Starting phenix.real_space_refine on Tue Feb 13 06:52:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yhp_33835/02_2024/7yhp_33835_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yhp_33835/02_2024/7yhp_33835.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yhp_33835/02_2024/7yhp_33835_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yhp_33835/02_2024/7yhp_33835_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yhp_33835/02_2024/7yhp_33835_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yhp_33835/02_2024/7yhp_33835.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yhp_33835/02_2024/7yhp_33835.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yhp_33835/02_2024/7yhp_33835_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yhp_33835/02_2024/7yhp_33835_updated.pdb" } resolution = 3.1 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 38 5.49 5 S 21 5.16 5 C 2310 2.51 5 N 687 2.21 5 O 755 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-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 3815 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 3028 Classifications: {'peptide': 374} Link IDs: {'PTRANS': 21, 'TRANS': 352} Chain breaks: 4 Chain: "B" Number of atoms: 434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 434 Classifications: {'DNA': 21} Link IDs: {'rna3p': 20} Chain: "C" Number of atoms: 345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 345 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} 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 1829 SG CYS A1054 20.379 29.195 44.503 1.00 39.23 S ATOM 1715 SG CYS A1038 25.319 32.541 43.195 1.00 34.11 S ATOM 1767 SG CYS A1045 22.505 32.740 49.043 1.00 36.39 S ATOM 1786 SG CYS A1048 19.860 35.961 44.189 1.00 37.83 S Time building chain proxies: 2.83, per 1000 atoms: 0.74 Number of scatterers: 3815 At special positions: 0 Unit cell: (69.472, 88.176, 88.844, 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 21 16.00 P 38 15.00 O 755 8.00 N 687 7.00 C 2310 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.64 Conformation dependent library (CDL) restraints added in 526.8 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 A1401 " pdb="FE1 SF4 A1401 " - pdb=" SG CYS A1054 " pdb="FE4 SF4 A1401 " - pdb=" SG CYS A1048 " pdb="FE3 SF4 A1401 " - pdb=" SG CYS A1045 " pdb="FE2 SF4 A1401 " - pdb=" SG CYS A1038 " Number of angles added : 12 728 Ramachandran restraints generated. 364 Oldfield, 0 Emsley, 364 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 706 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 21 helices and 2 sheets defined 48.4% alpha, 4.5% beta 10 base pairs and 32 stacking pairs defined. Time for finding SS restraints: 1.76 Creating SS restraints... Processing helix chain 'A' and resid 561 through 583 removed outlier: 3.646A pdb=" N PHE A 569 " --> pdb=" O GLU A 565 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU A 582 " --> pdb=" O ALA A 578 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL A 583 " --> pdb=" O ARG A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 605 Processing helix chain 'A' and resid 611 through 624 Processing helix chain 'A' and resid 885 through 890 Processing helix chain 'A' and resid 893 through 899 Processing helix chain 'A' and resid 901 through 903 No H-bonds generated for 'chain 'A' and resid 901 through 903' 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 961 Processing helix chain 'A' and resid 972 through 980 Processing helix chain 'A' and resid 1006 through 1015 Proline residue: A1013 - end of helix Processing helix chain 'A' and resid 1020 through 1036 Processing helix chain 'A' and resid 1051 through 1053 No H-bonds generated for 'chain 'A' and resid 1051 through 1053' Processing helix chain 'A' and resid 1056 through 1060 Processing helix chain 'A' and resid 1213 through 1217 removed outlier: 4.662A pdb=" N GLN A1217 " --> pdb=" O LEU A1214 " (cutoff:3.500A) Processing helix chain 'A' and resid 1286 through 1290 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 1341 No H-bonds generated for 'chain 'A' and resid 1338 through 1341' 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: 4.086A pdb=" N TYR A1229 " --> pdb=" O LEU A1208 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 1363 through 1365 removed outlier: 3.604A pdb=" N GLY A1370 " --> pdb=" O ASP A1365 " (cutoff:3.500A) 107 hydrogen bonds defined for protein. 