Starting phenix.real_space_refine (version: dev) on Tue Nov 29 13:31:15 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6f1y_4171/11_2022/6f1y_4171_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6f1y_4171/11_2022/6f1y_4171.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6f1y_4171/11_2022/6f1y_4171.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6f1y_4171/11_2022/6f1y_4171.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6f1y_4171/11_2022/6f1y_4171_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6f1y_4171/11_2022/6f1y_4171_neut.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.004 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "f ARG 786": "NH1" <-> "NH2" Residue "f ARG 790": "NH1" <-> "NH2" Residue "f ARG 862": "NH1" <-> "NH2" Residue "f ARG 909": "NH1" <-> "NH2" Residue "f ARG 914": "NH1" <-> "NH2" Residue "j ARG 157": "NH1" <-> "NH2" Residue "j ARG 171": "NH1" <-> "NH2" Residue "j ARG 175": "NH1" <-> "NH2" Residue "j TYR 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4778/modules/chem_data/mon_lib" Total number of atoms: 4316 Number of models: 1 Model: "" Number of chains: 2 Chain: "f" Number of atoms: 1924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 1924 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 113} Link IDs: {'PTRANS': 2, 'TRANS': 277} Chain breaks: 3 Unresolved non-hydrogen bonds: 228 Unresolved non-hydrogen angles: 340 Unresolved non-hydrogen dihedrals: 116 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'UNK:plan-1': 111} Unresolved non-hydrogen planarities: 111 Chain: "j" Number of atoms: 2392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2392 Classifications: {'peptide': 303} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 12, 'TRANS': 290} Chain breaks: 3 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 26 Time building chain proxies: 3.01, per 1000 atoms: 0.70 Number of scatterers: 4316 At special positions: 0 Unit cell: (142.04, 100.5, 80.4, 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 16 16.00 O 828 8.00 N 737 7.00 C 2735 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.93 Conformation dependent library (CDL) restraints added in 528.7 milliseconds 920 Ramachandran restraints generated. 460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1130 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 2 sheets defined 76.3% alpha, 7.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'f' and resid 780 through 797 Processing helix chain 'f' and resid 800 through 822 removed outlier: 4.266A pdb=" N LEU f 804 " --> pdb=" O THR f 800 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N GLY f 807 " --> pdb=" O LEU f 803 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N LEU f 808 " --> pdb=" O LEU f 804 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU f 822 " --> pdb=" O GLU f 818 " (cutoff:3.500A) Processing helix chain 'f' and resid 829 through 863 Processing helix chain 'f' and resid 870 through 891 removed outlier: 3.752A pdb=" N HIS f 891 " --> pdb=" O ASP f 887 " (cutoff:3.500A) Processing helix chain 'f' and resid 895 through 926 removed outlier: 3.501A pdb=" N TRP f 899 " --> pdb=" O ASN f 895 " (cutoff:3.500A) Processing helix chain 'f' and resid 973 through 1001 removed outlier: 3.717A pdb=" N UNK f 986 " --> pdb=" O UNK f 982 " (cutoff:3.500A) Processing helix chain 'f' and resid 1002 through 1006 removed outlier: 4.456A pdb=" N UNK f1005 " --> pdb=" O UNK f1002 " (cutoff:3.500A) Processing helix chain 'f' and resid 1035 through 1053 removed outlier: 4.041A pdb=" N SER f1045 " --> pdb=" O MET f1041 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLU f1048 " --> pdb=" O VAL f1044 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL f1053 " --> pdb=" O GLN f1049 " (cutoff:3.500A) Processing helix chain 'f' and resid 1076 through 1096 Processing helix chain 'f' and resid 1111 through 1137 removed outlier: 3.571A pdb=" N UNK f1125 " --> pdb=" O UNK f1121 " (cutoff:3.500A) Processing helix chain 'j' and resid 38 through 46 Processing helix chain 'j' and resid 66 through 75 Processing helix chain 'j' and resid 115 through 121 Processing helix chain 'j' and resid 141 through 164 removed outlier: 3.703A pdb=" N VAL j 145 " --> pdb=" O ARG j 141 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU j 147 " --> pdb=" O TRP j 143 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N GLN j 150 " --> pdb=" O MET j 146 " (cutoff:3.500A) Processing helix chain 'j' and resid 168 through 182 removed outlier: 3.693A pdb=" N GLU j 172 " --> pdb=" O GLU j 168 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N LYS j 176 " --> pdb=" O GLU j 172 " (cutoff:3.500A) Processing helix chain 'j' and resid 236 through 244 Processing helix