Starting phenix.real_space_refine on Sun Mar 10 16:31:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bdz_15995/03_2024/8bdz_15995.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bdz_15995/03_2024/8bdz_15995.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bdz_15995/03_2024/8bdz_15995.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bdz_15995/03_2024/8bdz_15995.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bdz_15995/03_2024/8bdz_15995.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bdz_15995/03_2024/8bdz_15995.pdb" } resolution = 3.13 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= 0.063 sd= 0.372 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 18 5.16 5 C 2157 2.51 5 N 546 2.21 5 O 588 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ASP 30": "OD1" <-> "OD2" Residue "C PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 38": "OE1" <-> "OE2" Residue "C ASP 223": "OD1" <-> "OD2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 3309 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1103 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 11, 'TRANS': 126} Chain breaks: 1 Chain: "B" Number of atoms: 1103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1103 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 11, 'TRANS': 126} Chain breaks: 1 Chain: "C" Number of atoms: 1103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1103 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 11, 'TRANS': 126} Chain breaks: 1 Time building chain proxies: 2.31, per 1000 atoms: 0.70 Number of scatterers: 3309 At special positions: 0 Unit cell: (87.4532, 76.3832, 91.8812, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 18 16.00 O 588 8.00 N 546 7.00 C 2157 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 59 " - pdb=" SG CYS B 59 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.29 Conformation dependent library (CDL) restraints added in 574.0 milliseconds 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 786 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 0 sheets defined 82.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 4 through 8 removed outlier: 3.600A pdb=" N GLY A 8 " --> pdb=" O LYS A 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 15 Processing helix chain 'A' and resid 16 through 17 No H-bonds generated for 'chain 'A' and resid 16 through 17' Processing helix chain 'A' and resid 18 through 22 removed outlier: 3.724A pdb=" N PHE A 22 " --> pdb=" O SER A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 41 removed outlier: 3.911A pdb=" N ARG A 37 " --> pdb=" O SER A 33 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N GLU A 38 " --> pdb=" O ALA A 34 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N ALA A 39 " --> pdb=" O LEU A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 73 removed outlier: 3.604A pdb=" N THR A 51 " --> pdb=" O SER A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 232 removed outlier: 3.918A pdb=" N ASN A 230 " --> pdb=" O VAL A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 251 Processing helix chain 'A' and resid 251 through 268 Processing helix chain 'B' and resid 4 through 8 Processing helix chain 'B' and resid 10 through 16 removed outlier: 3.606A pdb=" N PHE B 16 " --> pdb=" O GLU B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 22 removed outlier: 6.296A pdb=" N ASP B 20 " --> pdb=" O LEU B 17 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE B 22 " --> pdb=" O SER B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 41 removed outlier: 3.784A pdb=" N ARG B 37 " --> pdb=" O SER B 33 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N GLU B 38 " --> pdb=" O ALA B 34 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N ALA B 39 " --> pdb=" O LEU B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 72 removed outlier: 3.530A pdb=" N THR B 51 " --> pdb=" O SER B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 232 removed outlier: 3.837A pdb=" N VAL B 226 " --> pdb=" O ARG B 222 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N SER B 227 " --> pdb=" O ASP B 223 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ASN B 230 " --> pdb=" O VAL B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 251 Processing helix chain 'B' and resid 251 through 268 Processing helix chain 'B' and resid 269 through 273 Processing helix chain 'C' and resid 4 through 8 Processing helix chain 'C' and resid 10 through 16 removed outlier: 3.891A pdb=" N PHE C 16 " --> pdb=" O GLU C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 