Starting phenix.real_space_refine (version: 1.21rc1) on Mon Jul 3 20:10:06 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yhq_33836/07_2023/7yhq_33836_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yhq_33836/07_2023/7yhq_33836.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yhq_33836/07_2023/7yhq_33836_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yhq_33836/07_2023/7yhq_33836_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yhq_33836/07_2023/7yhq_33836_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yhq_33836/07_2023/7yhq_33836.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yhq_33836/07_2023/7yhq_33836.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yhq_33836/07_2023/7yhq_33836_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yhq_33836/07_2023/7yhq_33836_updated.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 43 5.49 5 S 23 5.16 5 C 2461 2.51 5 N 726 2.21 5 O 808 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 4065 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 3182 Classifications: {'peptide': 393} Link IDs: {'PTRANS': 25, 'TRANS': 367} Chain breaks: 4 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: 336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 336 Unusual residues: {'PED': 1} Classifications: {'DNA': 16, 'undetermined': 1} Link IDs: {'rna3p': 14, None: 2} Not linked: pdbres=" DC C 25 " pdbres="PED C 26 " Not linked: pdbres="PED C 26 " pdbres=" DG C 27 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 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 1949 SG CYS A1045 55.589 28.918 53.222 1.00 76.27 S ATOM 1897 SG CYS A1038 52.380 29.895 47.604 1.00 69.77 S ATOM 1968 SG CYS A1048 52.542 24.215 49.877 1.00 71.00 S ATOM 2011 SG CYS A1054 57.449 28.416 49.055 1.00 77.53 S Time building chain proxies: 2.60, per 1000 atoms: 0.64 Number of scatterers: 4065 At special positions: 0 Unit cell: (86.43, 72.36, 86.43, 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 43 15.00 O 808 8.00 N 726 7.00 C 2461 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.00 Conformation dependent library (CDL) restraints added in 442.7 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 A1401 " pdb="FE2 SF4 A1401 " - pdb=" SG CYS A1038 " pdb="FE3 SF4 A1401 " - pdb=" SG CYS A1048 " pdb="FE4 SF4 A1401 " - pdb=" SG CYS A1054 " pdb="FE1 SF4 A1401 " - pdb=" SG CYS A1045 " Number of angles added : 12 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 744 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 21 helices and 1 sheets defined 44.8% alpha, 2.8% beta 13 base pairs and 33 stacking pairs defined. Time for finding SS restraints: 1.51 Creating SS restraints... Processing helix chain 'A' and resid 561 through 579 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 924 Processing helix chain 'A' and resid 930 through 933 Processing helix chain 'A' and resid 937 through 945 Processing helix chain 'A' and resid 952 through 962 Processing helix chain 'A' and resid 972 through 980 Processing helix chain 'A' and resid 1007 through 1015 removed outlier: 4.851A pdb=" N TRP A1012 " --> pdb=" O LYS A1009 " (cutoff:3.500A) Proline residue: A1013 - end of helix Processing helix chain 'A' and resid 1020 through 1036 Processing helix chain 'A' and resid 1045 through 1047 No H-bonds generated for 'chain 'A' and resid 1045 through 1047' Processing helix chain 'A' and resid 1049 through 1052 removed outlier: 4.182A pdb=" N GLY A1052 " --> pdb=" O PRO A1049 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1049 through 1052' Processing helix chain 'A' and resid 1055 through 1059 removed outlier: 3.656A pdb=" N SER A1059 " --> pdb=" O ARG A1055 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1055 through 1059' Processing helix chain 'A' and resid 1213 through 1215 No H-bonds generated for 'chain 'A' and resid 1213 through 1215' Processing helix chain 'A' and resid 1286 through 1289 No H-bonds generated for 'chain 'A' and resid 1286 through 1289' Processing helix chain 'A' and resid 1295 through 1298 Processing helix chain 'A' and resid 1310 through 1314 Processing helix chain 'A' and resid 1338 through 1342 Processing helix chain 'A' and resid 1347 through 1355 Processing sheet with id= A, first strand: chain 'A' and resid 1206 through 1208 removed outlier: 3.948A pdb=" N TYR A1206 " --> pdb=" O LEU A1231 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N TYR A1229 " --> pdb=" O LEU A1208 " (cutoff:3.500A) 100 hydrogen bonds defined for protein. 