chain 'j' and resid 247 through 266 removed outlier: 3.785A pdb=" N ILE j 254 " --> pdb=" O HIS j 250 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLN j 255 " --> pdb=" O LEU j 251 " (cutoff:3.500A) Processing helix chain 'j' and resid 279 through 289 removed outlier: 3.876A pdb=" N LEU j 283 " --> pdb=" O ASN j 279 " (cutoff:3.500A) Processing helix chain 'j' and resid 318 through 324 Processing helix chain 'j' and resid 335 through 340 Processing helix chain 'j' and resid 361 through 371 Processing sheet with id=AA1, first strand: chain 'j' and resid 89 through 93 removed outlier: 3.858A pdb=" N VAL j 93 " --> pdb=" O THR j 102 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR j 102 " --> pdb=" O VAL j 93 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N LYS j 55 " --> pdb=" O ASN j 105 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N LEU j 109 " --> pdb=" O ILE j 57 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N VAL j 59 " --> pdb=" O LEU j 109 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'j' and resid 89 through 93 removed outlier: 3.858A pdb=" N VAL j 93 " --> pdb=" O THR j 102 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR j 102 " --> pdb=" O VAL j 93 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N LYS j 55 " --> pdb=" O ASN j 105 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N LEU j 228 " --> pdb=" O THR j 131 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N VAL j 133 " --> pdb=" O LEU j 228 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N VAL j 230 " --> pdb=" O VAL j 133 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N PHE j 135 " --> pdb=" O VAL j 230 " (cutoff:3.500A) removed outlier: 9.052A pdb=" N ILE j 270 " --> pdb=" O VAL j 227 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N VAL j 229 " --> pdb=" O ILE j 270 " (cutoff:3.500A) 271 hydrogen bonds defined for protein. 801 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: 1.02 Time building geometry restraints manager: 2.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1220 1.34 - 1.45: 801 1.45 - 1.57: 2332 1.57 - 1.69: 2 1.69 - 1.81: 26 Bond restraints: 4381 Sorted by residual: bond pdb=" CA PRO j 343 " pdb=" C PRO j 343 " ideal model delta sigma weight residual 1.517 1.572 -0.055 9.30e-03 1.16e+04 3.44e+01 bond pdb=" CA LYS j 342 " pdb=" C LYS j 342 " ideal model delta sigma weight residual 1.524 1.587 -0.063 1.26e-02 6.30e+03 2.53e+01 bond pdb=" C LYS j 342 " pdb=" N PRO j 343 " ideal model delta sigma weight residual 1.329 1.372 -0.043 1.18e-02 7.18e+03 1.31e+01 bond pdb=" C PRO j 166 " pdb=" N PRO j 167 " ideal model delta sigma weight residual 1.334 1.414 -0.080 2.34e-02 1.83e+03 1.17e+01 bond pdb=" CB PHE j 309 " pdb=" CG PHE j 309 " ideal model delta sigma weight residual 1.502 1.439 0.063 2.30e-02 1.89e+03 7.58e+00 ... (remaining 4376 not shown) Histogram of bond angle deviations from ideal: 96.55 - 105.14: 92 105.14 - 113.74: 2459 113.74 - 122.33: 2528 122.33 - 130.92: 848 130.92 - 139.51: 24 Bond angle restraints: 5951 Sorted by residual: angle pdb=" C LYS j 342 " pdb=" N PRO j 343 " pdb=" CA PRO j 343 " ideal model delta sigma weight residual 120.38 106.54 13.84 1.03e+00 9.43e-01 1.80e+02 angle pdb=" C PRO j 343 " pdb=" N PRO j 344 " pdb=" CA PRO j 344 " ideal model delta sigma weight residual 119.84 109.77 10.07 1.25e+00 6.40e-01 6.49e+01 angle pdb=" N GLU j 186 " pdb=" CA GLU j 186 " pdb=" C GLU j 186 " ideal model delta sigma weight residual 109.81 124.72 -14.91 2.21e+00 2.05e-01 4.55e+01 angle pdb=" N PRO j 343 " pdb=" CA PRO j 343 " pdb=" C PRO j 343 " ideal model delta sigma weight residual 110.70 118.27 -7.57 1.22e+00 6.72e-01 3.85e+01 angle pdb=" N HIS f 891 " pdb=" CA HIS f 891 " pdb=" C HIS f 891 " ideal model delta sigma weight residual 108.17 97.23 10.94 1.85e+00 2.92e-01 3.50e+01 ... (remaining 5946 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.32: 2395 14.32 - 28.63: 204 28.63 - 42.95: 46 42.95 - 57.27: 6 57.27 - 71.58: 3 Dihedral angle restraints: 2654 sinusoidal: 932 harmonic: 1722 Sorted by residual: dihedral pdb=" C TYR f 893 " pdb=" N TYR f 893 " pdb=" CA TYR f 893 " pdb=" CB TYR f 893 " ideal model delta harmonic sigma weight residual -122.60 -130.20 7.60 0 2.50e+00 1.60e-01 9.24e+00 dihedral pdb=" CG ARG f 880 " pdb=" CD ARG f 880 " pdb=" NE ARG f 880 " pdb=" CZ ARG f 880 " ideal model delta sinusoidal sigma weight residual -90.00 -130.99 40.99 2 1.50e+01 4.44e-03 9.18e+00 dihedral pdb=" C ILE j 165 " pdb=" N ILE j 165 " pdb=" CA ILE j 165 " pdb=" CB ILE j 165 " ideal model delta harmonic sigma weight residual -122.00 -129.55 7.55 0 2.50e+00 1.60e-01 9.12e+00 ... (remaining 2651 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 499 0.079 - 0.158: 158 