22 removed outlier: 6.033A pdb=" N ASP C 20 " --> pdb=" O LEU C 17 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE C 22 " --> pdb=" O SER C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 42 removed outlier: 3.875A pdb=" N ARG C 37 " --> pdb=" O SER C 33 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N GLU C 38 " --> pdb=" O ALA C 34 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N ALA C 39 " --> pdb=" O LEU C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 73 Processing helix chain 'C' and resid 222 through 230 removed outlier: 4.111A pdb=" N VAL C 226 " --> pdb=" O ARG C 222 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N SER C 227 " --> pdb=" O ASP C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 251 removed outlier: 3.789A pdb=" N LYS C 236 " --> pdb=" O ASN C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 268 Processing helix chain 'C' and resid 269 through 273 218 hydrogen bonds defined for protein. 618 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.82 Time building geometry restraints manager: 1.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1032 1.35 - 1.46: 865 1.46 - 1.58: 1487 1.58 - 1.70: 0 1.70 - 1.81: 27 Bond restraints: 3411 Sorted by residual: bond pdb=" CD GLU A 257 " pdb=" OE1 GLU A 257 " ideal model delta sigma weight residual 1.249 1.232 0.017 1.90e-02 2.77e+03 8.33e-01 bond pdb=" CD GLU C 257 " pdb=" OE1 GLU C 257 " ideal model delta sigma weight residual 1.249 1.233 0.016 1.90e-02 2.77e+03 7.43e-01 bond pdb=" CD GLU B 257 " pdb=" OE1 GLU B 257 " ideal model delta sigma weight residual 1.249 1.234 0.015 1.90e-02 2.77e+03 6.64e-01 bond pdb=" CA CYS B 46 " pdb=" CB CYS B 46 " ideal model delta sigma weight residual 1.530 1.543 -0.013 1.69e-02 3.50e+03 5.91e-01 bond pdb=" CB GLU A 257 " pdb=" CG GLU A 257 " ideal model delta sigma weight residual 1.520 1.542 -0.022 3.00e-02 1.11e+03 5.34e-01 ... (remaining 3406 not shown) Histogram of bond angle deviations from ideal: 99.35 - 106.27: 155 106.27 - 113.19: 1833 113.19 - 120.12: 1185 120.12 - 127.04: 1425 127.04 - 133.96: 64 Bond angle restraints: 4662 Sorted by residual: angle pdb=" C HIS B 45 " pdb=" N CYS B 46 " pdb=" CA CYS B 46 " ideal model delta sigma weight residual 121.54 127.91 -6.37 1.91e+00 2.74e-01 1.11e+01 angle pdb=" N GLU A 257 " pdb=" CA GLU A 257 " pdb=" CB GLU A 257 " ideal model delta sigma weight residual 110.39 114.79 -4.40 1.66e+00 3.63e-01 7.02e+00 angle pdb=" C HIS C 45 " pdb=" N CYS C 46 " pdb=" CA CYS C 46 " ideal model delta sigma weight residual 121.54 126.54 -5.00 1.91e+00 2.74e-01 6.86e+00 angle pdb=" N GLU B 257 " pdb=" CA GLU B 257 " pdb=" CB GLU B 257 " ideal model delta sigma weight residual 110.28 114.08 -3.80 1.55e+00 4.16e-01 6.00e+00 angle pdb=" C ILE A 256 " pdb=" N GLU A 257 " pdb=" CA GLU A 257 " ideal model delta sigma weight residual 120.72 116.80 3.92 1.67e+00 3.59e-01 5.51e+00 ... (remaining 4657 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.27: 1722 12.27 - 24.53: 194 24.53 - 36.80: 61 36.80 - 49.06: 18 49.06 - 61.32: 6 Dihedral angle restraints: 2001 sinusoidal: 792 harmonic: 1209 Sorted by residual: dihedral pdb=" CA ASP A 2 " pdb=" CB ASP A 2 " pdb=" CG ASP A 2 " pdb=" OD1 ASP A 2 " ideal model delta sinusoidal sigma weight residual -30.00 -87.40 57.40 1 2.00e+01 2.50e-03 1.11e+01 dihedral pdb=" CB CYS A 59 " pdb=" SG CYS A 59 " pdb=" SG CYS B 59 " pdb=" CB CYS B 59 " ideal model delta sinusoidal sigma weight residual 93.00 118.39 -25.39 1 1.00e+01 1.00e-02 9.27e+00 dihedral pdb=" CA SER A 47 " pdb=" C SER A 47 " pdb=" N PRO A 48 " pdb=" CA PRO A 48 " ideal model delta harmonic sigma weight residual 180.00 165.01 14.99 0 5.00e+00 4.00e-02 8.99e+00 ... (remaining 1998 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 395 0.037 - 0.074: 104 0.074 - 0.112: 22 0.112 - 0.149: 2 0.149 - 0.186: 2 Chirality restraints: 525 Sorted by residual: chirality pdb=" CA GLU A 257 " pdb=" N GLU A 257 " pdb=" C GLU A 257 " pdb=" CB GLU A 257 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.65e-01 chirality pdb=" CA GLU C 257 " pdb=" N GLU C 257 " pdb=" C GLU C 257 " pdb=" CB GLU C 257 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.17e-01 chirality pdb=" CA GLU B 257 " pdb=" N GLU B 257 " pdb=" C GLU B 257 " pdb=" CB GLU B 257 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.52e-01 ... (remaining 522 not shown) Planarity restraints: 585 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU B 253 " 0.008 2.00e-02 2.50e+03 1.61e-02 2.59e+00 pdb=" C GLU B 253 " -0.028 2.00e-02 2.50e+03 