306 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 22 hydrogen bonds 44 hydrogen bond angles 0 basepair planarities 10 basepair parallelities 32 stacking parallelities Total time for adding SS restraints: 1.20 Time building geometry restraints manager: 1.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.42: 1741 1.42 - 1.64: 2212 1.64 - 1.85: 24 1.85 - 2.07: 0 2.07 - 2.28: 12 Bond restraints: 3989 Sorted by residual: bond pdb=" C3' 5CM C 26 " pdb=" C2' 5CM C 26 " ideal model delta sigma weight residual 1.323 1.516 -0.193 2.00e-02 2.50e+03 9.28e+01 bond pdb=" O4' 5CM C 26 " pdb=" C1' 5CM C 26 " ideal model delta sigma weight residual 1.587 1.431 0.156 2.00e-02 2.50e+03 6.12e+01 bond pdb=" C4' 5CM C 26 " pdb=" O4' 5CM C 26 " ideal model delta sigma weight residual 1.279 1.432 -0.153 2.00e-02 2.50e+03 5.82e+01 bond pdb=" C1' 5CM C 26 " pdb=" N1 5CM C 26 " ideal model delta sigma weight residual 1.321 1.466 -0.145 2.00e-02 2.50e+03 5.26e+01 bond pdb=" C2 5CM C 26 " pdb=" N3 5CM C 26 " ideal model delta sigma weight residual 1.494 1.349 0.145 2.00e-02 2.50e+03 5.22e+01 ... (remaining 3984 not shown) Histogram of bond angle deviations from ideal: 73.66 - 85.73: 12 85.73 - 97.80: 0 97.80 - 109.86: 884 109.86 - 121.93: 3858 121.93 - 133.99: 812 Bond angle restraints: 5566 Sorted by residual: angle pdb=" N THR A1299 " pdb=" CA THR A1299 " pdb=" C THR A1299 " ideal model delta sigma weight residual 113.16 107.09 6.07 1.24e+00 6.50e-01 2.40e+01 angle pdb=" N LEU A 952 " pdb=" CA LEU A 952 " pdb=" C LEU A 952 " ideal model delta sigma weight residual 111.28 116.56 -5.28 1.09e+00 8.42e-01 2.35e+01 angle pdb=" CA TYR A1300 " pdb=" CB TYR A1300 " pdb=" CG TYR A1300 " ideal model delta sigma weight residual 113.90 120.76 -6.86 1.80e+00 3.09e-01 1.45e+01 angle pdb=" OP1 5CM C 26 " pdb=" P 5CM C 26 " pdb=" OP2 5CM C 26 " ideal model delta sigma weight residual 109.44 118.72 -9.28 3.00e+00 1.11e-01 9.58e+00 angle pdb=" C TYR A1300 " pdb=" CA TYR A1300 " pdb=" CB TYR A1300 " ideal model delta sigma weight residual 110.38 105.52 4.86 2.04e+00 2.40e-01 5.67e+00 ... (remaining 5561 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.68: 2057 28.68 - 57.36: 197 57.36 - 86.04: 16 86.04 - 114.72: 0 114.72 - 143.41: 1 Dihedral angle restraints: 2271 sinusoidal: 1187 harmonic: 1084 Sorted by residual: dihedral pdb=" C4' DT C 17 " pdb=" C3' DT C 17 " pdb=" O3' DT C 17 " pdb=" P DT C 18 " ideal model delta sinusoidal sigma weight residual 220.00 76.59 143.41 1 3.50e+01 8.16e-04 1.41e+01 dihedral pdb=" CA ARG A 903 " pdb=" CB ARG A 903 " pdb=" CG ARG A 903 " pdb=" CD ARG A 903 " ideal model delta sinusoidal sigma weight residual -60.00 -114.87 54.87 3 1.50e+01 4.44e-03 9.31e+00 dihedral pdb=" CA LEU A 952 " pdb=" CB LEU A 952 " pdb=" CG LEU A 952 " pdb=" CD1 LEU A 952 " ideal model delta sinusoidal sigma weight residual 180.00 133.27 46.73 3 1.50e+01 4.44e-03 8.38e+00 ... (remaining 2268 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 530 0.049 - 0.098: 66 0.098 - 0.148: 12 0.148 - 0.197: 2 0.197 - 0.246: 1 Chirality restraints: 611 Sorted by residual: chirality pdb=" CA LEU A 952 " pdb=" N LEU A 952 " pdb=" C LEU A 952 " pdb=" CB LEU A 952 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CA ASN A1297 " pdb=" N ASN A1297 " pdb=" C ASN A1297 " pdb=" CB ASN A1297 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.86e-01 chirality pdb=" C3' 5CM C 26 " pdb=" C4' 5CM C 26 " pdb=" O3' 5CM C 26 " pdb=" C2' 5CM C 26 " both_signs ideal model delta sigma weight residual False -2.49 -2.65 0.16 2.00e-01 2.50e+01 6.29e-01 ... (remaining 608 not shown) Planarity restraints: 572 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A1300 " 0.028 2.00e-02 2.50e+03 1.62e-02 5.24e+00 pdb=" CG TYR A1300 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR A1300 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR A1300 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR A1300 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A1300 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR A1300 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR A1300 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 950 " -0.007 2.00e-02 2.50e+03 1.48e-02 2.18e+00 pdb=" C LEU A 950 " 0.026 2.00e-02 2.50e+03 pdb=" O LEU A 950 " -0.009 2.00e-02 2.50e+03 pdb=" N GLY A 951 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A1296 " 0.007 2.00e-02 2.50e+03 1.31e-02 1.72e+00 pdb=" C LEU A1296 " -0.023 2.00e-02 2.50e+03 pdb=" O LEU