Starting phenix.real_space_refine on Thu Mar 14 15:31:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5v6p_8637/03_2024/5v6p_8637.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5v6p_8637/03_2024/5v6p_8637.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5v6p_8637/03_2024/5v6p_8637.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5v6p_8637/03_2024/5v6p_8637.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5v6p_8637/03_2024/5v6p_8637.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5v6p_8637/03_2024/5v6p_8637.pdb" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.009 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: 5 Type Number sf(0) Gaussians S 26 5.16 5 C 3030 2.51 5 N 698 2.21 5 O 764 1.98 5 H 4676 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9194 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 4597 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 3, 'TRANS': 266} Chain breaks: 1 Chain: "B" Number of atoms: 4597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 4597 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 3, 'TRANS': 266} Chain breaks: 1 Time building chain proxies: 4.79, per 1000 atoms: 0.52 Number of scatterers: 9194 At special positions: 0 Unit cell: (87.75, 90.45, 76.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 26 16.00 O 764 8.00 N 698 7.00 C 3030 6.00 H 4676 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.48 Conformation dependent library (CDL) restraints added in 1.1 seconds 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1060 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 0 sheets defined 94.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 10 through 31 Processing helix chain 'A' and resid 34 through 45 Processing helix chain 'A' and resid 45 through 69 removed outlier: 3.702A pdb=" N MET A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 99 Proline residue: A 87 - end of helix removed outlier: 3.623A pdb=" N LEU A 99 " --> pdb=" O PHE A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 135 removed outlier: 8.314A pdb=" N PHE A 106 " --> pdb=" O GLU A 102 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N THR A 107 " --> pdb=" O ARG A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 140 Processing helix chain 'A' and resid 142 through 147 Processing helix chain 'A' and resid 147 through 176 removed outlier: 3.638A pdb=" N SER A 151 " --> pdb=" O PHE A 147 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ASN A 153 " --> pdb=" O ARG A 149 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N LEU A 156 " --> pdb=" O PHE A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 220 removed outlier: 3.642A pdb=" N LEU A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 289 Processing helix chain 'A' and resid 295 through 324 removed outlier: 4.106A pdb=" N LYS A 301 " --> pdb=" O MET A 297 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N ASP A 302 " --> pdb=" O MET A 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 31 Processing helix chain 'B' and resid 34 through 45 Processing helix chain 'B' and resid 45 through 69 removed outlier: 3.702A pdb=" N MET B 49 " --> pdb=" O GLY B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 99 Proline residue: B 87 - end of helix removed outlier: 3.624A pdb=" N LEU B 99 " --> pdb=" O PHE B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 135 removed outlier: 8.314A pdb=" N PHE B 106 " --> pdb=" O GLU B 102 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N THR B 107 " --> pdb=" O ARG B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 140 Processing helix chain 'B' and resid 142 through 147 Processing helix chain 'B' and resid 147 through 176 removed outlier: 3.638A pdb=" N SER B 151 " --> pdb=" O PHE B 147 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ASN B 153 " --> pdb=" O ARG B 149 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N LEU B 156 " --> pdb=" O PHE B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 220 removed outlier: 3.641A pdb=" N LEU B 185 " --> pdb=" O GLU B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 289 Processing helix chain 'B' and resid 295 through 324 removed outlier: 4.106A pdb=" N LYS B 301 " --> pdb=" O MET B 297 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N ASP B 302 " --> pdb=" O MET B 298 " (cutoff:3.500A) 395 hydrogen bonds defined for protein. 