pdb=" O GLU B 253 " 0.010 2.00e-02 2.50e+03 pdb=" N THR B 254 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR C 268 " 0.022 5.00e-02 4.00e+02 3.30e-02 1.74e+00 pdb=" N PRO C 269 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO C 269 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 269 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA HIS C 45 " 0.006 2.00e-02 2.50e+03 1.31e-02 1.71e+00 pdb=" C HIS C 45 " -0.023 2.00e-02 2.50e+03 pdb=" O HIS C 45 " 0.008 2.00e-02 2.50e+03 pdb=" N CYS C 46 " 0.008 2.00e-02 2.50e+03 ... (remaining 582 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 825 2.79 - 3.32: 3428 3.32 - 3.85: 5678 3.85 - 4.37: 6494 4.37 - 4.90: 11051 Nonbonded interactions: 27476 Sorted by model distance: nonbonded pdb=" OG SER C 47 " pdb=" ND1 HIS C 50 " model vdw 2.264 2.520 nonbonded pdb=" OG SER B 47 " pdb=" ND1 HIS B 50 " model vdw 2.300 2.520 nonbonded pdb=" O PHE A 22 " pdb=" NH2 ARG A 238 " model vdw 2.301 2.520 nonbonded pdb=" O GLU A 62 " pdb=" OG1 THR A 65 " model vdw 2.302 2.440 nonbonded pdb=" OE2 GLU A 62 " pdb=" NZ LYS B 236 " model vdw 2.319 2.520 ... (remaining 27471 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 17.220 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.780 Find NCS groups from input model: 0.190 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: 37.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 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 : 0.002 0.022 3411 Z= 0.142 Angle : 0.522 6.373 4662 Z= 0.279 Chirality : 0.037 0.186 525 Planarity : 0.004 0.033 585 Dihedral : 12.414 61.325 1212 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.43), residues: 402 helix: 1.50 (0.31), residues: 291 sheet: None (None), residues: 0 loop : 1.86 (0.65), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 265 HIS 0.003 0.001 HIS B 45 PHE 0.007 0.001 PHE A 237 TYR 0.006 0.001 TYR A 258 ARG 0.002 0.000 ARG A 37 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 5 LYS cc_start: 0.7412 (tmtt) cc_final: 0.6803 (tmtt) REVERT: C 233 MET cc_start: 0.8428 (mpp) cc_final: 0.7894 (mpp) outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.2300 time to fit residues: 11.3658 Evaluate side-chains 28 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 9.9990 chunk 29 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 10 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 15 optimal weight: 8.9990 chunk 30 optimal weight: 10.0000 chunk 11 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 35 optimal weight: 9.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.0977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3411 Z= 0.184 Angle : 0.527 4.767 4662 Z= 0.273 Chirality : 0.038 0.149 525 Planarity : 0.004 0.035 585 Dihedral : 3.852 13.540 447 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.82 % Allowed : 6.56 % Favored : 92.62 % 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: 2.68 (0.43), residues: 402 helix: 1.83 (0.31), residues: 292 sheet: None (None), residues: 0 loop : 1.96 (0.63), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 265 HIS 0.004 0.001 HIS A 244 PHE 0.005 0.001 PHE C 237 TYR 0.008 0.001 TYR A 36 ARG 0.002 0.000 ARG C 26 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 30 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 MET cc_start: 0.7975 (mtm) cc_final: 0.7769 (mtm) REVERT: C 233 MET cc_start: 0.8384 (mpp) cc_final: 0.7880 (mpp) outliers start: 3 outliers final: 3 residues processed: 31 average time/residue: 0.1593 time to fit residues: 6.1248 Evaluate side-chains 32 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 29 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain C residue 20 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 19 optimal weight: 5.9990 chunk 10 optimal weight: 10.0000 chunk 29 optimal weight: 9.9990 chunk 24 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 35 optimal weight: 9.9990 chunk 38 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 12 optimal weight: 7.9990 chunk 28 optimal weight: 5.9990 chunk 26 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3411 Z= 0.265 Angle : 0.541 4.427 4662 Z= 0.283 Chirality : 0.039 0.124 525 Planarity : 0.004 0.035 585 Dihedral : 3.899 15.121 447 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.37 % Allowed : 9.02 % Favored : 89.62 % 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: 2.75 (0.43), residues: 402 helix: 1.90 (0.30), residues: 292 sheet: None (None), residues: 0 loop : 1.91 (0.64), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 