Starting phenix.real_space_refine on Tue Feb 13 06:14:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7urv_26719/02_2024/7urv_26719.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7urv_26719/02_2024/7urv_26719.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7urv_26719/02_2024/7urv_26719.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7urv_26719/02_2024/7urv_26719.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7urv_26719/02_2024/7urv_26719.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7urv_26719/02_2024/7urv_26719.pdb" } resolution = 3.05 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= 0.002 sd= 0.069 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 17 5.16 5 C 2202 2.51 5 N 579 2.21 5 O 662 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D GLU 117": "OE1" <-> "OE2" Residue "D GLU 166": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 3460 Number of models: 1 Model: "" Number of chains: 2 Chain: "C" Number of atoms: 1701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1701 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 197} Chain breaks: 3 Chain: "D" Number of atoms: 1759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1759 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 218} Chain breaks: 1 Time building chain proxies: 2.57, per 1000 atoms: 0.74 Number of scatterers: 3460 At special positions: 0 Unit cell: (52.608, 92.064, 90.968, 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 17 16.00 O 662 8.00 N 579 7.00 C 2202 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS C 38 " - pdb=" SG CYS C 261 " distance=2.03 Simple disulfide: pdb=" SG CYS C 97 " - pdb=" SG CYS C 200 " distance=2.03 Simple disulfide: pdb=" SG CYS D 61 " - pdb=" SG CYS D 126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 182 " - pdb=" SG CYS D 255 " 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: 1.03 Conformation dependent library (CDL) restraints added in 663.1 milliseconds 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 808 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 10 sheets defined 4.5% alpha, 44.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'C' and resid 88 through 92 removed outlier: 3.629A pdb=" N GLY C 92 " --> pdb=" O GLN C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 206 removed outlier: 4.269A pdb=" N SER C 206 " --> pdb=" O PRO C 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 121 removed outlier: 3.954A pdb=" N ILE D 121 " --> pdb=" O GLN D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 250 removed outlier: 3.742A pdb=" N THR D 250 " --> pdb=" O THR D 247 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 24 through 29 removed outlier: 3.717A pdb=" N THR C 275 " --> pdb=" O VAL C 28 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LYS C 258 " --> pdb=" O GLU C 55 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N GLU C 55 " --> pdb=" O LYS C 258 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ARG C 54 " --> pdb=" O PRO C 60 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N HIS C 218 " --> pdb=" O GLY C 221 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N TRP C 214 " --> pdb=" O LEU C 225 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N SER C 227 " --> pdb=" O LEU C 212 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N LEU C 212 " --> pdb=" O SER C 227 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N GLY C 93 " --> pdb=" O THR C 112 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N THR C 112 " --> pdb=" O GLY C 93 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N TYR C 95 " --> pdb=" O GLY C 110 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N LEU C 188 " --> pdb=" O GLY C 110 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N THR C 112 " --> pdb=" O LEU C 188 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N MET C 190 " --> pdb=" O THR C 112 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N ASN C 114 " --> pdb=" O MET C 190 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 195 through 198 Processing sheet with id=AA3, first strand: chain 'C' and resid 120 through 123 removed outlier: 6.175A pdb=" N LEU C 121 " --> pdb=" O TYR C 157 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N TRP C 159 " --> pdb=" O LEU C 121 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N ARG C 123 " --> pdb=" O TRP C 159 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 42 