1185 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: 3.15 Time building geometry restraints manager: 8.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.96 - 1.13: 4670 1.13 - 1.30: 681 1.30 - 1.48: 1955 1.48 - 1.65: 1952 1.65 - 1.83: 46 Bond restraints: 9304 Sorted by residual: bond pdb=" NE2 HIS A 79 " pdb=" HE2 HIS A 79 " ideal model delta sigma weight residual 0.860 1.052 -0.192 2.00e-02 2.50e+03 9.24e+01 bond pdb=" NE2 HIS B 79 " pdb=" HE2 HIS B 79 " ideal model delta sigma weight residual 0.860 1.052 -0.192 2.00e-02 2.50e+03 9.20e+01 bond pdb=" NH1 ARG A 128 " pdb="HH12 ARG A 128 " ideal model delta sigma weight residual 0.860 1.043 -0.183 2.00e-02 2.50e+03 8.42e+01 bond pdb=" NH1 ARG B 128 " pdb="HH12 ARG B 128 " ideal model delta sigma weight residual 0.860 1.043 -0.183 2.00e-02 2.50e+03 8.39e+01 bond pdb=" NE2 HIS B 122 " pdb=" HE2 HIS B 122 " ideal model delta sigma weight residual 0.860 1.043 -0.183 2.00e-02 2.50e+03 8.36e+01 ... (remaining 9299 not shown) Histogram of bond angle deviations from ideal: 94.47 - 102.35: 18 102.35 - 110.23: 9138 110.23 - 118.11: 2985 118.11 - 125.99: 4576 125.99 - 133.87: 95 Bond angle restraints: 16812 Sorted by residual: angle pdb=" CA ASP B 161 " pdb=" CB ASP B 161 " pdb=" CG ASP B 161 " ideal model delta sigma weight residual 112.60 118.59 -5.99 1.00e+00 1.00e+00 3.59e+01 angle pdb=" CA ASP A 161 " pdb=" CB ASP A 161 " pdb=" CG ASP A 161 " ideal model delta sigma weight residual 112.60 118.57 -5.97 1.00e+00 1.00e+00 3.57e+01 angle pdb=" C ILE A 291 " pdb=" N PRO A 292 " pdb=" CA PRO A 292 " ideal model delta sigma weight residual 119.78 125.76 -5.98 1.03e+00 9.43e-01 3.37e+01 angle pdb=" C ILE B 291 " pdb=" N PRO B 292 " pdb=" CA PRO B 292 " ideal model delta sigma weight residual 119.78 125.73 -5.95 1.03e+00 9.43e-01 3.33e+01 angle pdb=" C ILE A 53 " pdb=" CA ILE A 53 " pdb=" CB ILE A 53 " ideal model delta sigma weight residual 111.97 105.84 6.13 1.28e+00 6.10e-01 2.30e+01 ... (remaining 16807 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.41: 3978 11.41 - 22.81: 276 22.81 - 34.22: 58 34.22 - 45.62: 18 45.62 - 57.03: 14 Dihedral angle restraints: 4344 sinusoidal: 2276 harmonic: 2068 Sorted by residual: dihedral pdb=" CD2 HIS A 286 " pdb=" CG HIS A 286 " pdb=" ND1 HIS A 286 " pdb=" HD1 HIS A 286 " ideal model delta harmonic sigma weight residual -180.00 -139.78 -40.22 0 5.00e+00 4.00e-02 6.47e+01 dihedral pdb=" CD2 HIS B 286 " pdb=" CG HIS B 286 " pdb=" ND1 HIS B 286 " pdb=" HD1 HIS B 286 " ideal model delta harmonic sigma weight residual -180.00 -139.82 -40.18 0 5.00e+00 4.00e-02 6.46e+01 dihedral pdb=" CD2 HIS B 101 " pdb=" CG HIS B 101 " pdb=" ND1 HIS B 101 " pdb=" HD1 HIS B 101 " ideal model delta harmonic sigma weight residual 180.00 142.02 37.98 0 5.00e+00 4.00e-02 5.77e+01 ... (remaining 4341 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 416 0.061 - 0.121: 227 0.121 - 0.182: 80 0.182 - 0.243: 19 0.243 - 0.304: 8 Chirality restraints: 750 Sorted by residual: chirality pdb=" CG LEU A 129 " pdb=" CB LEU A 129 " pdb=" CD1 LEU A 129 " pdb=" CD2 LEU A 129 " both_signs ideal model delta sigma weight residual False -2.59 -2.89 0.30 2.00e-01 2.50e+01 2.30e+00 chirality pdb=" CG LEU B 129 " pdb=" CB LEU B 129 " pdb=" CD1 LEU B 129 " pdb=" CD2 LEU B 129 " both_signs ideal model delta sigma weight residual False -2.59 -2.89 0.30 2.00e-01 2.50e+01 2.30e+00 chirality pdb=" CG LEU A 197 " pdb=" CB LEU A 197 " pdb=" CD1 LEU A 197 " pdb=" CD2 LEU A 197 " both_signs ideal model delta sigma weight residual False -2.59 -2.87 0.28 2.00e-01 2.50e+01 1.96e+00 ... (remaining 747 not shown) Planarity restraints: 1268 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS A 286 " 0.157 2.00e-02 2.50e+03 1.59e-01 5.69e+02 pdb=" CG HIS A 286 " 0.091 2.00e-02 2.50e+03 pdb=" ND1 HIS A 286 " 0.141 2.00e-02 2.50e+03 pdb=" CD2 HIS A 286 " -0.038 2.00e-02 2.50e+03 pdb=" CE1 HIS A 286 " 0.075 2.00e-02 2.50e+03 pdb=" NE2 