285 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 32 hydrogen bonds 64 hydrogen bond angles 0 basepair planarities 13 basepair parallelities 33 stacking parallelities Total time for adding SS restraints: 1.29 Time building geometry restraints manager: 2.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.43: 1865 1.43 - 1.64: 2351 1.64 - 1.85: 28 1.85 - 2.07: 0 2.07 - 2.28: 12 Bond restraints: 4256 Sorted by residual: bond pdb=" CA ASN A1044 " pdb=" C ASN A1044 " ideal model delta sigma weight residual 1.531 1.474 0.057 1.12e-02 7.97e+03 2.57e+01 bond pdb=" N THR A 962 " pdb=" CA THR A 962 " ideal model delta sigma weight residual 1.457 1.489 -0.031 1.17e-02 7.31e+03 7.22e+00 bond pdb=" O5' PED C 26 " pdb=" P PED C 26 " ideal model delta sigma weight residual 1.648 1.595 0.053 2.00e-02 2.50e+03 7.12e+00 bond pdb=" C TRP A 562 " pdb=" O TRP A 562 " ideal model delta sigma weight residual 1.237 1.267 -0.030 1.17e-02 7.31e+03 6.70e+00 bond pdb=" C PHE A 625 " pdb=" N PRO A 626 " ideal model delta sigma weight residual 1.329 1.361 -0.032 1.25e-02 6.40e+03 6.55e+00 ... (remaining 4251 not shown) Histogram of bond angle deviations from ideal: 73.50 - 86.00: 12 86.00 - 98.49: 1 98.49 - 110.99: 1926 110.99 - 123.48: 3688 123.48 - 135.98: 320 Bond angle restraints: 5947 Sorted by residual: angle pdb=" N ASN A1044 " pdb=" CA ASN A1044 " pdb=" C ASN A1044 " ideal model delta sigma weight residual 110.70 100.96 9.74 1.55e+00 4.16e-01 3.95e+01 angle pdb=" C PHE A 625 " pdb=" N PRO A 626 " pdb=" CA PRO A 626 " ideal model delta sigma weight residual 120.14 113.74 6.40 1.06e+00 8.90e-01 3.65e+01 angle pdb=" N TRP A 561 " pdb=" CA TRP A 561 " pdb=" C TRP A 561 " ideal model delta sigma weight residual 111.82 106.16 5.66 1.16e+00 7.43e-01 2.38e+01 angle pdb=" N ASN A1046 " pdb=" CA ASN A1046 " pdb=" C ASN A1046 " ideal model delta sigma weight residual 111.82 106.35 5.47 1.16e+00 7.43e-01 2.22e+01 angle pdb=" C3' DT B 5 " pdb=" O3' DT B 5 " pdb=" P DG B 6 " ideal model delta sigma weight residual 120.20 113.50 6.70 1.50e+00 4.44e-01 2.00e+01 ... (remaining 5942 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.85: 2137 35.85 - 71.69: 222 71.69 - 107.53: 8 107.53 - 143.38: 0 143.38 - 179.22: 2 Dihedral angle restraints: 2369 sinusoidal: 1227 harmonic: 1142 Sorted by residual: dihedral pdb=" CA TYR A1001 " pdb=" C TYR A1001 " pdb=" N PRO A1002 " pdb=" CA PRO A1002 " ideal model delta harmonic sigma weight residual -180.00 -159.52 -20.48 0 5.00e+00 4.00e-02 1.68e+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 -140.00 39.22 -179.22 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DT B 12 " pdb=" C3' DT B 12 " pdb=" O3' DT B 12 " pdb=" P DC B 13 " ideal model delta sinusoidal sigma weight residual 220.00 51.30 168.70 1 3.50e+01 8.16e-04 1.55e+01 ... (remaining 2366 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 626 0.102 - 0.203: 23 0.203 - 0.305: 3 0.305 - 0.406: 1 0.406 - 0.508: 3 Chirality restraints: 656 Sorted by residual: 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 -2.85 -0.51 2.00e-01 2.50e+01 6.45e+00 chirality pdb=" P DT B 5 " pdb=" OP1 DT B 5 " pdb=" OP2 DT B 5 " pdb=" O5' DT B 5 " both_signs ideal model delta sigma weight residual True 2.35 -2.83 -0.48 2.00e-01 2.50e+01 5.76e+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 5.62e+00 ... (remaining 653 not shown) Planarity restraints: 604 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TRP A 561 " -0.010 2.00e-02 2.50e+03 1.94e-02 3.76e+00 pdb=" C TRP A 561 " 0.034 2.00e-02 2.50e+03 pdb=" O TRP A 561 " -0.012 2.00e-02 2.50e+03 pdb=" N TRP A 562 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG C 27 " 0.018 2.00e-02 2.50e+03 1.02e-02 3.11e+00 pdb=" N9 DG C 27 " -0.008 2.00e-02 2.50e+03 pdb=" C8 DG C 27 " 0.001 2.00e-02 2.50e+03 pdb=" N7 DG C 27 " 0.002 2.00e-02 2.50e+03 pdb=" C5 DG C 27 " -0.020 2.00e-02 2.50e+03 pdb=" C6 DG C 27 " 0.015 2.00e-02 2.50e+03 pdb=" O6 DG C 27 " 0.002 2.00e-02 2.50e+03 pdb=" N1 DG C 27 " 0.009 2.00e-02 2.50e+03 pdb=" C2 DG C 27 " -0.001 2.00e-02 2.50e+03 pdb=" N2 DG C 27 " -0.003 2.00e-02 2.50e+03 pdb=" N3 DG C 27 " -0.002 2.00e-02 2.50e+03 pdb=" C4 DG C 27 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 627 " 0.027 5.00e-02 4.00e+02 4.09e-02 2.68e+00 pdb=" N PRO A 628 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 628 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 