0.037 0.181 637 Planarity : 0.004 0.036 561 Dihedral : 26.996 179.040 874 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.57 % Allowed : 26.96 % Favored : 71.47 % 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: -0.04 (0.45), residues: 349 helix: 0.95 (0.41), residues: 183 sheet: 0.33 (1.12), residues: 19 loop : -1.33 (0.48), residues: 147 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 698 Ramachandran restraints generated. 349 Oldfield, 0 Emsley, 349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 698 Ramachandran restraints generated. 349 Oldfield, 0 Emsley, 349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 59 time to evaluate : 0.371 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 61 average time/residue: 0.1560 time to fit residues: 12.0091 Evaluate side-chains 59 residues out of total 319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 55 time to evaluate : 0.346 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0395 time to fit residues: 0.7254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 32 optimal weight: 0.0970 chunk 17 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 12 optimal weight: 0.0870 chunk 20 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 4 optimal weight: 0.0050 chunk 22 optimal weight: 0.0870 chunk 28 optimal weight: 0.5980 overall best weight: 0.1748 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1027 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7103 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4124 Z= 0.158 Angle : 0.553 7.484 5796 Z= 0.310 Chirality : 0.036 0.175 637 Planarity : 0.004 0.034 561 Dihedral : 26.918 179.825 874 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.25 % Allowed : 26.65 % Favored : 72.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.45), residues: 349 helix: 0.89 (0.39), residues: 190 sheet: 0.37 (1.10), residues: 19 loop : -1.35 (0.49), residues: 140 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 698 Ramachandran restraints generated. 349 Oldfield, 0 Emsley, 349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 698 Ramachandran restraints generated. 349 Oldfield, 0 Emsley, 349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 58 time to evaluate : 0.342 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 61 average time/residue: 0.1438 time to fit residues: 11.2955 Evaluate side-chains 55 residues out of total 319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 52 time to evaluate : 0.398 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0422 time to fit residues: 0.7360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 1.9990 chunk 32 optimal weight: 0.3980 chunk 38 optimal weight: 3.9990 chunk 24 optimal weight: 0.0570 chunk 23 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 7 optimal weight: 0.0570 chunk 26 optimal weight: 0.5980 chunk 19 optimal weight: 3.9990 overall best weight: 0.3816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 924 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7123 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4124 Z= 0.175 Angle : 0.559 6.307 5796 Z= 0.312 Chirality : 0.036 0.173 637 Planarity : 0.004 0.035 561 Dihedral : 26.865 179.826 874 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.88 % Allowed : 27.59 % Favored : 70.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.45), residues: 349 helix: 0.93 (0.40), residues: 189 sheet: 0.13 (1.05), residues: 19 loop : -1.52 (0.48), residues: 141 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 698 Ramachandran restraints generated. 349 Oldfield, 0 Emsley, 349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 698 Ramachandran restraints generated. 349 Oldfield, 0 Emsley, 349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 55 time to evaluate : 0.376 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 57 average time/residue: 0.1487 time to fit residues: 10.8793 Evaluate side-chains 56 residues out of total 319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 52 time to evaluate : 0.362 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0413 time to fit residues: 0.7926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 0.0970 chunk 30 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 36 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 924 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4124 Z= 0.207 Angle : 0.577 6.467 5796 Z= 0.323 Chirality : 0.037 0.171 637 Planarity : 0.004 0.036 561 Dihedral : 26.812 179.979 874 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 0.94 % Allowed : 27.27 % Favored : 71.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.45), residues: 349 helix: 0.90 (0.40), residues: 188 sheet: 0.06 (1.03), residues: 19 loop : -1.60 (0.47), residues: 142 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 698 Ramachandran restraints generated. 349 Oldfield, 0 Emsley, 349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 698 Ramachandran restraints generated. 349 Oldfield, 0 Emsley, 349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 52 time to evaluate : 0.384 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 53 average time/residue: 0.1394 time to fit residues: 9.6587 Evaluate side-chains 53 residues out of total 319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 52 time to evaluate : 0.348 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0402 time to fit residues: 0.5297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 18 optimal weight: 0.0170 chunk 26 optimal weight: 0.0770 chunk 39 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 31 optimal weight: 0.6980 chunk 3 optimal weight: 0.0870 chunk 24 optimal weight: 4.9990 chunk 19 optimal weight: 0.0770 chunk 25 optimal weight: 0.9990 overall best weight: 0.1912 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 924 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4124 Z= 0.170 Angle : 0.546 6.813 5796 Z= 0.307 Chirality : 0.036 0.162 637 Planarity : 0.004 0.033 561 Dihedral : 26.639 179.280 874 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.00 % Allowed : 27.59 % Favored : 72.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.45), residues: 349 helix: 1.04 (0.40), residues: 186 sheet: -0.08 (1.02), residues: 19 loop : -1.40 (0.47), residues: 144 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 698 Ramachandran restraints generated. 349 Oldfield, 0 Emsley, 349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 698 Ramachandran restraints generated. 349 Oldfield, 0 Emsley, 349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.394 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.1485 time to fit residues: 10.5664 Evaluate side-chains 53 residues out of total 319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 0.366 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 31 optimal weight: 0.0770 chunk 13 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 chunk 27 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 924 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 4124 Z= 0.222 Angle : 0.586 7.399 5796 Z= 0.324 Chirality : 0.036 0.165 637 Planarity : 0.004 0.035 561 Dihedral : 26.634 179.318 874 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.31 % Allowed : 27.27 % Favored : 72.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.45), residues: 349 helix: 1.01 (0.40), residues: 189 sheet: -0.11 (0.99), residues: 19 loop : -1.48 (0.48), residues: 141 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 698 Ramachandran restraints generated. 349 Oldfield, 0 Emsley, 349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 698 Ramachandran restraints generated. 349 Oldfield, 0 Emsley, 349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 52 time to evaluate : 0.480 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 52 average time/residue: 0.1520 time to fit residues: 10.2817 Evaluate side-chains 52 residues out of total 319 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 51 time to evaluate : 0.395 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0415 time to fit residues: 0.6024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 0.8980 chunk 36 optimal weight: 4.9990 chunk 21 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 924 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.160512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.135067 restraints weight = 8116.308| |-----------------------------------------------------------------------------| r_work (start): 0.4180 rms_B_bonded: 2.32 r_work: 0.4051 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.4051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.3231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 4124 Z= 0.316 Angle : 0.658 6.588 5796 Z= 0.362 Chirality : 0.040 0.169 637 Planarity : 0.005 0.041 561 Dihedral : 26.770 179.583 874 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 0.63 % Allowed : 27.90 % Favored : 71.47 % 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: -0.59 (0.45), residues: 349 helix: 0.59 (0.39), residues: 188 sheet: -0.77 (0.94), residues: 19 loop : -1.68 (0.49), residues: 142 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1404.78 seconds wall clock time: 27 minutes 58.50 seconds (1678.50 seconds total)