Starting phenix.real_space_refine (version: 1.21rc1) on Mon Oct 2 22:43:57 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yhq_33836/10_2023/7yhq_33836_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yhq_33836/10_2023/7yhq_33836.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yhq_33836/10_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_33836/10_2023/7yhq_33836_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yhq_33836/10_2023/7yhq_33836_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yhq_33836/10_2023/7yhq_33836.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yhq_33836/10_2023/7yhq_33836.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yhq_33836/10_2023/7yhq_33836_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yhq_33836/10_2023/7yhq_33836_updated.pdb" } resolution = 3.9 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 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-1.21rc1-5097/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: 2.96, per 1000 atoms: 0.73 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: 2.21 Conformation dependent library (CDL) restraints added in 456.4 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: 1.94 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: 1.34 Time building geometry restraints manager: 2.21 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: 3.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 12.360 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 18.020 Find NCS groups from input model: 0.100 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.270 ------------------------------------------------------------------------------- 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 % Allowed : 1.71 % Favored : 96.29 % 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 : 0.322 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 72 average time/residue: 0.1686 time to fit residues: 14.5474 Evaluate side-chains 48 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 45 time to evaluate : 0.307 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1111 time to fit residues: 0.8090 ------------------------------------------------------------------------------- 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: 0.7311 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 4256 Z= 0.225 Angle : 0.651 8.471 5947 Z= 0.343 Chirality : 0.040 0.136 656 Planarity : 0.005 0.036 604 Dihedral : 27.038 178.105 839 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.88 % Favored : 91.12 % Rotamer: Outliers : 1.71 % Allowed : 11.14 % Favored : 87.14 % 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: -0.60 (0.46), residues: 383 helix: 1.03 (0.42), residues: 170 sheet: -3.29 (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 56 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 50 time to evaluate : 0.416 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 55 average time/residue: 0.1500 time to fit residues: 10.6816 Evaluate side-chains 41 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 38 time to evaluate : 0.417 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0414 time to fit residues: 0.7664 ------------------------------------------------------------------------------- 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: 0.6980 chunk 25 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 38 optimal weight: 0.1980 chunk 41 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 28 optimal weight: 0.0870 chunk 19 optimal weight: 0.0980 overall best weight: 0.3758 ------------------------------------------------------------------------------- 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: 0.7273 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4256 Z= 0.175 Angle : 0.584 7.936 5947 Z= 0.310 Chirality : 0.038 0.153 656 Planarity : 0.004 0.034 604 Dihedral : 26.870 176.576 839 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Rotamer: Outliers : 1.71 % Allowed : 13.71 % Favored : 84.57 % 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: -0.55 (0.47), residues: 383 helix: 0.91 (0.41), residues: 178 sheet: -3.72 (0.67), residues: 26 loop : -1.11 (0.53), residues: 179 *********************** 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 48 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 42 time to evaluate : 0.296 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 46 average time/residue: 0.0972 time to fit residues: 6.1907 Evaluate side-chains 39 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 37 time to evaluate : 0.298 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0338 time to fit residues: 0.5067 ------------------------------------------------------------------------------- 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: 0.2980 chunk 40 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 33 optimal weight: 6.9990 chunk 23 optimal weight: 0.0070 chunk 0 optimal weight: 3.9990 overall best weight: 0.8200 ------------------------------------------------------------------------------- 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: 0.7350 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 4256 Z= 0.219 Angle : 0.619 8.624 5947 Z= 0.327 Chirality : 0.040 0.235 656 Planarity : 0.004 0.031 604 Dihedral : 26.642 175.130 839 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.40 % Favored : 90.60 % Rotamer: Outliers : 2.57 % Allowed : 16.29 % Favored : 81.14 % 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: -0.69 (0.46), residues: 