HIS A 286 " -0.028 2.00e-02 2.50e+03 pdb=" HD1 HIS A 286 " -0.371 2.00e-02 2.50e+03 pdb=" HD2 HIS A 286 " -0.134 2.00e-02 2.50e+03 pdb=" HE1 HIS A 286 " 0.108 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 286 " -0.156 2.00e-02 2.50e+03 1.59e-01 5.68e+02 pdb=" CG HIS B 286 " -0.091 2.00e-02 2.50e+03 pdb=" ND1 HIS B 286 " -0.141 2.00e-02 2.50e+03 pdb=" CD2 HIS B 286 " 0.038 2.00e-02 2.50e+03 pdb=" CE1 HIS B 286 " -0.075 2.00e-02 2.50e+03 pdb=" NE2 HIS B 286 " 0.027 2.00e-02 2.50e+03 pdb=" HD1 HIS B 286 " 0.371 2.00e-02 2.50e+03 pdb=" HD2 HIS B 286 " 0.134 2.00e-02 2.50e+03 pdb=" HE1 HIS B 286 " -0.107 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 101 " -0.140 2.00e-02 2.50e+03 1.43e-01 4.60e+02 pdb=" CG HIS A 101 " -0.074 2.00e-02 2.50e+03 pdb=" ND1 HIS A 101 " -0.125 2.00e-02 2.50e+03 pdb=" CD2 HIS A 101 " 0.038 2.00e-02 2.50e+03 pdb=" CE1 HIS A 101 " -0.074 2.00e-02 2.50e+03 pdb=" NE2 HIS A 101 " 0.029 2.00e-02 2.50e+03 pdb=" HD1 HIS A 101 " 0.334 2.00e-02 2.50e+03 pdb=" HD2 HIS A 101 " 0.115 2.00e-02 2.50e+03 pdb=" HE1 HIS A 101 " -0.104 2.00e-02 2.50e+03 ... (remaining 1265 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.24: 732 2.24 - 2.83: 20114 2.83 - 3.42: 26087 3.42 - 4.01: 33152 4.01 - 4.60: 50653 Nonbonded interactions: 130738 Sorted by model distance: nonbonded pdb=" O VAL A 190 " pdb=" HG1 THR A 194 " model vdw 1.653 1.850 nonbonded pdb=" O VAL B 190 " pdb=" HG1 THR B 194 " model vdw 1.653 1.850 nonbonded pdb=" O LEU A 203 " pdb=" HG1 THR A 207 " model vdw 1.665 1.850 nonbonded pdb=" O LEU B 203 " pdb=" HG1 THR B 207 " model vdw 1.665 1.850 nonbonded pdb=" OD1 ASP B 199 " pdb=" HZ1 LYS B 282 " model vdw 1.668 1.850 ... (remaining 130733 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.310 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: 0.120 Extract box with map and model: 1.990 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 35.300 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.030 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6254 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 : 0.015 0.076 4628 Z= 0.921 Angle : 1.365 7.304 6272 Z= 0.975 Chirality : 0.083 0.304 750 Planarity : 0.010 0.069 738 Dihedral : 9.648 55.820 1640 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 1.41 Ramachandran Plot: Outliers : 0.38 % Allowed : 2.63 % Favored : 96.99 % 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: 0.18 (0.33), residues: 532 helix: 0.44 (0.22), residues: 456 sheet: None (None), residues: 0 loop : -1.20 (0.74), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.008 TRP A 212 HIS 0.009 0.004 HIS B 286 PHE 0.025 0.005 PHE A 95 TYR 0.030 0.005 TYR B 270 ARG 0.004 0.001 ARG A 167 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 346 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 GLN cc_start: 0.8858 (mt0) cc_final: 0.8480 (mp10) REVERT: A 68 LYS cc_start: 0.8880 (mttt) cc_final: 0.8422 (mmmt) REVERT: A 116 LEU cc_start: 0.8482 (tt) cc_final: 0.8222 (mt) REVERT: A 206 GLN cc_start: 0.8574 (mt0) cc_final: 0.8371 (tm-30) REVERT: B 58 ASN cc_start: 0.7585 (m-40) cc_final: 0.7370 (m-40) REVERT: B 64 GLN cc_start: 0.8874 (mt0) cc_final: 0.8507 (mp10) REVERT: B 68 LYS cc_start: 0.8898 (mttt) cc_final: 0.8464 (mmmt) REVERT: B 116 LEU cc_start: 0.8442 (tt) cc_final: 0.8192 (mt) outliers start: 0 outliers final: 0 residues processed: 346 average time/residue: 0.3713 time to fit residues: 158.8921 Evaluate side-chains 262 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 262 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 0.9990 chunk 40 optimal weight: 5.9990 chunk 22 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 42 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 ASN B 324 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6407 moved from start: 0.5155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 4628 Z= 0.254 Angle : 0.732 11.308 6272 Z= 0.421 Chirality : 0.037 0.152 750 Planarity : 0.005 0.035 738 Dihedral : 4.599 25.052 578 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.38 % Allowed : 1.88 % Favored : 97.74 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.33), residues: 