through 43 removed outlier: 3.901A pdb=" N ASP D 108 " --> pdb=" O SER D 105 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER D 105 " --> pdb=" O ASP D 108 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 48 through 51 Processing sheet with id=AA6, first strand: chain 'D' and resid 48 through 51 removed outlier: 3.904A pdb=" N THR D 135 " --> pdb=" O GLN D 128 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 86 through 87 Processing sheet with id=AA8, first strand: chain 'D' and resid 163 through 167 Processing sheet with id=AA9, first strand: chain 'D' and resid 217 through 219 removed outlier: 6.631A pdb=" N TRP D 196 " --> pdb=" O LEU D 208 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N VAL D 210 " --> pdb=" O VAL D 194 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL D 194 " --> pdb=" O VAL D 210 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N CYS D 255 " --> pdb=" O TRP D 270 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N TRP D 270 " --> pdb=" O CYS D 255 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N LYS D 257 " --> pdb=" O ASP D 268 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 217 through 219 removed outlier: 6.631A pdb=" N TRP D 196 " --> pdb=" O LEU D 208 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N VAL D 210 " --> pdb=" O VAL D 194 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL D 194 " --> pdb=" O VAL D 210 " (cutoff:3.500A) 128 hydrogen bonds defined for protein. 315 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: 0.98 Time building geometry restraints manager: 1.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 559 1.31 - 1.44: 990 1.44 - 1.56: 1976 1.56 - 1.69: 0 1.69 - 1.81: 25 Bond restraints: 3550 Sorted by residual: bond pdb=" C TYR D 70 " pdb=" O TYR D 70 " ideal model delta sigma weight residual 1.234 1.187 0.047 1.19e-02 7.06e+03 1.54e+01 bond pdb=" CA SER D 68 " pdb=" CB SER D 68 " ideal model delta sigma weight residual 1.529 1.467 0.062 1.62e-02 3.81e+03 1.46e+01 bond pdb=" N PRO C 235 " pdb=" CA PRO C 235 " ideal model delta sigma weight residual 1.468 1.428 0.040 1.20e-02 6.94e+03 1.09e+01 bond pdb=" CA SER D 47 " pdb=" CB SER D 47 " ideal model delta sigma weight residual 1.533 1.483 0.050 1.58e-02 4.01e+03 1.01e+01 bond pdb=" C ARG C 234 " pdb=" N PRO C 235 " ideal model delta sigma weight residual 1.331 1.366 -0.035 1.20e-02 6.94e+03 8.63e+00 ... (remaining 3545 not shown) Histogram of bond angle deviations from ideal: 99.03 - 106.02: 128 106.02 - 113.01: 1915 113.01 - 120.00: 1146 120.00 - 126.99: 1574 126.99 - 133.98: 68 Bond angle restraints: 4831 Sorted by residual: angle pdb=" N PRO C 172 " pdb=" CA PRO C 172 " pdb=" C PRO C 172 " ideal model delta sigma weight residual 112.47 99.03 13.44 2.06e+00 2.36e-01 4.26e+01 angle pdb=" CA ARG C 234 " pdb=" C ARG C 234 " pdb=" N PRO C 235 " ideal model delta sigma weight residual 118.23 112.84 5.39 9.20e-01 1.18e+00 3.44e+01 angle pdb=" N PRO C 235 " pdb=" CA PRO C 235 " pdb=" C PRO C 235 " ideal model delta sigma weight residual 111.03 102.28 8.75 1.54e+00 4.22e-01 3.23e+01 angle pdb=" C THR D 46 " pdb=" CA THR D 46 " pdb=" CB THR D 46 " ideal model delta sigma weight residual 109.53 118.01 -8.48 1.69e+00 3.50e-01 2.52e+01 angle pdb=" C PRO C 172 " pdb=" CA PRO C 172 " pdb=" CB PRO C 172 " ideal model delta sigma weight residual 111.56 119.80 -8.24 1.65e+00 3.67e-01 2.49e+01 ... (remaining 4826 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.02: 1861 16.02 - 32.03: 175 32.03 - 48.04: 55 48.04 - 64.06: 8 64.06 - 80.07: 4 Dihedral angle restraints: 2103 sinusoidal: 836 harmonic: 1267 Sorted by residual: dihedral pdb=" CB CYS D 182 " pdb=" SG CYS D 182 " pdb=" SG CYS D 255 " pdb=" CB CYS D 255 " ideal model delta sinusoidal sigma weight residual 93.00 160.69 -67.69 1 1.00e+01 1.00e-02 5.96e+01 dihedral pdb=" C ARG C 237 " pdb=" N ARG C 237 " pdb=" CA ARG C 237 " pdb=" CB ARG C 237 " ideal model delta harmonic sigma weight residual -122.60 -108.82 -13.78 0 2.50e+00 1.60e-01 3.04e+01 dihedral pdb=" N ARG C 237 " pdb=" C ARG C 237 " pdb=" CA ARG C 237 " pdb=" CB ARG C 237 " ideal model delta harmonic sigma weight residual 122.80 113.56 9.24 0 2.50e+00 1.60e-01 1.37e+01 ... (remaining 2100 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 469 0.090 - 0.180: 52 0.180 - 0.270: 6 0.270 - 0.360: 3 0.360 - 0.450: 1 Chirality restraints: 531 Sorted by residual: chirality pdb=" CA ARG C 237 " pdb=" N ARG