0.158 - 0.237: 41 0.237 - 0.315: 7 0.315 - 0.394: 3 Chirality restraints: 708 Sorted by residual: chirality pdb=" CA GLU j 186 " pdb=" N GLU j 186 " pdb=" C GLU j 186 " pdb=" CB GLU j 186 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.88e+00 chirality pdb=" CB VAL j 288 " pdb=" CA VAL j 288 " pdb=" CG1 VAL j 288 " pdb=" CG2 VAL j 288 " both_signs ideal model delta sigma weight residual False -2.63 -2.26 -0.37 2.00e-01 2.50e+01 3.36e+00 chirality pdb=" CB VAL j 145 " pdb=" CA VAL j 145 " pdb=" CG1 VAL j 145 " pdb=" CG2 VAL j 145 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.36 2.00e-01 2.50e+01 3.18e+00 ... (remaining 705 not shown) Planarity restraints: 766 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR f 832 " -0.027 2.00e-02 2.50e+03 2.90e-02 1.68e+01 pdb=" CG TYR f 832 " 0.069 2.00e-02 2.50e+03 pdb=" CD1 TYR f 832 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 TYR f 832 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR f 832 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR f 832 " -0.016 2.00e-02 2.50e+03 pdb=" CZ TYR f 832 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR f 832 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS j 257 " -0.031 2.00e-02 2.50e+03 2.74e-02 1.12e+01 pdb=" CG HIS j 257 " 0.042 2.00e-02 2.50e+03 pdb=" ND1 HIS j 257 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 HIS j 257 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 HIS j 257 " -0.034 2.00e-02 2.50e+03 pdb=" NE2 HIS j 257 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE j 225 " 0.050 5.00e-02 4.00e+02 7.63e-02 9.32e+00 pdb=" N PRO j 226 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO j 226 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO j 226 " 0.043 5.00e-02 4.00e+02 ... (remaining 763 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 115 2.64 - 3.20: 4227 3.20 - 3.77: 7159 3.77 - 4.33: 8945 4.33 - 4.90: 13536 Nonbonded interactions: 33982 Sorted by model distance: nonbonded pdb=" OD2 ASP j 138 " pdb=" OG SER j 140 " model vdw 2.069 2.440 nonbonded pdb=" OG SER f 894 " pdb=" OE2 GLU j 357 " model vdw 2.077 2.440 nonbonded pdb=" NZ LYS j 164 " pdb=" O PRO j 167 " model vdw 2.249 2.520 nonbonded pdb=" O SER f 863 " pdb=" OG1 THR f 866 " model vdw 2.252 2.440 nonbonded pdb=" O ARG f 920 " pdb=" OG1 THR f 923 " model vdw 2.272 2.440 ... (remaining 33977 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 Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 16 5.16 5 C 2735 2.51 5 N 737 2.21 5 O 828 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 9.620 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: 41.890 Check model and map are aligned: 0.070 Convert atoms to be neutral: 0.090 Process input model: 18.540 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Set scattering table: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 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 : 0.011 0.131 4381 Z= 0.718 Angle : 1.943 14.913 5951 Z= 1.085 Chirality : 0.086 0.394 708 Planarity : 0.009 0.076 766 Dihedral : 11.719 71.584 1524 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.22 % Allowed : 17.17 % Favored : 82.61 % Rotamer Outliers : 0.74 % 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: -4.92 (0.29), residues: 460 helix: -2.14 (0.25), residues: 277 sheet: -3.54 (0.67), residues: 38 loop : -5.26 (0.30), residues: 145 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 920 Ramachandran restraints generated. 460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 920 Ramachandran restraints generated. 460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 108 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 111 average time/residue: 0.2240 time to fit residues: 29.4193 Evaluate side-chains 52 residues out of total 429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 51 time to evaluate : 0.503 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0422 time to fit residues: 0.6907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 15 optimal weight: 4.9990 chunk 23 optimal weight: 0.0570 chunk 9 optimal weight: 0.8980 chunk 14 optimal weight: 0.5980 chunk 17 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 879 ASN j 94 HIS j 115 HIS j 150 GLN j 221 HIS ** j 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.3840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.059 4381 Z= 0.247 Angle : 0.845 10.347 5951 Z= 0.439 Chirality : 0.044 0.248 708 Planarity : 0.007 0.085 766 Dihedral : 5.283 27.794 612 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 18.31 Ramachandran Plot: Outliers : 0.22 % Allowed : 9.35 % Favored : 90.43 % Rotamer Outliers : 3.43 % 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: -3.24 (0.35), residues: 460 helix: -0.72 (0.29), residues: 282 sheet: -3.14 (0.70), residues: 41 loop : -4.85 (0.35), residues: 137 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 920 Ramachandran restraints generated. 