532 helix: 1.74 (0.21), residues: 462 sheet: None (None), residues: 0 loop : -1.54 (0.69), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 305 HIS 0.005 0.001 HIS A 286 PHE 0.022 0.002 PHE B 100 TYR 0.019 0.002 TYR A 23 ARG 0.005 0.001 ARG B 149 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 299 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 LEU cc_start: 0.8000 (mt) cc_final: 0.7747 (mt) REVERT: A 68 LYS cc_start: 0.8925 (mttt) cc_final: 0.8459 (mmmt) REVERT: A 76 LEU cc_start: 0.8351 (tt) cc_final: 0.7871 (tp) REVERT: A 149 ARG cc_start: 0.7069 (mmm160) cc_final: 0.6853 (tpt-90) REVERT: A 164 ILE cc_start: 0.8442 (mm) cc_final: 0.8234 (mm) REVERT: B 68 LYS cc_start: 0.8940 (mttt) cc_final: 0.8441 (mmmt) REVERT: B 76 LEU cc_start: 0.8215 (tt) cc_final: 0.7725 (tp) REVERT: B 297 MET cc_start: 0.6858 (ptp) cc_final: 0.5935 (mtp) outliers start: 0 outliers final: 0 residues processed: 299 average time/residue: 0.3448 time to fit residues: 127.9002 Evaluate side-chains 248 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 248 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 27 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 13 optimal weight: 7.9990 chunk 49 optimal weight: 5.9990 chunk 53 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 overall best weight: 1.1782 ------------------------------------------------------------------------------- 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: 0.6500 moved from start: 0.6285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 4628 Z= 0.232 Angle : 0.663 11.884 6272 Z= 0.374 Chirality : 0.036 0.259 750 Planarity : 0.004 0.027 738 Dihedral : 4.534 25.940 578 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.38 % Allowed : 2.07 % Favored : 97.56 % Rotamer: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % 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: 2.55 (0.33), residues: 532 helix: 2.11 (0.21), residues: 452 sheet: None (None), residues: 0 loop : -0.78 (0.72), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 305 HIS 0.005 0.002 HIS A 79 PHE 0.032 0.002 PHE A 54 TYR 0.014 0.002 TYR A 23 ARG 0.002 0.000 ARG A 149 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 287 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 LYS cc_start: 0.8979 (mttt) cc_final: 0.8352 (mmmt) REVERT: A 111 PHE cc_start: 0.6971 (m-80) cc_final: 0.6635 (m-80) REVERT: A 165 ILE cc_start: 0.8455 (mt) cc_final: 0.8212 (mt) REVERT: B 68 LYS cc_start: 0.8959 (mttt) cc_final: 0.8392 (mmmt) REVERT: B 167 ARG cc_start: 0.7045 (tpt-90) cc_final: 0.6752 (ttt180) outliers start: 0 outliers final: 0 residues processed: 287 average time/residue: 0.3712 time to fit residues: 133.3176 Evaluate side-chains 221 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 221 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 48 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 25 optimal weight: 7.9990 chunk 5 optimal weight: 2.9990 chunk 23 optimal weight: 0.0010 chunk 32 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 43 optimal weight: 7.9990 overall best weight: 0.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6511 moved from start: 0.6973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 4628 Z= 0.206 Angle : 0.606 7.598 6272 Z= 0.352 Chirality : 0.035 0.124 750 Planarity : 0.004 0.027 738 Dihedral : 4.637 27.143 578 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.38 % Allowed : 2.26 % Favored : 97.37 % Rotamer: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % 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: 2.79 (0.34), residues: 532 helix: 2.20 (0.22), residues: 464 sheet: None (None), residues: 0 loop : -0.62 (0.82), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 305 HIS 0.006 0.002 HIS A 286 PHE 0.022 0.002 PHE B 214 TYR 0.013 0.002 TYR B 23 ARG 0.004 0.000 ARG A 85 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 274 time to evaluate : 0.