C 237 " pdb=" C ARG C 237 " pdb=" CB ARG C 237 " both_signs ideal model delta sigma weight residual False 2.51 2.96 -0.45 2.00e-01 2.50e+01 5.07e+00 chirality pdb=" CA TRP C 240 " pdb=" N TRP C 240 " pdb=" C TRP C 240 " pdb=" CB TRP C 240 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.38e+00 chirality pdb=" CA LEU C 248 " pdb=" N LEU C 248 " pdb=" C LEU C 248 " pdb=" CB LEU C 248 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.13e+00 ... (remaining 528 not shown) Planarity restraints: 610 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG C 234 " -0.017 2.00e-02 2.50e+03 3.51e-02 1.23e+01 pdb=" C ARG C 234 " 0.061 2.00e-02 2.50e+03 pdb=" O ARG C 234 " -0.024 2.00e-02 2.50e+03 pdb=" N PRO C 235 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR D 43 " 0.016 2.00e-02 2.50e+03 3.14e-02 9.84e+00 pdb=" C THR D 43 " -0.054 2.00e-02 2.50e+03 pdb=" O THR D 43 " 0.020 2.00e-02 2.50e+03 pdb=" N GLN D 44 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS C 218 " -0.037 5.00e-02 4.00e+02 5.65e-02 5.11e+00 pdb=" N PRO C 219 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO C 219 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 219 " -0.031 5.00e-02 4.00e+02 ... (remaining 607 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 1007 2.82 - 3.34: 2872 3.34 - 3.86: 5733 3.86 - 4.38: 6736 4.38 - 4.90: 11779 Nonbonded interactions: 28127 Sorted by model distance: nonbonded pdb=" OD1 ASN C 114 " pdb=" NH1 ARG C 123 " model vdw 2.300 2.520 nonbonded pdb=" NH1 ARG C 54 " pdb=" OE2 GLU C 55 " model vdw 2.337 2.520 nonbonded pdb=" OH TYR D 74 " pdb=" OE1 GLN D 127 " model vdw 2.353 2.440 nonbonded pdb=" O GLY C 100 " pdb=" OG SER C 213 " model vdw 2.400 2.440 nonbonded pdb=" O MET C 91 " pdb=" OH TYR C 95 " model vdw 2.402 2.440 ... (remaining 28122 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: 1.520 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: 6.560 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 14.250 Find NCS groups from input model: 0.110 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 3550 Z= 0.327 Angle : 0.968 13.445 4831 Z= 0.601 Chirality : 0.062 0.450 531 Planarity : 0.006 0.056 610 Dihedral : 14.079 80.070 1283 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.93 % Favored : 92.84 % Rotamer: Outliers : 0.78 % Allowed : 2.85 % Favored : 96.37 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.42), residues: 433 helix: None (None), residues: 0 sheet: -0.26 (0.37), residues: 206 loop : -1.06 (0.43), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP C 240 HIS 0.003 0.001 HIS C 216 PHE 0.010 0.001 PHE C 61 TYR 0.017 0.002 TYR D 259 ARG 0.002 0.000 ARG C 234 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 57 time to evaluate : 0.379 Fit side-chains REVERT: C 162 ASP cc_start: 0.8179 (t0) cc_final: 0.7952 (t0) outliers start: 3 outliers final: 2 residues processed: 58 average time/residue: 0.1620 time to fit residues: 12.0347 Evaluate side-chains 47 residues out of total 386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 45 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 242 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 36 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 11 optimal weight: 0.3980 chunk 21 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 130 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.1191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3550 Z= 0.292 Angle : 0.669 7.415 4831 Z= 0.337 Chirality : 0.045 0.151 531 Planarity : 0.006 0.061 610 Dihedral : 5.608 43.002 482 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 1.30 % Allowed : 10.36 % Favored : 88.34 % 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: -0.97 (0.42), residues: 433 helix: None (None), residues: 0 sheet: -0.18 (0.37), residues: 202 loop : -1.04 (0.43), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 207 HIS 0.003 0.001 HIS D 88 PHE 0.009 0.002 PHE C 61 TYR 0.014 0.002 TYR D 261 ARG 0.002 0.000 ARG C 234 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 52 time to evaluate : 0.366 Fit side-chains REVERT: C 162 ASP cc_start: 0.8049 (t0) cc_final: 0.7816 (t0) outliers start: 5 outliers final: 3 residues processed: 56 average time/residue: 0.1391 time to fit residues: 9.6992 Evaluate side-chains 51 residues out of total 386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 48 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain D residue 246 