A1296 " 0.009 2.00e-02 2.50e+03 pdb=" N ASN A1297 " 0.008 2.00e-02 2.50e+03 ... (remaining 569 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 1160 2.84 - 3.35: 3393 3.35 - 3.87: 6556 3.87 - 4.38: 7916 4.38 - 4.90: 12404 Nonbonded interactions: 31429 Sorted by model distance: nonbonded pdb=" NE2 HIS A 581 " pdb=" OD1 ASP A 586 " model vdw 2.320 2.520 nonbonded pdb=" OE1 GLN A 624 " pdb=" OG1 THR A 899 " model vdw 2.325 2.440 nonbonded pdb=" O LEU A 582 " pdb=" NE1 TRP A1355 " model vdw 2.335 2.520 nonbonded pdb=" N2 DG B 22 " pdb=" O2 DC C 19 " model vdw 2.338 2.520 nonbonded pdb=" OG SER A 926 " pdb=" OD1 ASP A 928 " model vdw 2.355 2.440 ... (remaining 31424 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 12.530 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.660 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 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 : 0.008 0.193 3989 Z= 0.411 Angle : 0.546 9.284 5566 Z= 0.307 Chirality : 0.037 0.246 611 Planarity : 0.004 0.029 572 Dihedral : 19.251 143.405 1565 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.81 % Allowed : 4.53 % Favored : 93.66 % 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: 0.44 (0.45), residues: 364 helix: 1.66 (0.41), residues: 172 sheet: -1.60 (1.15), residues: 20 loop : -0.90 (0.47), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 592 HIS 0.004 0.001 HIS A 612 PHE 0.013 0.001 PHE A1033 TYR 0.035 0.002 TYR A1300 ARG 0.002 0.000 ARG A 587 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 728 Ramachandran restraints generated. 364 Oldfield, 0 Emsley, 364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 728 Ramachandran restraints generated. 364 Oldfield, 0 Emsley, 364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 51 time to evaluate : 0.357 Fit side-chains REVERT: A 620 SER cc_start: 0.8502 (m) cc_final: 0.8284 (p) outliers start: 6 outliers final: 5 residues processed: 57 average time/residue: 0.2581 time to fit residues: 17.0115 Evaluate side-chains 42 residues out of total 331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 37 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 1299 THR Chi-restraints excluded: chain A residue 1368 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 0.8980 chunk 30 optimal weight: 0.0670 chunk 16 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 31 optimal weight: 0.5980 chunk 12 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 971 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.0965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3989 Z= 0.207 Angle : 0.527 5.331 5566 Z= 0.293 Chirality : 0.037 0.128 611 Planarity : 0.004 0.036 572 Dihedral : 23.585 144.646 828 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.42 % Allowed : 8.76 % Favored : 88.82 % 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: 0.53 (0.45), residues: 364 helix: 1.83 (0.40), residues: 172 sheet: -0.89 (1.07), residues: 23 loop : -1.05 (0.47), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 592 HIS 0.004 0.001 HIS A 612 PHE 0.015 0.002 PHE A1033 TYR 0.018 0.002 TYR A1300 ARG 0.006 0.001 ARG A1330 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 728 Ramachandran restraints generated. 364 Oldfield, 0 Emsley, 364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 728 Ramachandran restraints generated. 364 Oldfield, 0 Emsley, 364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 37 time to evaluate : 0.399 Fit side-chains REVERT: A 620 SER cc_start: 0.8541 (m) cc_final: 0.8281 (p) REVERT: A 1305 GLU cc_start: 0.6411 (OUTLIER) cc_final: 0.5884 (tt0) outliers start: 8 outliers final: 5 residues processed: 44 average time/residue: 0.2176 time to fit residues: 11.4949 Evaluate side-chains 40 residues out of total 331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 34 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 1228 SER Chi-restraints excluded: chain A residue 1305 GLU Chi-restraints excluded: chain A residue 1368 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 36 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 29 optimal weight: 0.0870 chunk 35 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.1262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3989 Z= 0.221 Angle : 0.528 5.392 5566 Z= 0.295 Chirality : 0.037 0.130 611 Planarity : 0.004 0.032 572 Dihedral : 23.794 143.157 827 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.42 % Allowed : 10.88 % Favored : 86.71 % 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: 0.34 (0.44), residues: 364 helix: 1.67 (0.40), residues: 171 sheet: -0.87 (1.09), residues: 23 loop : -1.15 (0.46), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 592 HIS 0.004 0.001 HIS A 612 PHE 0.015 0.002 PHE A1033 TYR 0.019 0.002 TYR A1300 ARG 0.007 0.001 ARG A1330 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 728 Ramachandran restraints generated. 