460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 920 Ramachandran restraints generated. 460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 72 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 7 residues processed: 83 average time/residue: 0.1816 time to fit residues: 18.7588 Evaluate side-chains 60 residues out of total 429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 53 time to evaluate : 0.456 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0532 time to fit residues: 1.3259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 22 optimal weight: 0.0270 chunk 18 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 27 optimal weight: 0.0170 chunk 29 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 26 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 14 optimal weight: 0.0040 overall best weight: 0.2488 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 889 ASN j 159 HIS ** j 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.4932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 4381 Z= 0.194 Angle : 0.739 10.649 5951 Z= 0.379 Chirality : 0.042 0.217 708 Planarity : 0.005 0.077 766 Dihedral : 4.818 24.659 612 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 15.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.48 % Favored : 91.52 % Rotamer Outliers : 1.96 % 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: -2.02 (0.38), residues: 460 helix: 0.27 (0.31), residues: 278 sheet: -2.41 (0.77), residues: 41 loop : -4.40 (0.37), residues: 141 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 920 Ramachandran restraints generated. 460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 920 Ramachandran restraints generated. 460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 63 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 70 average time/residue: 0.1735 time to fit residues: 15.2342 Evaluate side-chains 55 residues out of total 429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 52 time to evaluate : 0.488 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0513 time to fit residues: 0.8838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 3 optimal weight: 0.9990 chunk 13 optimal weight: 0.0370 chunk 18 optimal weight: 2.9990 chunk 27 optimal weight: 0.0670 chunk 28 optimal weight: 2.9990 chunk 14 optimal weight: 0.0010 chunk 25 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 overall best weight: 0.6206 ------------------------------------------------------------------------------- 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: 0.7390 moved from start: 0.5445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 4381 Z= 0.222 Angle : 0.745 9.382 5951 Z= 0.382 Chirality : 0.042 0.238 708 Planarity : 0.005 0.068 766 Dihedral : 4.816 24.764 612 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 18.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.13 % Favored : 90.87 % Rotamer Outliers : 4.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.38), residues: 460 helix: 0.62 (0.31), residues: 282 sheet: -1.99 (0.81), residues: 41 loop : -4.32 (0.38), residues: 137 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 920 Ramachandran restraints generated. 460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 920 Ramachandran restraints generated. 460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 54 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 6 residues processed: 68 average time/residue: 0.1583 time to fit residues: 13.8303 Evaluate side-chains 59 residues out of total 429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 53 time to evaluate : 0.499 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0426 time to fit residues: 1.1236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 21 optimal weight: 0.2980 chunk 11 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 0 optimal weight: 0.8980 chunk 14 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 889 ASN ** f1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.5910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 4381 Z= 0.214 Angle : 0.752 12.433 5951 Z= 0.380 Chirality : 0.042 0.188 708 Planarity : 0.005 0.067 766 Dihedral : 4.808 24.062 612 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 18.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.13 % Favored : 90.87 % Rotamer Outliers : 2.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.39), residues: 460 helix: 0.67 (0.31), residues: 282 sheet: -1.84 (0.79), residues: 41 loop : -4.17 (0.40), residues: 137 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 920 Ramachandran restraints generated. 