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 LYS cc_start: 0.8777 (mttt) cc_final: 0.8324 (mmmt) REVERT: A 111 PHE cc_start: 0.7102 (m-80) cc_final: 0.6882 (m-80) REVERT: A 200 LEU cc_start: 0.8684 (tp) cc_final: 0.8434 (tp) REVERT: B 36 LEU cc_start: 0.7986 (mt) cc_final: 0.7753 (mt) REVERT: B 68 LYS cc_start: 0.8781 (mttt) cc_final: 0.8348 (mmmt) REVERT: B 203 LEU cc_start: 0.8604 (mt) cc_final: 0.8364 (mt) outliers start: 0 outliers final: 0 residues processed: 274 average time/residue: 0.3373 time to fit residues: 115.3557 Evaluate side-chains 232 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 232 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 38 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 44 optimal weight: 6.9990 chunk 36 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 13 optimal weight: 5.9990 chunk 17 optimal weight: 6.9990 chunk 47 optimal weight: 3.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 189 GLN ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6601 moved from start: 0.7619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4628 Z= 0.217 Angle : 0.591 8.283 6272 Z= 0.342 Chirality : 0.033 0.150 750 Planarity : 0.003 0.032 738 Dihedral : 4.549 27.010 578 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.20 % Favored : 96.43 % Rotamer: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % 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: 2.95 (0.34), residues: 532 helix: 2.25 (0.22), residues: 470 sheet: None (None), residues: 0 loop : -0.36 (0.95), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 305 HIS 0.006 0.002 HIS A 79 PHE 0.018 0.002 PHE A 214 TYR 0.008 0.001 TYR A 162 ARG 0.002 0.000 ARG B 103 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 269 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 LYS cc_start: 0.8793 (mttt) cc_final: 0.8344 (mmmt) REVERT: A 191 MET cc_start: 0.6706 (tmm) cc_final: 0.6134 (tmm) REVERT: A 289 MET cc_start: 0.4642 (mtp) cc_final: 0.4429 (mtp) REVERT: B 64 GLN cc_start: 0.8805 (mp10) cc_final: 0.8581 (mp10) REVERT: B 68 LYS cc_start: 0.8795 (mttt) cc_final: 0.8358 (mmmt) REVERT: B 85 ARG cc_start: 0.8053 (mtt90) cc_final: 0.7764 (mtt90) REVERT: B 86 LEU cc_start: 0.8996 (tt) cc_final: 0.8663 (tp) REVERT: B 96 MET cc_start: 0.5271 (mmt) cc_final: 0.5069 (mmt) REVERT: B 111 PHE cc_start: 0.6921 (m-80) cc_final: 0.6627 (m-80) outliers start: 0 outliers final: 0 residues processed: 269 average time/residue: 0.3441 time to fit residues: 116.8352 Evaluate side-chains 209 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 209 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 10 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 12 optimal weight: 0.0040 chunk 52 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 50 optimal weight: 0.0000 chunk 5 optimal weight: 0.6980 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6557 moved from start: 0.7953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4628 Z= 0.186 Angle : 0.559 7.973 6272 Z= 0.322 Chirality : 0.034 0.134 750 Planarity : 0.003 0.020 738 Dihedral : 4.543 27.969 578 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.38 % Allowed : 2.44 % Favored : 97.18 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % 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: 3.17 (0.35), residues: 532 helix: 2.31 (0.21), residues: 474 sheet: None (None), residues: 0 loop : 0.28 (1.04), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 305 HIS 0.007 0.002 HIS A 122 PHE 0.021 0.002 PHE B 214 TYR 0.007 0.001 TYR B 23 ARG 0.004 0.000 ARG A 85 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 269 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 GLN cc_start: 0.8617 (mp10) cc_final: 0.8386 (mp10) REVERT: A 68 LYS cc_start: 0.8763 (mttt) cc_final: 0.8296 (mmmt) REVERT: B 64 GLN cc_start: 0.8615 (mp10) cc_final: 0.8376 (mp10) REVERT: B 68 LYS cc_start: 0.8824 (mttt) cc_final: 0.8329 (mmmt) REVERT: B 128 ARG cc_start: 0.7668 (mmt-90) cc_final: 0.7399 (mmt-90) REVERT: B 213 GLU cc_start: 0.7686 (tm-30) cc_final: 0.7395 (tm-30) outliers start: 0 outliers final: 0 residues processed: 269 average time/residue: 0.3425 time to fit residues: 114.8537 Evaluate side-chains 219 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 219 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 0.0170 chunk 38 