383 helix: 0.79 (0.41), residues: 178 sheet: -3.78 (0.75), residues: 22 loop : -1.27 (0.51), residues: 183 *********************** 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 52 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 43 time to evaluate : 0.459 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 4 residues processed: 49 average time/residue: 0.1195 time to fit residues: 8.0941 Evaluate side-chains 41 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 37 time to evaluate : 0.419 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0487 time to fit residues: 0.8763 ------------------------------------------------------------------------------- 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: 2.9990 chunk 34 optimal weight: 0.9980 chunk 28 optimal weight: 6.9990 chunk 0 optimal weight: 3.9990 chunk 20 optimal weight: 0.1980 chunk 36 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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: 0.7435 moved from start: 0.2979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 4256 Z= 0.281 Angle : 0.674 9.958 5947 Z= 0.354 Chirality : 0.042 0.153 656 Planarity : 0.005 0.033 604 Dihedral : 26.573 174.702 839 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.66 % Favored : 90.34 % Rotamer: Outliers : 2.29 % Allowed : 18.86 % Favored : 78.86 % 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: -0.99 (0.46), residues: 383 helix: 0.51 (0.40), residues: 176 sheet: -3.88 (0.67), residues: 26 loop : -1.30 (0.52), residues: 181 *********************** 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 46 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 38 time to evaluate : 0.375 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 44 average time/residue: 0.1176 time to fit residues: 7.2995 Evaluate side-chains 39 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 35 time to evaluate : 0.412 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0413 time to fit residues: 0.8376 ------------------------------------------------------------------------------- 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: 0.7980 chunk 40 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 13 optimal weight: 0.0770 chunk 21 optimal weight: 0.3980 chunk 39 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 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 567 ASN ** 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: 0.7373 moved from start: 0.3157 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= 0.188 Angle : 0.625 8.752 5947 Z= 0.324 Chirality : 0.039 0.147 656 Planarity : 0.004 0.034 604 Dihedral : 26.554 174.044 839 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.88 % Favored : 91.12 % Rotamer: Outliers : 1.71 % Allowed : 22.00 % Favored : 76.29 % 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: -0.73 (0.46), residues: 383 helix: 0.73 (0.40), residues: 178 sheet: -3.74 (0.68), residues: 26 loop : -1.18 (0.52), residues: 179 *********************** 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 45 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 39 time to evaluate : 0.411 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 42 average time/residue: 0.1319 time to fit residues: 7.5991 Evaluate side-chains 41 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 36 time to evaluate : 0.437 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1088 time to fit residues: 1.2614 ------------------------------------------------------------------------------- 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: 0.6980 chunk 34 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 18 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 7 optimal weight: 0.0060 chunk 27 optimal weight: 2.9990 chunk 20 optimal weight: 0.0030 overall best weight: 0.4606 ------------------------------------------------------------------------------- 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 ** A1029 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.3290 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= 0.175 Angle : 0.613 8.555 5947 Z= 0.318 Chirality : 0.038 0.146 656 Planarity : 0.004 0.034 604 Dihedral : 26.468 173.602 839 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer: Outliers : 0.29 % Allowed : 23.14 % Favored : 76.57 % 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: -0.69 (0.46), residues: 383 helix: 0.77 (0.40), residues: 177 sheet: -3.70 (0.69), residues: 26 loop : -1.18 (0.52), residues: 180 *********************** 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 43 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 42 time to evaluate : 0.405 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 43 average time/residue: 0.1191 time to fit residues: 7.2220 Evaluate side-chains 35 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 0.399 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5146 ------------------------------------------------------------------------------- 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: 2.9990 chunk 31 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 29 optimal weight: 0.1980 chunk 11 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 584 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: 0.7400 moved from start: 0.3529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 4256 Z= 0.223 Angle : 0.657 9.924 5947 Z= 0.338 Chirality : 0.039 0.146 656 Planarity : 0.004 0.035 604 Dihedral : 26.446 172.580 839 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.14 % Favored : 90.86 % Rotamer: Outliers : 0.86 % Allowed : 24.29 % Favored : 74.86 % 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: -0.69 (0.46), residues: 383 helix: 0.73 (0.40), residues: 178 sheet: -3.63 (0.70), residues: 26 loop : -1.14 (0.53), residues: 179 *********************** 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 39 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 36 time to evaluate : 0.382 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 38 average time/residue: 0.1201 time to fit residues: 6.4740 Evaluate side-chains 36 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 34 time to evaluate : 0.425 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0575 time to fit residues: 0.6782 ------------------------------------------------------------------------------- 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: 0.0970 chunk 37 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 chunk 39 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 27 optimal weight: 0.0670 chunk 41 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 overall best weight: 0.5316 ------------------------------------------------------------------------------- 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 584 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: 0.7352 moved from start: 0.3630 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= 0.181 Angle : 0.635 9.574 5947 Z= 0.323 Chirality : 0.038 0.145 656 Planarity : 0.004 0.035 604 Dihedral : 26.437 172.309 839 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer: Outliers : 0.57 % Allowed : 24.86 % Favored : 74.57 % 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: -0.60 (0.46), residues: 383 helix: 0.83 (0.41), residues: 178 sheet: -3.63 (0.69), residues: 26 loop : -1.12 (0.53), residues: 179 *********************** 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 44 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 42 time to evaluate : 0.411 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 42 average time/residue: 0.1469 time to fit residues: 8.2811 Evaluate side-chains 42 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 40 time to evaluate : 0.414 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0681 time to fit residues: 0.7370 ------------------------------------------------------------------------------- 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: 0.3980 chunk 26 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 4 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 6 optimal weight: 0.3980 overall best weight: 0.6984 ------------------------------------------------------------------------------- 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 584 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: 0.7374 moved from start: 0.3778 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= 0.200 Angle : 0.646 9.953 5947 Z= 0.331 Chirality : 0.040 0.163 656 Planarity : 0.004 0.034 604 Dihedral : 26.411 170.853 839 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.88 % Favored : 91.12 % Rotamer: Outliers : 0.29 % Allowed : 25.14 % Favored : 74.57 % 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: -0.65 (0.46), residues: 383 helix: 0.79 (0.40), residues: 178 sheet: -3.72 (0.68), residues: 26 loop : -1.12 (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 43 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 42 time to evaluate : 0.384 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 43 average time/residue: 0.1574 time to fit residues: 8.7905 Evaluate side-chains 37 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 36 time to evaluate : 0.555 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0534 time to fit residues: 0.6048 ------------------------------------------------------------------------------- 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: 2.9990 chunk 1 optimal weight: 0.6980 chunk 24 optimal weight: 0.4980 chunk 38 optimal weight: 3.9990 chunk 22 optimal weight: 0.5980 chunk 28 optimal weight: 0.0980 chunk 26 optimal weight: 1.9990 chunk 25 optimal weight: 0.0040 chunk 16 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 41 optimal weight: 3.9990 overall best weight: 0.3792 ------------------------------------------------------------------------------- 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 584 GLN ** 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 = 0.4096 r_free = 0.4096 target = 0.127176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.104036 restraints weight = 11958.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.106370 restraints weight = 7268.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.108062 restraints weight = 5239.734| |-----------------------------------------------------------------------------| r_work (final): 0.3793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.3924 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= 0.169 Angle : 0.635 10.053 5947 Z= 0.325 Chirality : 0.039 0.157 656 Planarity : 0.004 0.035 604 Dihedral : 26.382 170.399 839 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 0.00 % Allowed : 26.29 % Favored : 73.71 % 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: -0.61 (0.46), residues: 383 helix: 0.92 (0.41), residues: 176 sheet: -3.34 (0.62), residues: 31 loop : -1.19 (0.53), residues: 176 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1259.90 seconds wall clock time: 30 minutes 21.41 seconds (1821.41 seconds total)