460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 920 Ramachandran restraints generated. 460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 56 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 6 residues processed: 65 average time/residue: 0.1363 time to fit residues: 11.8233 Evaluate side-chains 57 residues out of total 429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 51 time to evaluate : 0.378 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0399 time to fit residues: 0.9000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 0.5980 chunk 29 optimal weight: 0.4980 chunk 24 optimal weight: 0.7980 chunk 13 optimal weight: 0.4980 chunk 2 optimal weight: 0.0980 chunk 9 optimal weight: 0.2980 chunk 15 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 3 optimal weight: 0.0970 chunk 16 optimal weight: 1.9990 chunk 21 optimal weight: 0.0570 overall best weight: 0.2096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** j 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.6375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 4381 Z= 0.178 Angle : 0.780 12.768 5951 Z= 0.370 Chirality : 0.041 0.184 708 Planarity : 0.004 0.060 766 Dihedral : 4.562 21.653 612 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 16.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.26 % Favored : 91.74 % Rotamer Outliers : 0.98 % 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: -1.11 (0.40), residues: 460 helix: 0.89 (0.32), residues: 287 sheet: -1.70 (0.77), residues: 41 loop : -4.22 (0.41), residues: 132 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 920 Ramachandran restraints generated. 460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 920 Ramachandran restraints generated. 460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 59 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 62 average time/residue: 0.1673 time to fit residues: 13.3303 Evaluate side-chains 52 residues out of total 429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 50 time to evaluate : 0.520 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0428 time to fit residues: 0.8057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 16 optimal weight: 0.9980 chunk 24 optimal weight: 0.0670 chunk 28 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 13 optimal weight: 0.2980 chunk 11 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 14 optimal weight: 0.2980 overall best weight: 0.5320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** j 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.6599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 4381 Z= 0.202 Angle : 0.776 11.415 5951 Z= 0.376 Chirality : 0.041 0.180 708 Planarity : 0.004 0.058 766 Dihedral : 4.618 21.592 612 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 17.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer Outliers : 1.72 % 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: -1.13 (0.40), residues: 460 helix: 0.83 (0.31), residues: 287 sheet: -1.71 (0.74), residues: 41 loop : -4.11 (0.44), residues: 132 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 920 Ramachandran restraints generated. 460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 920 Ramachandran restraints generated. 460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 54 time to evaluate : 0.529 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 59 average time/residue: 0.1677 time to fit residues: 12.8990 Evaluate side-chains 53 residues out of total 429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 50 time to evaluate : 0.509 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0453 time to fit residues: 0.9065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 2 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 27 optimal weight: 0.0980 chunk 25 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 11 optimal weight: 0.5980 chunk 21 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** j 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.6813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 4381 Z= 0.216 Angle : 0.831 11.741 5951 Z= 0.404 Chirality : 0.042 0.185 708 Planarity : 0.004 0.053 766 Dihedral : 4.644 21.593 612 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 18.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.78 % Favored : 90.22 % Rotamer Outliers : 0.74 % 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: -1.21 (0.39), residues: 460 helix: 0.74 (0.31), residues: 284 sheet: -1.57 (0.75), residues: 41 loop : -4.03 (0.45), residues: 135 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 920 Ramachandran restraints generated. 