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 21 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 38 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 31 optimal weight: 0.0870 overall best weight: 0.6358 ------------------------------------------------------------------------------- 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: 0.7585 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 3550 Z= 0.258 Angle : 0.618 7.246 4831 Z= 0.311 Chirality : 0.044 0.182 531 Planarity : 0.005 0.063 610 Dihedral : 4.839 23.354 479 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 2.33 % Allowed : 11.66 % Favored : 86.01 % 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: -0.93 (0.41), residues: 433 helix: None (None), residues: 0 sheet: -0.12 (0.36), residues: 202 loop : -1.04 (0.43), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 167 HIS 0.003 0.001 HIS C 216 PHE 0.015 0.002 PHE C 83 TYR 0.013 0.001 TYR D 261 ARG 0.002 0.000 ARG C 234 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 48 time to evaluate : 0.360 Fit side-chains REVERT: C 32 ASP cc_start: 0.8816 (OUTLIER) cc_final: 0.8051 (m-30) REVERT: C 162 ASP cc_start: 0.7983 (t0) cc_final: 0.7716 (t0) outliers start: 9 outliers final: 5 residues processed: 53 average time/residue: 0.1609 time to fit residues: 10.5522 Evaluate side-chains 53 residues out of total 386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 47 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 32 ASP Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 246 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 38 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 4 optimal weight: 0.4980 chunk 18 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 11 optimal weight: 0.1980 chunk 34 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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: 0.7582 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3550 Z= 0.250 Angle : 0.598 7.299 4831 Z= 0.298 Chirality : 0.043 0.165 531 Planarity : 0.005 0.063 610 Dihedral : 4.666 23.379 477 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.93 % Favored : 92.84 % Rotamer: Outliers : 2.33 % Allowed : 14.77 % Favored : 82.90 % 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: -0.90 (0.41), residues: 433 helix: None (None), residues: 0 sheet: -0.08 (0.36), residues: 202 loop : -1.05 (0.43), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 167 HIS 0.003 0.001 HIS C 216 PHE 0.020 0.002 PHE C 83 TYR 0.013 0.001 TYR D 261 ARG 0.002 0.000 ARG D 198 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 51 time to evaluate : 0.409 Fit side-chains REVERT: C 32 ASP cc_start: 0.8833 (OUTLIER) cc_final: 0.8018 (m-30) REVERT: C 162 ASP cc_start: 0.8016 (t0) cc_final: 0.7720 (t0) outliers start: 9 outliers final: 7 residues processed: 57 average time/residue: 0.1537 time to fit residues: 10.9899 Evaluate side-chains 52 residues out of total 386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 44 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 32 ASP Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 246 GLN Chi-restraints excluded: chain D residue 250 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 23 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 30 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 35 optimal weight: 0.2980 chunk 28 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 8 optimal weight: 0.3980 overall best weight: 0.6182 ------------------------------------------------------------------------------- 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: 0.7581 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3550 Z= 0.254 Angle : 0.598 7.225 4831 Z= 0.298 Chirality : 0.043 0.162 531 Planarity : 0.005 0.062 610 Dihedral : 4.607 23.357 477 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.24 % Favored : 93.53 % Rotamer: Outliers : 3.37 % Allowed : 13.73 % Favored : 82.90 % 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: -0.88 (0.41), residues: 433 helix: None (None), residues: 0 sheet: -0.04 (0.36), residues: 202 loop : -1.07 (0.43), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 167 HIS 0.003 0.001 HIS C 216 PHE 0.037 0.002 PHE C 83 TYR 0.013 0.001 TYR D 261 ARG 0.002 0.000 ARG C 234 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 46 time to evaluate : 0.423 Fit side-chains REVERT: C 32 ASP cc_start: 0.8838 (OUTLIER) cc_final: 0.8004 (m-30) REVERT: C 162 ASP cc_start: 0.8010 (t0) cc_final: 0.7714 (t0) outliers start: 13 outliers final: 10 residues processed: 56 average time/residue: 0.1389 time to fit residues: 10.0431 Evaluate side-chains 55 residues out of total 386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 44 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 32 ASP Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 246 GLN Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 278 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 24 optimal weight: 0.9990 chunk 10 optimal weight: 0.4980 chunk 41 optimal weight: 1.9990 chunk 34 optimal weight: 0.1980 chunk 19 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 176 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3550 Z= 0.256 Angle : 0.596 7.238 4831 Z= 0.297 Chirality : 0.043 0.160 531 Planarity : 0.005 0.062 610 Dihedral : 4.596 23.301 477 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.70 % Favored : 93.07 % Rotamer: Outliers : 3.11 % Allowed : 15.03 % Favored : 81.87 % 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: -0.87 (0.41), residues: 433 helix: None (None), residues: 0 sheet: -0.01 (0.36), residues: 202 loop : -1.08 (0.43), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 167 HIS 0.003 0.001 HIS C 216 PHE 0.036 0.002 PHE C 83 TYR 0.013 0.001 TYR D 261 ARG 0.002 0.000 ARG D 198 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 48 time to evaluate : 0.417 Fit side-chains REVERT: C 32 ASP cc_start: 0.8830 (OUTLIER) cc_final: 0.8040 (m-30) REVERT: C 162 ASP cc_start: 0.7995 (t0) cc_final: 0.7697 (t0) outliers start: 12 outliers final: 11 residues processed: 55 average time/residue: 0.1296 time to fit residues: 9.4327 Evaluate side-chains 58 residues out of total 386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 46 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 32 ASP Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 242 MET Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 246 GLN Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 278 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 30 optimal weight: 0.6980 chunk 23 optimal weight: 3.9990 chunk 35 optimal weight: 0.0370 chunk 41 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 24 optimal weight: 0.5980 chunk 12 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 overall best weight: 0.5458 ------------------------------------------------------------------------------- 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: 0.7570 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3550 Z= 0.232 Angle : 0.588 7.124 4831 Z= 0.291 Chirality : 0.043 0.155 531 Planarity : 0.005 0.061 610 Dihedral : 4.524 23.350 477 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 3.37 % Allowed : 15.28 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.41), residues: 433 helix: None (None), residues: 0 sheet: 0.06 (0.36), residues: 218 loop : -1.10 (0.44), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 167 HIS 0.003 0.001 HIS C 216 PHE 0.032 0.002 PHE C 83 TYR 0.012 0.001 TYR D 261 ARG 0.002 0.000 ARG D 198 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 45 time to evaluate : 0.432 Fit side-chains outliers start: 13 outliers final: 10 residues processed: 54 average time/residue: 0.1233 time to fit residues: 8.7479 Evaluate side-chains 54 residues out of total 386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 44 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 242 MET Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 278 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 28 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 36 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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: 0.7586 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3550 Z= 0.273 Angle : 0.601 7.282 4831 Z= 0.298 Chirality : 0.043 0.147 531 Planarity : 0.005 0.062 610 Dihedral : 4.589 23.280 477 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 2.85 % Allowed : 15.54 % Favored : 81.61 % 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: -0.83 (0.41), residues: 433 helix: None (None), residues: 0 sheet: 0.03 (0.36), residues: 211 loop : -1.11 (0.43), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 167 HIS 0.003 0.001 HIS C 216 PHE 0.037 0.003 PHE C 83 TYR 0.013 0.001 TYR D 261 ARG 0.002 0.000 ARG C 234 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 