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 32 optimal weight: 0.1980 chunk 31 optimal weight: 3.9990 chunk 24 optimal weight: 7.9990 chunk 20 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 overall best weight: 1.2422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6602 moved from start: 0.8196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4628 Z= 0.194 Angle : 0.555 7.524 6272 Z= 0.322 Chirality : 0.033 0.138 750 Planarity : 0.003 0.022 738 Dihedral : 4.530 28.103 578 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.38 % Allowed : 2.82 % Favored : 96.80 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % 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: 3.23 (0.34), residues: 532 helix: 2.40 (0.21), residues: 472 sheet: None (None), residues: 0 loop : -0.04 (1.02), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 318 HIS 0.006 0.002 HIS B 122 PHE 0.019 0.002 PHE B 111 TYR 0.006 0.001 TYR A 162 ARG 0.002 0.000 ARG A 85 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 264 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 LYS cc_start: 0.8731 (mttt) cc_final: 0.8313 (mmmt) REVERT: B 68 LYS cc_start: 0.8782 (mttt) cc_final: 0.8364 (mmmt) REVERT: B 85 ARG cc_start: 0.8378 (mtt90) cc_final: 0.7562 (mtt90) REVERT: B 128 ARG cc_start: 0.7678 (mmt-90) cc_final: 0.7412 (mmt-90) REVERT: B 133 LEU cc_start: 0.8334 (tp) cc_final: 0.8068 (tp) REVERT: B 203 LEU cc_start: 0.8575 (mt) cc_final: 0.8364 (mt) REVERT: B 213 GLU cc_start: 0.7724 (tm-30) cc_final: 0.7451 (tm-30) outliers start: 0 outliers final: 0 residues processed: 264 average time/residue: 0.3346 time to fit residues: 110.7285 Evaluate side-chains 206 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 206 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 35 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6651 moved from start: 0.8424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4628 Z= 0.211 Angle : 0.561 7.228 6272 Z= 0.331 Chirality : 0.033 0.125 750 Planarity : 0.004 0.056 738 Dihedral : 4.592 27.919 578 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.38 % Allowed : 2.26 % Favored : 97.37 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % 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: 3.21 (0.34), residues: 532 helix: 2.35 (0.21), residues: 474 sheet: None (None), residues: 0 loop : 0.19 (1.01), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 318 HIS 0.008 0.003 HIS B 122 PHE 0.017 0.002 PHE B 214 TYR 0.009 0.001 TYR A 162 ARG 0.008 0.001 ARG B 103 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 258 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 LYS cc_start: 0.8851 (mttt) cc_final: 0.8349 (mmmt) REVERT: B 61 LEU cc_start: 0.8897 (mt) cc_final: 0.8675 (mm) REVERT: B 68 LYS cc_start: 0.8861 (mttt) cc_final: 0.8404 (mmmt) REVERT: B 85 ARG cc_start: 0.8059 (mtt90) cc_final: 0.7712 (mtt90) REVERT: B 103 ARG cc_start: 0.6864 (mtt90) cc_final: 0.5901 (tpp-160) REVERT: B 210 ASN cc_start: 0.7175 (m110) cc_final: 0.6274 (m110) outliers start: 0 outliers final: 0 residues processed: 258 average time/residue: 0.3419 time to fit residues: 110.3141 Evaluate side-chains 202 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 202 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 14 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 51 optimal weight: 0.1980 chunk 24 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 42 optimal weight: 0.6980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6646 moved from start: 0.8834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4628 Z= 0.181 Angle : 0.563 7.921 6272 Z= 0.323 Chirality : 0.033 0.126 750 Planarity : 0.004 0.050 738 Dihedral : 4.488 26.981 578 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.38 % Allowed : 1.88 % Favored : 97.74 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % 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: 3.21 (0.33), residues: 532 helix: 2.34 (0.21), residues: 476 sheet: None (None), residues: 0 loop : 0.22 (1.02), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 305 HIS 0.008 0.001 HIS A 286 PHE 0.020 0.002 PHE A 46 TYR 0.008 0.001 