364 Oldfield, 0 Emsley, 364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 728 Ramachandran restraints generated. 364 Oldfield, 0 Emsley, 364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 35 time to evaluate : 0.291 Fit side-chains REVERT: A 1305 GLU cc_start: 0.6463 (OUTLIER) cc_final: 0.5912 (tt0) outliers start: 8 outliers final: 5 residues processed: 42 average time/residue: 0.1979 time to fit residues: 10.3159 Evaluate side-chains 39 residues out of total 331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 33 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 1228 SER Chi-restraints excluded: chain A residue 1305 GLU Chi-restraints excluded: chain A residue 1368 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 32 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3989 Z= 0.242 Angle : 0.545 5.375 5566 Z= 0.304 Chirality : 0.037 0.132 611 Planarity : 0.004 0.040 572 Dihedral : 24.052 142.777 827 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.72 % Allowed : 12.08 % Favored : 85.20 % 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: 0.11 (0.44), residues: 364 helix: 1.42 (0.40), residues: 171 sheet: -0.76 (1.10), residues: 23 loop : -1.24 (0.46), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 592 HIS 0.004 0.001 HIS A 612 PHE 0.016 0.002 PHE A1033 TYR 0.021 0.002 TYR A1300 ARG 0.004 0.001 ARG A 933 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 728 Ramachandran restraints generated. 364 Oldfield, 0 Emsley, 364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 728 Ramachandran restraints generated. 364 Oldfield, 0 Emsley, 364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 33 time to evaluate : 0.383 Fit side-chains REVERT: A 1305 GLU cc_start: 0.6510 (OUTLIER) cc_final: 0.5937 (tt0) outliers start: 9 outliers final: 6 residues processed: 42 average time/residue: 0.1851 time to fit residues: 9.5656 Evaluate side-chains 40 residues out of total 331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 33 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 603 VAL Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 983 TRP Chi-restraints excluded: chain A residue 1228 SER Chi-restraints excluded: chain A residue 1305 GLU Chi-restraints excluded: chain A residue 1368 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 32 optimal weight: 0.0870 chunk 26 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 19 optimal weight: 0.5980 chunk 34 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 overall best weight: 0.8360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1297 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3989 Z= 0.244 Angle : 0.546 5.389 5566 Z= 0.305 Chirality : 0.037 0.133 611 Planarity : 0.004 0.041 572 Dihedral : 24.168 142.039 827 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.42 % Allowed : 13.60 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.44), residues: 364 helix: 1.35 (0.40), residues: 171 sheet: -0.63 (1.14), residues: 23 loop : -1.28 (0.46), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 592 HIS 0.005 0.001 HIS A 612 PHE 0.016 0.002 PHE A1033 TYR 0.021 0.002 TYR A1300 ARG 0.002 0.000 ARG A 933 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 728 Ramachandran restraints generated. 364 Oldfield, 0 Emsley, 364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 728 Ramachandran restraints generated. 