46 time to evaluate : 0.430 Fit side-chains REVERT: C 32 ASP cc_start: 0.8839 (OUTLIER) cc_final: 0.8033 (m-30) outliers start: 11 outliers final: 10 residues processed: 52 average time/residue: 0.1274 time to fit residues: 8.7458 Evaluate side-chains 56 residues out of total 386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 45 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 32 ASP Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 242 MET Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 278 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 11 optimal weight: 0.0470 chunk 34 optimal weight: 0.0670 chunk 36 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 42 optimal weight: 0.6980 chunk 39 optimal weight: 0.7980 overall best weight: 0.4416 ------------------------------------------------------------------------------- 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: 0.7557 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3550 Z= 0.213 Angle : 0.579 6.954 4831 Z= 0.290 Chirality : 0.043 0.178 531 Planarity : 0.005 0.062 610 Dihedral : 4.459 23.415 477 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 2.85 % Allowed : 15.54 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.41), residues: 433 helix: None (None), residues: 0 sheet: 0.17 (0.36), residues: 213 loop : -1.13 (0.43), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 167 HIS 0.004 0.001 HIS C 216 PHE 0.034 0.002 PHE C 83 TYR 0.011 0.001 TYR D 261 ARG 0.001 0.000 ARG C 234 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 46 time to evaluate : 0.399 Fit side-chains outliers start: 11 outliers final: 9 residues processed: 53 average time/residue: 0.1275 time to fit residues: 8.8760 Evaluate side-chains 55 residues out of total 386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 46 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 242 MET Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 278 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 34 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 5 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 14 optimal weight: 0.0670 overall best weight: 0.6118 ------------------------------------------------------------------------------- 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: 0.7574 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3550 Z= 0.250 Angle : 0.595 7.095 4831 Z= 0.297 Chirality : 0.043 0.178 531 Planarity : 0.005 0.063 610 Dihedral : 4.517 23.346 477 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 2.33 % Allowed : 16.32 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.41), residues: 433 helix: None (None), residues: 0 sheet: 0.17 (0.37), residues: 213 loop : -1.17 (0.43), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 167 HIS 0.003 0.001 HIS C 216 PHE 0.035 0.002 PHE C 83 TYR 0.013 0.001 TYR D 261 ARG 0.002 0.000 ARG D 198 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 45 time to evaluate : 0.416 Fit side-chains outliers start: 9 outliers final: 9 residues processed: 51 average time/residue: 0.1258 time to fit residues: 8.5148 Evaluate side-chains 53 residues out of total 386 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 44 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 242 MET Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 278 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 35 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 39 optimal weight: 0.7980 chunk 22 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3817 r_free = 0.3817 target = 0.144693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.116146 restraints weight = 4672.510| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 2.63 r_work: 0.3361 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3550 Z= 0.287 Angle : 0.617 7.345 4831 Z= 0.307 Chirality : 0.043 0.176 531 Planarity : 0.005 0.063 610 Dihedral : 4.639 23.230 477 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 2.59 % Allowed : 15.80 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.41), residues: 433 helix: None (None), residues: 0 sheet: 0.21 (0.37), residues: 207 loop : -1.20 (0.42), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 167 HIS 0.002 0.001 HIS C 74 PHE 0.034 0.002 PHE C 83 TYR 0.013 0.002 TYR D 261 ARG 0.002 0.000 ARG C 234 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1286.23 seconds wall clock time: 23 minutes 57.64 seconds (1437.64 seconds total)