460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 920 Ramachandran restraints generated. 460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 47 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 48 average time/residue: 0.1603 time to fit residues: 10.0565 Evaluate side-chains 49 residues out of total 429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 46 time to evaluate : 0.469 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0537 time to fit residues: 0.9481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 28 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 13 optimal weight: 0.0170 chunk 19 optimal weight: 0.9990 chunk 29 optimal weight: 0.0270 chunk 27 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 14 optimal weight: 0.3980 chunk 25 optimal weight: 0.9990 overall best weight: 0.4278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** j 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.7073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 4381 Z= 0.198 Angle : 0.807 12.343 5951 Z= 0.386 Chirality : 0.041 0.183 708 Planarity : 0.004 0.053 766 Dihedral : 4.513 20.440 612 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 17.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.48 % Favored : 91.52 % Rotamer Outliers : 0.98 % 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: -1.06 (0.39), residues: 460 helix: 0.91 (0.31), residues: 283 sheet: -1.46 (0.76), residues: 41 loop : -4.09 (0.43), residues: 136 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 920 Ramachandran restraints generated. 460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 920 Ramachandran restraints generated. 460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 49 time to evaluate : 0.427 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 51 average time/residue: 0.1546 time to fit residues: 10.2425 Evaluate side-chains 49 residues out of total 429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 46 time to evaluate : 0.427 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0459 time to fit residues: 0.7962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 1 optimal weight: 0.3980 chunk 17 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** j 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.7137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 4381 Z= 0.233 Angle : 0.853 15.761 5951 Z= 0.411 Chirality : 0.043 0.205 708 Planarity : 0.004 0.052 766 Dihedral : 4.726 26.456 612 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 19.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.78 % Favored : 90.22 % Rotamer Outliers : 0.00 % 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: -1.18 (0.39), residues: 460 helix: 0.77 (0.31), residues: 286 sheet: -1.41 (0.77), residues: 41 loop : -4.17 (0.44), residues: 133 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 920 Ramachandran restraints generated. 460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 920 Ramachandran restraints generated. 460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 0.516 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.1653 time to fit residues: 10.4405 Evaluate side-chains 45 residues out of total 429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 0.525 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 0 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 29 optimal weight: 0.0060 chunk 1 optimal weight: 0.0670 chunk 28 optimal weight: 2.9990 overall best weight: 0.5134 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** j 264 GLN ** 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 = 0.3883 r_free = 0.3883 target = 0.063200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.055521 restraints weight = 36803.816| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 6.26 r_work: 0.3716 rms_B_bonded: 6.06 restraints_weight: 2.0000 r_work: 0.3715 rms_B_bonded: 5.68 restraints_weight: 4.0000 r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.7355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 4381 Z= 0.222 Angle : 0.828 13.836 5951 Z= 0.399 Chirality : 0.043 0.204 708 Planarity : 0.004 0.051 766 Dihedral : 4.645 21.211 612 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 16.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.78 % Favored : 90.22 % Rotamer Outliers : 0.25 % 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: -1.19 (0.39), residues: 460 helix: 0.79 (0.31), residues: 282 sheet: -1.34 (0.78), residues: 41 loop : -4.13 (0.42), residues: 137 =============================================================================== Job complete usr+sys time: 1632.63 seconds wall clock time: 30 minutes 35.61 seconds (1835.61 seconds total)