628 " 0.024 5.00e-02 4.00e+02 ... (remaining 601 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 857 2.78 - 3.31: 3879 3.31 - 3.84: 7253 3.84 - 4.37: 8300 4.37 - 4.90: 12633 Nonbonded interactions: 32922 Sorted by model distance: nonbonded pdb=" O TYR A 943 " pdb=" OG SER A 946 " model vdw 2.249 2.440 nonbonded pdb=" OH TYR A1024 " pdb=" OD1 ASN A1297 " model vdw 2.280 2.440 nonbonded pdb=" O MET A1050 " pdb=" N CYS A1054 " model vdw 2.287 2.520 nonbonded pdb=" OG SER A 623 " pdb=" O THR A1368 " model vdw 2.295 2.440 nonbonded pdb=" OE1 GLN A 987 " pdb=" N SER A 992 " model vdw 2.341 2.520 ... (remaining 32917 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.270 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: 12.590 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 16.780 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 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 0.057 4256 Z= 0.313 Angle : 0.908 10.976 5947 Z= 0.535 Chirality : 0.060 0.508 656 Planarity : 0.005 0.041 604 Dihedral : 23.626 179.224 1625 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 15.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer Outliers : 2.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.46), residues: 383 helix: 1.04 (0.43), residues: 170 sheet: -2.96 (0.87), residues: 20 loop : -1.43 (0.48), residues: 193 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 65 time to evaluate : 0.380 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 72 average time/residue: 0.2127 time to fit residues: 18.3004 Evaluate side-chains 48 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 45 time to evaluate : 0.411 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1273 time to fit residues: 1.0105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 32 optimal weight: 0.0870 chunk 12 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 973 ASN A1008 GLN ** A1029 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 4256 Z= 0.220 Angle : 0.653 7.989 5947 Z= 0.344 Chirality : 0.039 0.144 656 Planarity : 0.005 0.036 604 Dihedral : 27.037 178.542 839 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer Outliers : 2.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.46), residues: 383 helix: 1.00 (0.42), residues: 170 sheet: -3.24 (0.79), residues: 22 loop : -1.38 (0.50), residues: 191 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 50 time to evaluate : 0.408 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 56 average time/residue: 0.1488 time to fit residues: 10.8652 Evaluate side-chains 42 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 37 time to evaluate : 0.406 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0410 time to fit residues: 0.9104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 38 optimal weight: 0.0030 chunk 41 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 28 optimal weight: 0.0980 chunk 19 optimal weight: 0.8980 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 973 ASN ** A1029 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 4256 Z= 0.202 Angle : 0.612 8.413 5947 Z= 0.323 Chirality : 0.040 0.218 656 Planarity : 0.004 0.032 604 Dihedral : 26.884 176.419 839 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer Outliers : 2.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.46), residues: 383 helix: 1.05 (0.41), residues: 171 sheet: -3.62 (0.74), residues: 22 loop : -1.30 (0.51), residues: 190 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 38 time to evaluate : 0.410 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 42 average time/residue: 0.1300 time to fit residues: 7.5301 Evaluate side-chains 39 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 35 time to evaluate : 0.423 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0457 time to fit residues: 0.8613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 38 optimal weight: 0.0000 chunk 40 optimal weight: 2.9990 chunk 20 optimal weight: 0.0570 chunk 36 optimal weight: 0.4980 chunk 10 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 0 optimal weight: 0.5980 overall best weight: 0.3502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 973 ASN ** A1029 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 4256 Z= 0.174 Angle : 0.578 7.670 5947 Z= 0.309 Chirality : 0.037 0.145 656 Planarity : 0.004 0.032 604 Dihedral : 26.587 175.144 839 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Rotamer