TYR B 104 ARG 0.005 0.000 ARG B 103 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 246 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 LEU cc_start: 0.7874 (mt) cc_final: 0.7624 (mp) REVERT: A 68 LYS cc_start: 0.8768 (mttt) cc_final: 0.8327 (mmmt) REVERT: B 61 LEU cc_start: 0.8875 (mt) cc_final: 0.8642 (mm) REVERT: B 68 LYS cc_start: 0.8819 (mttt) cc_final: 0.8366 (mmmt) REVERT: B 85 ARG cc_start: 0.8217 (mtt90) cc_final: 0.7992 (mtt90) REVERT: B 103 ARG cc_start: 0.7129 (mtt90) cc_final: 0.5766 (tpp-160) REVERT: B 128 ARG cc_start: 0.7646 (mmt-90) cc_final: 0.7268 (mmt-90) REVERT: B 156 LEU cc_start: 0.8458 (mp) cc_final: 0.8238 (mp) REVERT: B 289 MET cc_start: 0.5273 (mtp) cc_final: 0.4810 (mtp) outliers start: 0 outliers final: 0 residues processed: 246 average time/residue: 0.3466 time to fit residues: 106.4636 Evaluate side-chains 204 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 204 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 4 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 26 optimal weight: 0.5980 chunk 34 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 17 optimal weight: 3.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6628 moved from start: 0.9042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4628 Z= 0.181 Angle : 0.546 7.770 6272 Z= 0.317 Chirality : 0.033 0.130 750 Planarity : 0.003 0.018 738 Dihedral : 4.522 29.765 578 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.07 % Favored : 97.74 % 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: 3.41 (0.34), residues: 532 helix: 2.45 (0.21), residues: 476 sheet: None (None), residues: 0 loop : 0.55 (1.04), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 305 HIS 0.003 0.001 HIS B 101 PHE 0.019 0.002 PHE B 46 TYR 0.004 0.001 TYR A 186 ARG 0.003 0.000 ARG B 103 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 253 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 LEU cc_start: 0.7916 (mt) cc_final: 0.7643 (mp) REVERT: A 68 LYS cc_start: 0.8859 (mttt) cc_final: 0.8395 (mmmt) REVERT: A 130 GLU cc_start: 0.8666 (tp30) cc_final: 0.8429 (tp30) REVERT: B 68 LYS cc_start: 0.8882 (mttt) cc_final: 0.8415 (mmmt) REVERT: B 85 ARG cc_start: 0.8189 (mtt90) cc_final: 0.7958 (mtt90) REVERT: B 103 ARG cc_start: 0.7026 (mtt90) cc_final: 0.6490 (tpp-160) REVERT: B 289 MET cc_start: 0.5405 (mtp) cc_final: 0.5106 (mtp) outliers start: 0 outliers final: 0 residues processed: 253 average time/residue: 0.3557 time to fit residues: 111.5358 Evaluate side-chains 204 residues out of total 514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 204 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 44 optimal weight: 5.9990 chunk 5 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 2 optimal weight: 0.0570 chunk 30 optimal weight: 4.9990 chunk 49 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 overall best weight: 0.9900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.149838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.129497 restraints weight = 33548.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.134834 restraints weight = 14821.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.138112 restraints weight = 8608.178| |-----------------------------------------------------------------------------| r_work (final): 0.4058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6939 moved from start: 0.9126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 4628 Z= 0.188 Angle : 0.615 12.494 6272 Z= 0.344 Chirality : 0.034 0.188 750 Planarity : 0.003 0.023 738 Dihedral : 4.545 29.971 578 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % 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: 3.30 (0.34), residues: 532 helix: 2.44 (0.21), residues: 478 sheet: None (None), residues: 0 loop : -0.24 (1.00), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 305 HIS 0.006 0.001 HIS A 286 PHE 0.018 0.002 PHE A 54 TYR 0.005 0.001 TYR B 104 ARG 0.003 0.000 ARG B 128 =============================================================================== Job complete usr+sys time: 3173.33 seconds wall clock time: 56 minutes 9.28 seconds (3369.28 seconds total)