364 Oldfield, 0 Emsley, 364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 33 time to evaluate : 0.369 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 41 average time/residue: 0.2148 time to fit residues: 10.8659 Evaluate side-chains 39 residues out of total 331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 33 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 983 TRP Chi-restraints excluded: chain A residue 1228 SER Chi-restraints excluded: chain A residue 1341 ILE Chi-restraints excluded: chain A residue 1368 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 3 optimal weight: 0.0770 chunk 12 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 22 optimal weight: 0.4980 chunk 28 optimal weight: 0.6980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3989 Z= 0.180 Angle : 0.500 5.186 5566 Z= 0.281 Chirality : 0.035 0.129 611 Planarity : 0.004 0.040 572 Dihedral : 24.030 141.270 826 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.11 % Allowed : 13.90 % Favored : 83.99 % 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: 0.24 (0.44), residues: 364 helix: 1.53 (0.40), residues: 171 sheet: -0.67 (1.15), residues: 23 loop : -1.18 (0.46), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 592 HIS 0.003 0.001 HIS A 612 PHE 0.013 0.001 PHE A 618 TYR 0.017 0.002 TYR A1300 ARG 0.002 0.000 ARG A1330 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 728 Ramachandran restraints generated. 364 Oldfield, 0 Emsley, 364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 728 Ramachandran restraints generated. 364 Oldfield, 0 Emsley, 364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 34 time to evaluate : 0.376 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 41 average time/residue: 0.2171 time to fit residues: 10.7461 Evaluate side-chains 40 residues out of total 331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 35 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 983 TRP Chi-restraints excluded: chain A residue 1228 SER Chi-restraints excluded: chain A residue 1368 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 1.9990 chunk 32 optimal weight: 0.4980 chunk 38 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 584 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 3989 Z= 0.285 Angle : 0.574 5.474 5566 Z= 0.320 Chirality : 0.039 0.133 611 Planarity : 0.005 0.043 572 Dihedral : 24.358 141.834 826 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.72 % Allowed : 13.60 % Favored : 83.69 % 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: -0.07 (0.44), residues: 364 helix: 1.23 (0.40), residues: 171 sheet: -0.53 (1.17), residues: 23 loop : -1.33 (0.45), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 592 HIS 0.005 0.001 HIS A 612 PHE 0.018 0.002 PHE A1033 TYR 0.021 0.003 TYR A1300 ARG 0.003 0.000 ARG A 933 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 728 Ramachandran restraints generated. 364 Oldfield, 0 Emsley, 364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 728 Ramachandran restraints generated. 364 Oldfield, 0 Emsley, 364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 33 time to evaluate : 0.403 Fit side-chains REVERT: A 1305 GLU cc_start: 0.6506 (OUTLIER) cc_final: 0.6014 (tt0) outliers start: 9 outliers final: 6 residues processed: 42 average time/residue: 0.1959 time to fit residues: 10.1519 Evaluate side-chains 39 residues out of total 331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 32 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 983 TRP Chi-restraints excluded: chain A residue 1228 SER Chi-restraints excluded: chain A residue 1305 GLU Chi-restraints excluded: chain A residue 1341 ILE Chi-restraints excluded: chain A residue 1368 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 36 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 28 optimal weight: 0.2980 chunk 11 optimal weight: 0.1980 chunk 32 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 584 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3989 Z= 0.179 Angle : 0.501 5.280 5566 Z= 0.281 Chirality : 0.035 0.130 611 Planarity : 0.004 0.043 572 Dihedral : 24.137 140.599 826 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.21 % Allowed : 15.41 % Favored : 83.38 % 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: 0.22 (0.44), residues: 364 helix: 1.50 (0.40), residues: 171 sheet: -0.59 (1.16), residues: 23 loop : -1.19 (0.46), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 592 HIS 0.004 0.001 HIS A 612 PHE 0.020 0.002 PHE A1057 TYR 0.018 0.002 TYR A1300 ARG 0.003 0.000 ARG A1362 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 728 Ramachandran restraints generated. 364 Oldfield, 0 Emsley, 364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 728 Ramachandran restraints generated. 