Outliers : 1.71 % 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: -0.69 (0.46), residues: 383 helix: 0.82 (0.41), residues: 176 sheet: -3.74 (0.66), residues: 26 loop : -1.22 (0.51), residues: 181 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 45 time to evaluate : 0.382 Fit side-chains outliers start: 6 outliers final: 1 residues processed: 50 average time/residue: 0.1224 time to fit residues: 8.5067 Evaluate side-chains 39 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 38 time to evaluate : 0.418 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0432 time to fit residues: 0.6203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 28 optimal weight: 9.9990 chunk 0 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 23 optimal weight: 0.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 612 HIS A 973 ASN ** A1029 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.051 4256 Z= 0.413 Angle : 0.776 10.930 5947 Z= 0.405 Chirality : 0.047 0.189 656 Planarity : 0.005 0.046 604 Dihedral : 26.671 173.669 839 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 17.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.18 % Favored : 89.82 % Rotamer Outliers : 3.14 % 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: -1.25 (0.45), residues: 383 helix: 0.20 (0.39), residues: 178 sheet: -3.54 (0.77), residues: 22 loop : -1.49 (0.52), residues: 183 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 41 time to evaluate : 0.409 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 7 residues processed: 49 average time/residue: 0.1306 time to fit residues: 8.6777 Evaluate side-chains 45 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 38 time to evaluate : 0.422 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0458 time to fit residues: 1.1107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 18 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 13 optimal weight: 0.0980 chunk 21 optimal weight: 0.5980 chunk 39 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 23 optimal weight: 0.0060 chunk 29 optimal weight: 2.9990 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 924 HIS A 973 ASN ** A1029 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 4256 Z= 0.184 Angle : 0.629 8.595 5947 Z= 0.327 Chirality : 0.040 0.164 656 Planarity : 0.004 0.033 604 Dihedral : 26.620 173.877 839 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer Outliers : 0.86 % 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: -0.84 (0.45), residues: 383 helix: 0.69 (0.41), residues: 175 sheet: -3.74 (0.67), residues: 26 loop : -1.29 (0.51), residues: 182 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 41 time to evaluate : 0.428 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 43 average time/residue: 0.1218 time to fit residues: 7.4289 Evaluate side-chains 37 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 36 time to evaluate : 0.407 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0417 time to fit residues: 0.5994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 25 optimal weight: 0.0010 chunk 24 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 16 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 7 optimal weight: 0.0870 chunk 27 optimal weight: 0.9980 chunk 20 optimal weight: 0.3980 overall best weight: 0.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 973 ASN ** A1029 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.3427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 4256 Z= 0.173 Angle : 0.625 8.572 5947 Z= 0.325 Chirality : 0.039 0.154 656 Planarity : 0.004 0.034 604 Dihedral : 26.517 173.174 839 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer Outliers : 1.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.45), residues: 383 helix: 0.76 (0.41), residues: 175 sheet: -3.75 (0.68), residues: 26 loop : -1.23 (0.51), residues: 182 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 46 time to evaluate : 0.434 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 50 average time/residue: 0.1335 time to fit residues: 8.9538 Evaluate side-chains 44 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 42 time to evaluate : 0.403 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0535 time to fit residues: 0.7081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 38 optimal weight: 0.5980 chunk 35 optimal weight: 0.3980 chunk 37 