60 HIS 0.004 0.001 HIS A 244 PHE 0.008 0.001 PHE B 237 TYR 0.011 0.001 TYR C 272 ARG 0.003 0.000 ARG B 238 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 29 time to evaluate : 0.383 Fit side-chains REVERT: C 233 MET cc_start: 0.8402 (mpp) cc_final: 0.7865 (mpp) outliers start: 5 outliers final: 2 residues processed: 31 average time/residue: 0.1865 time to fit residues: 7.1680 Evaluate side-chains 30 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 28 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain B residue 45 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 18 optimal weight: 9.9990 chunk 3 optimal weight: 5.9990 chunk 16 optimal weight: 10.0000 chunk 23 optimal weight: 8.9990 chunk 35 optimal weight: 6.9990 chunk 37 optimal weight: 7.9990 chunk 33 optimal weight: 0.9980 chunk 10 optimal weight: 9.9990 chunk 31 optimal weight: 7.9990 chunk 21 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 overall best weight: 5.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 ASN A 239 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 3411 Z= 0.369 Angle : 0.582 4.310 4662 Z= 0.302 Chirality : 0.041 0.121 525 Planarity : 0.005 0.039 585 Dihedral : 4.080 17.498 447 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.82 % Allowed : 13.39 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.62 (0.42), residues: 402 helix: 1.85 (0.30), residues: 292 sheet: None (None), residues: 0 loop : 1.72 (0.62), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 60 HIS 0.005 0.002 HIS A 244 PHE 0.009 0.002 PHE B 22 TYR 0.011 0.002 TYR C 272 ARG 0.003 0.001 ARG B 238 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 31 time to evaluate : 0.415 Fit side-chains REVERT: C 233 MET cc_start: 0.8474 (mpp) cc_final: 0.7892 (mpp) outliers start: 3 outliers final: 2 residues processed: 33 average time/residue: 0.1780 time to fit residues: 7.3098 Evaluate side-chains 32 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 30 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain B residue 45 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 28 optimal weight: 4.9990 chunk 15 optimal weight: 10.0000 chunk 32 optimal weight: 8.9990 chunk 26 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 19 optimal weight: 5.9990 chunk 33 optimal weight: 20.0000 chunk 9 optimal weight: 3.9990 chunk 12 optimal weight: 0.3980 chunk 7 optimal weight: 0.0040 chunk 22 optimal weight: 0.8980 overall best weight: 2.0596 ------------------------------------------------------------------------------- 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: 0.8339 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3411 Z= 0.176 Angle : 0.500 4.422 4662 Z= 0.261 Chirality : 0.036 0.110 525 Planarity : 0.004 0.036 585 Dihedral : 3.914 16.850 447 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.82 % Allowed : 13.93 % Favored : 85.25 % 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: 2.85 (0.42), residues: 402 helix: 2.01 (0.30), residues: 292 sheet: None (None), residues: 0 loop : 1.83 (0.63), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 60 HIS 0.003 0.001 HIS A 244 PHE 0.013 0.001 PHE B 237 TYR 0.007 0.001 TYR A 228 ARG 0.001 0.000 ARG C 37 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 29 time to evaluate : 0.389 Fit side-chains REVERT: C 233 MET cc_start: 0.8482 (mpp) cc_final: 0.7919 (mpp) outliers start: 3 outliers final: 2 residues processed: 31 average time/residue: 0.1658 time to fit residues: 6.5308 Evaluate side-chains 31 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 29 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain B residue 45 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 9 optimal weight: 2.9990 chunk 37 optimal weight: 6.9990 chunk 31 optimal weight: 9.9990 chunk 17 optimal weight: 7.9990 chunk 3 optimal weight: 7.9990 chunk 12 optimal weight: 0.0980 chunk 19 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 21 optimal weight: 20.0000 chunk 27 optimal weight: 5.9990 overall best weight: 2.2188 ------------------------------------------------------------------------------- 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: 0.8337 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3411 Z= 0.185 Angle : 0.525 6.422 4662 Z= 0.270 Chirality : 0.036 0.132 525 Planarity : 0.004 0.032 585 Dihedral : 3.846 16.509 447 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.91 % Allowed : 13.11 % Favored : 84.97 % 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: 2.92 (0.43), residues: 402 helix: 2.05 (0.30), residues: 292 sheet: None (None), residues: 0 loop : 1.91 (0.64), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 60 HIS 0.004 0.001 HIS A 244 PHE 0.012 0.001 PHE B 237 TYR 0.008 0.001 TYR C 272 ARG 0.001 0.000 ARG B 238 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 31 time to evaluate : 0.390 Fit side-chains REVERT: C 44 GLU cc_start: 0.7410 (OUTLIER) cc_final: 0.7199 (pp20) REVERT: C 233 MET cc_start: 0.8440 (mpp) cc_final: 0.7945 (mpp) outliers start: 7 outliers final: 3 residues processed: 36 average time/residue: 0.1880 time to fit residues: 8.3253 Evaluate side-chains 34 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 30 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 HIS Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain B residue 45 HIS Chi-restraints excluded: chain C residue 44 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 21 optimal weight: 9.9990 chunk 31 optimal weight: 9.9990 chunk 37 optimal weight: 9.9990 chunk 23 optimal weight: 10.0000 chunk 22 optimal weight: 2.9990 chunk 17 optimal weight: 8.9990 chunk 15 optimal weight: 8.9990 chunk 11 optimal weight: 6.9990 chunk 7 optimal weight: 40.0000 chunk 25 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 overall best weight: 4.7988 ------------------------------------------------------------------------------- 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: 0.8373 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 3411 Z= 0.307 Angle : 0.567 6.135 4662 Z= 0.293 Chirality : 0.039 0.131 525 Planarity : 0.005 0.045 585 Dihedral : 3.975 17.594 447 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.37 % Allowed : 12.84 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.83 (0.42), residues: 402 helix: 2.02 (0.30), residues: 292 sheet: None (None), residues: 0 loop : 1.76 (0.62), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 60 HIS 0.005 0.001 HIS A 244 PHE 0.012 0.001 PHE B 237 TYR 0.011 0.002 TYR C 272 ARG 0.006 0.001 ARG C 252 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 30 time to evaluate : 0.368 Fit side-chains REVERT: C 44 GLU cc_start: 0.7411 (OUTLIER) cc_final: 0.7197 (pp20) REVERT: C 233 MET cc_start: 0.8422 (mpp) cc_final: 0.7946 (mpp) outliers start: 5 outliers final: 4 residues processed: 32 average time/residue: 0.1654 time to fit residues: 6.7199 Evaluate side-chains 35 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 30 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 HIS Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 267 ARG Chi-restraints excluded: chain B residue 45 HIS Chi-restraints excluded: chain C residue 44 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 chunk 34 optimal weight: 9.9990 chunk 36 optimal weight: 1.9990 chunk 32 optimal weight: 20.0000 chunk 35 optimal weight: 2.9990 chunk 21 optimal weight: 10.0000 chunk 15 optimal weight: 7.9990 chunk 27 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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: 0.8367 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3411 Z= 0.268 Angle : 0.566 6.601 4662 Z= 0.294 Chirality : 0.038 0.124 525 Planarity : 0.005 0.039 585 Dihedral : 3.995 17.926 447 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.91 % Allowed : 12.57 % Favored : 85.52 % 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: 2.83 (0.42), residues: 402 helix: 2.01 (0.30), residues: 292 sheet: None (None), residues: 0 loop : 1.79 (0.62), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 60 HIS 0.004 0.001 HIS A 244 PHE 0.011 0.001 PHE B 237 TYR 0.010 0.001 TYR C 272 ARG 0.005 0.000 ARG C 252 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 31 time to evaluate : 0.350 Fit side-chains REVERT: C 44 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.7173 (pp20) REVERT: C 233 MET cc_start: 0.8494 (mpp) cc_final: 0.7920 (mpp) outliers start: 7 outliers final: 4 residues processed: 35 average time/residue: 0.1533 time to fit residues: 6.7758 Evaluate side-chains 35 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 30 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 HIS Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 267 ARG Chi-restraints excluded: chain B residue 45 HIS Chi-restraints excluded: chain C residue 44 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 33 optimal weight: 0.0570 chunk 34 optimal weight: 10.0000 chunk 23 optimal weight: 8.9990 chunk 37 optimal weight: 8.9990 chunk 22 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 25 optimal weight: 0.0000 chunk 38 optimal weight: 4.9990 chunk 