364 Oldfield, 0 Emsley, 364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 32 time to evaluate : 0.394 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 36 average time/residue: 0.1907 time to fit residues: 8.6487 Evaluate side-chains 38 residues out of total 331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 34 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 1228 SER Chi-restraints excluded: chain A residue 1368 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 36 optimal weight: 0.2980 chunk 31 optimal weight: 2.9990 chunk 3 optimal weight: 0.0980 chunk 24 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 584 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3989 Z= 0.236 Angle : 0.536 5.332 5566 Z= 0.299 Chirality : 0.037 0.134 611 Planarity : 0.004 0.044 572 Dihedral : 24.422 141.539 826 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.81 % Allowed : 15.11 % Favored : 83.08 % 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: 0.10 (0.44), residues: 364 helix: 1.37 (0.40), residues: 171 sheet: -0.46 (1.18), residues: 23 loop : -1.25 (0.46), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 592 HIS 0.004 0.001 HIS A 612 PHE 0.016 0.002 PHE A1033 TYR 0.019 0.002 TYR A1300 ARG 0.002 0.000 ARG A 588 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 728 Ramachandran restraints generated. 364 Oldfield, 0 Emsley, 364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 728 Ramachandran restraints generated. 364 Oldfield, 0 Emsley, 364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 34 time to evaluate : 0.353 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 40 average time/residue: 0.1918 time to fit residues: 9.4331 Evaluate side-chains 37 residues out of total 331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 33 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 1228 SER Chi-restraints excluded: chain A residue 1368 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 0.9990 chunk 9 optimal weight: 0.2980 chunk 29 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 27 optimal weight: 0.4980 chunk 1 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3989 Z= 0.227 Angle : 0.527 5.354 5566 Z= 0.294 Chirality : 0.036 0.135 611 Planarity : 0.004 0.045 572 Dihedral : 24.522 140.772 826 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.81 % Allowed : 15.71 % Favored : 82.48 % 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: 0.10 (0.44), residues: 364 helix: 1.35 (0.40), residues: 171 sheet: -0.41 (1.18), residues: 23 loop : -1.23 (0.46), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 592 HIS 0.004 0.001 HIS A 612 PHE 0.016 0.002 PHE A1033 TYR 0.019 0.002 TYR A1300 ARG 0.003 0.000 ARG A1362 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 728 Ramachandran restraints generated. 364 Oldfield, 0 Emsley, 364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 728 Ramachandran restraints generated. 364 Oldfield, 0 Emsley, 364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 33 time to evaluate : 0.382 Fit side-chains REVERT: A 1305 GLU cc_start: 0.6572 (OUTLIER) cc_final: 0.6021 (tt0) outliers start: 6 outliers final: 4 residues processed: 39 average time/residue: 0.2031 time to fit residues: 9.7777 Evaluate side-chains 38 residues out of total 331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 33 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 1228 SER Chi-restraints excluded: chain A residue 1305 GLU Chi-restraints excluded: chain A residue 1368 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 27 optimal weight: 0.4980 chunk 1 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 39 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.194045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.162466 restraints weight = 4418.160| |-----------------------------------------------------------------------------| r_work (start): 0.4060 rms_B_bonded: 1.29 r_work: 0.3943 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3813 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3989 Z= 0.234 Angle : 0.535 5.349 5566 Z= 0.298 Chirality : 0.037 0.137 611 Planarity : 0.004 0.046 572 Dihedral : 24.562 141.190 826 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.81 % Allowed : 15.71 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.44), residues: 364 helix: 1.29 (0.40), residues: 171 sheet: -0.39 (1.17), residues: 23 loop : -1.25 (0.46), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 592 HIS 0.005 0.001 HIS A 612 PHE 0.016 0.002 PHE A1033 TYR 0.019 0.002 TYR A1300 ARG 0.002 0.000 ARG A1362 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1332.92 seconds wall clock time: 24 minutes 31.56 seconds (1471.56 seconds total)