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 973 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.3544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 4256 Z= 0.190 Angle : 0.634 9.566 5947 Z= 0.326 Chirality : 0.039 0.145 656 Planarity : 0.004 0.034 604 Dihedral : 26.455 172.332 839 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Rotamer Outliers : 1.14 % 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: -0.78 (0.45), residues: 383 helix: 0.67 (0.41), residues: 173 sheet: -3.74 (0.66), residues: 26 loop : -1.14 (0.51), residues: 184 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 44 time to evaluate : 0.414 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 46 average time/residue: 0.1675 time to fit residues: 9.9099 Evaluate side-chains 42 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 40 time to evaluate : 0.407 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0421 time to fit residues: 0.6888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.4980 chunk 37 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 chunk 18 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 25 optimal weight: 0.0070 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 973 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.3684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 4256 Z= 0.194 Angle : 0.653 9.703 5947 Z= 0.332 Chirality : 0.039 0.145 656 Planarity : 0.004 0.034 604 Dihedral : 26.422 171.938 839 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer Outliers : 0.57 % 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: -0.72 (0.46), residues: 383 helix: 0.63 (0.41), residues: 175 sheet: -3.64 (0.67), residues: 26 loop : -1.03 (0.52), residues: 182 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 41 time to evaluate : 0.420 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 43 average time/residue: 0.1419 time to fit residues: 8.2672 Evaluate side-chains 41 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 39 time to evaluate : 0.419 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2021 time to fit residues: 0.9799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 0.2980 chunk 26 optimal weight: 7.9990 chunk 35 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 33 optimal weight: 0.1980 chunk 13 optimal weight: 0.3980 chunk 34 optimal weight: 4.9990 chunk 6 optimal weight: 0.6980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.3820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 4256 Z= 0.180 Angle : 0.641 9.922 5947 Z= 0.328 Chirality : 0.039 0.157 656 Planarity : 0.004 0.034 604 Dihedral : 26.398 171.123 839 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.46), residues: 383 helix: 0.73 (0.41), residues: 173 sheet: -3.20 (0.62), residues: 31 loop : -1.09 (0.53), residues: 179 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.429 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.1247 time to fit residues: 7.1027 Evaluate side-chains 39 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.388 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 chunk 38 optimal weight: 4.9990 chunk 22 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 41 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 973 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.125364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.102888 restraints weight = 12135.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.105154 restraints weight = 7458.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.106581 restraints weight = 5370.207| |-----------------------------------------------------------------------------| r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.3966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 4256 Z= 0.196 Angle : 0.655 9.883 5947 Z= 0.335 Chirality : 0.039 0.152 656 Planarity : 0.004 0.034 604 Dihedral : 26.376 170.226 839 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 16.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.14 % Favored : 90.86 % Rotamer Outliers : 0.57 % 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: -0.74 (0.46), residues: 383 helix: 0.63 (0.41), residues: 175 sheet: -3.18 (0.63), residues: 31 loop : -1.07 (0.53), residues: 177 =============================================================================== Job complete usr+sys time: 1270.88 seconds wall clock time: 23 minutes 34.33 seconds (1414.33 seconds total)