35 optimal weight: 7.9990 chunk 30 optimal weight: 3.9990 chunk 3 optimal weight: 7.9990 overall best weight: 1.2108 ------------------------------------------------------------------------------- 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: 0.8322 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 3411 Z= 0.157 Angle : 0.529 6.857 4662 Z= 0.273 Chirality : 0.035 0.118 525 Planarity : 0.004 0.032 585 Dihedral : 3.819 16.529 447 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.64 % Allowed : 13.11 % Favored : 85.25 % 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: 3.00 (0.43), residues: 402 helix: 2.12 (0.31), residues: 292 sheet: None (None), residues: 0 loop : 1.92 (0.64), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 60 HIS 0.003 0.001 HIS A 244 PHE 0.010 0.001 PHE B 237 TYR 0.009 0.001 TYR A 228 ARG 0.006 0.000 ARG C 252 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 35 time to evaluate : 0.356 Fit side-chains REVERT: C 44 GLU cc_start: 0.7315 (OUTLIER) cc_final: 0.7092 (pp20) REVERT: C 233 MET cc_start: 0.8426 (mpp) cc_final: 0.8022 (mpp) outliers start: 6 outliers final: 4 residues processed: 37 average time/residue: 0.2098 time to fit residues: 9.3051 Evaluate side-chains 37 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 32 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 HIS Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 267 ARG Chi-restraints excluded: chain B residue 45 HIS Chi-restraints excluded: chain C residue 44 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 23 optimal weight: 3.9990 chunk 18 optimal weight: 10.0000 chunk 24 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 8 optimal weight: 8.9990 chunk 30 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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: 0.8341 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3411 Z= 0.203 Angle : 0.556 7.163 4662 Z= 0.289 Chirality : 0.037 0.148 525 Planarity : 0.004 0.031 585 Dihedral : 3.807 16.320 447 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.37 % Allowed : 13.39 % Favored : 85.25 % 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: 2.92 (0.43), residues: 402 helix: 2.05 (0.30), residues: 292 sheet: None (None), residues: 0 loop : 1.92 (0.64), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 60 HIS 0.004 0.001 HIS A 244 PHE 0.011 0.001 PHE B 237 TYR 0.009 0.001 TYR A 228 ARG 0.005 0.000 ARG C 252 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 34 time to evaluate : 0.401 Fit side-chains REVERT: C 44 GLU cc_start: 0.7357 (OUTLIER) cc_final: 0.7129 (pp20) REVERT: C 233 MET cc_start: 0.8409 (mpp) cc_final: 0.7999 (mpp) outliers start: 5 outliers final: 4 residues processed: 36 average time/residue: 0.1867 time to fit residues: 8.2912 Evaluate side-chains 38 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 33 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 HIS Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 267 ARG Chi-restraints excluded: chain B residue 45 HIS Chi-restraints excluded: chain C residue 44 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 9.9990 chunk 5 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 1 optimal weight: 0.0060 chunk 22 optimal weight: 9.9990 chunk 35 optimal weight: 0.9980 chunk 20 optimal weight: 30.0000 chunk 26 optimal weight: 7.9990 chunk 24 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 15 optimal weight: 7.9990 overall best weight: 1.3798 ------------------------------------------------------------------------------- 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 = 0.3416 r_free = 0.3416 target = 0.054985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.044905 restraints weight = 16410.623| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 2.73 r_work: 0.2971 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3411 Z= 0.165 Angle : 0.544 6.990 4662 Z= 0.281 Chirality : 0.036 0.147 525 Planarity : 0.004 0.032 585 Dihedral : 3.774 15.803 447 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.91 % Allowed : 13.39 % Favored : 84.70 % 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: 3.02 (0.43), residues: 402 helix: 2.11 (0.30), residues: 292 sheet: None (None), residues: 0 loop : 1.98 (0.64), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 60 HIS 0.003 0.001 HIS A 244 PHE 0.010 0.001 PHE B 237 TYR 0.011 0.001 TYR C 36 ARG 0.004 0.000 ARG C 252 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1043.25 seconds wall clock time: 19 minutes 37.36 seconds (1177.36 seconds total)