Starting phenix.real_space_refine on Fri Apr 5 20:18:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p70_17513/04_2024/8p70_17513_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p70_17513/04_2024/8p70_17513.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p70_17513/04_2024/8p70_17513_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p70_17513/04_2024/8p70_17513_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p70_17513/04_2024/8p70_17513_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p70_17513/04_2024/8p70_17513.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p70_17513/04_2024/8p70_17513.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p70_17513/04_2024/8p70_17513_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p70_17513/04_2024/8p70_17513_updated.pdb" } resolution = 2.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 31 5.16 5 C 3309 2.51 5 N 876 2.21 5 O 1066 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H GLU 262": "OE1" <-> "OE2" Residue "I GLU 17": "OE1" <-> "OE2" Residue "I GLU 234": "OE1" <-> "OE2" Residue "I TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 269": "OE1" <-> "OE2" Residue "J TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 147": "OE1" <-> "OE2" Residue "J TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 266": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 5282 Number of models: 1 Model: "" Number of chains: 7 Chain: "H" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 512 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 5, 'TRANS': 59} Chain: "I" Number of atoms: 2281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2281 Unusual residues: {'ACE': 1} Classifications: {'peptide': 279, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 264} Chain breaks: 1 Chain: "J" Number of atoms: 2283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2283 Classifications: {'peptide': 286} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 267} Chain breaks: 2 Chain: "J" Number of atoms: 52 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1, 26 Unusual residues: {'X4Q': 1} Classifications: {'undetermined': 1} Conformer: "B" Number of residues, atoms: 1, 26 Unusual residues: {'X4Q': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "I" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 62 Classifications: {'water': 62} Link IDs: {None: 61} Chain: "J" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 76 Classifications: {'water': 76} Link IDs: {None: 75} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" C01AX4Q J 401 " occ=0.81 ... (50 atoms not shown) pdb=" N25BX4Q J 401 " occ=0.19 Time building chain proxies: 3.78, per 1000 atoms: 0.72 Number of scatterers: 5282 At special positions: 0 Unit cell: (84.7875, 93.3375, 66.975, 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 31 16.00 O 1066 8.00 N 876 7.00 C 3309 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: 2.37 Conformation dependent library (CDL) restraints added in 888.8 milliseconds 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1196 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 34 helices and 2 sheets defined 53.5% alpha, 4.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'H' and resid 264 through 269 removed outlier: 4.024A pdb=" N GLY H 267 " --> pdb=" O GLU H 264 " (cutoff:3.500A) Processing helix chain 'H' and resid 271 through 274 Processing helix chain 'H' and resid 280 through 284 Processing helix chain 'H' and resid 289 through 301 Processing helix chain 'I' and resid 2 through 4 No H-bonds generated for 'chain 'I' and resid 2 through 4' Processing helix chain 'I' and resid 6 through 10 Processing helix chain 'I' and resid 16 through 37 Processing helix chain 'I' and resid 50 through 70 Processing helix chain 'I' and resid 77 through 92 Processing helix chain 'I' and resid 101 through 115 removed outlier: 3.794A pdb=" N LEU I 106 " --> pdb=" O ARG I 102 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 128 removed outlier: 3.847A pdb=" N ASN I 128 " --> pdb=" O GLN I 124 " (cutoff:3.500A) Processing helix chain 'I' and resid 133 through 153 removed outlier: 4.622A pdb=" N LEU I 148 " --> pdb=" O LEU I 144 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N LEU I 149 " --> pdb=" O GLU I 145 " (cutoff:3.500A) Processing helix chain 'I' and resid 163 through 177 Processing helix chain 'I' and resid 184 through 200 removed outlier: 4.721A pdb=" N LYS I 189 " --> pdb=" O ILE I 186 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N THR I 190 " --> pdb=" O LEU I 187 " (cutoff:3.500A) Processing helix chain 'I' and resid 203 through 205 No H-bonds generated for 'chain 'I' and resid 203 through 205' Processing helix chain 'I' and resid 209 through 223 Processing helix chain 'I' and resid 229 through 233 Processing helix chain 'I' and resid 242 through 261 removed outlier: 3.869A pdb=" N ILE I 251 " --> pdb=" O GLN I 247 " (cutoff:3.500A) Processing helix chain 'I' and resid 267 through 283 Processing helix chain 'J' and resid 57 through 66 Processing helix chain 'J' and resid 98 through 103 Processing helix chain 'J' and resid 111 through 130 Processing helix chain 'J' and resid 140 through 142 No H-bonds generated for 'chain 'J' and resid 140 through 142' Processing helix chain 'J' and resid 156 through 158 No H-bonds generated for 'chain 'J' and resid 156 through 158' Processing helix chain 'J' and resid 176 through 178 No H-bonds generated for 'chain 'J' and resid 176 through 178' Processing helix chain 'J' and resid 181 through 184 No H-bonds generated for 'chain 'J' and resid 181 through 184' Processing helix chain 'J' and resid 192 through 208 removed outlier: 4.036A pdb=" N TRP J 197 " --> pdb=" O VAL J 194 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU J 208 " --> pdb=" O GLU J 205 " (cutoff:3.500A) Processing helix chain 'J' and resid 218 through 229 Processing helix chain 'J' and resid 240 through 242 No H-bonds generated for 'chain 'J' and resid 240 through 242' Processing helix chain 'J' and resid 257 through 260 No H-bonds generated for 'chain 'J' and resid 257 through 260' Processing helix chain 'J' and resid 266 through 275 Processing helix chain 'J' and resid 286 through 290 Processing helix chain 'J' and resid 293 through 296 No H-bonds generated for 'chain 'J' and resid 293 through 296' Processing helix chain 'J' and resid 304 through 306 No H-bonds generated for 'chain 'J' and resid 304 through 306' Processing sheet with id= A, first strand: chain 'J' and resid 77 through 83 removed outlier: 6.877A pdb=" N VAL J 90 " --> pdb=" O LEU J 78 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ALA J 80 " --> pdb=" O SER J 88 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N SER J 88 " --> pdb=" O ALA J 80 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N GLY J 82 " --> pdb=" O ASN J 86 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ASN J 86 " --> pdb=" O GLY J 82 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N ARG J 30 " --> pdb=" O LYS J 14 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N LYS J 14 " --> pdb=" O ARG J 30 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'J' and resid 143 through 145 217 hydrogen bonds defined for protein. 564 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: 1.40 Time building geometry restraints manager: 2.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1644 1.34 - 1.46: 1122 1.46 - 1.58: 2438 1.58 - 1.69: 2 1.69 - 1.81: 49 Bond restraints: 5255 Sorted by residual: bond pdb=" C09BX4Q J 401 " pdb=" C10BX4Q J 401 " ideal model delta sigma weight residual 1.314 1.532 -0.218 2.00e-02 2.50e+03 1.19e+02 bond pdb=" C09AX4Q J 401 " pdb=" C10AX4Q J 401 " ideal model delta sigma weight residual 1.314 1.531 -0.217 2.00e-02 2.50e+03 1.18e+02 bond pdb=" C13BX4Q J 401 " pdb=" N12BX4Q J 401 " ideal model delta sigma weight residual 1.336 1.507 -0.171 2.00e-02 2.50e+03 7.30e+01 bond pdb=" C13AX4Q J 401 " pdb=" N12AX4Q J 401 " ideal model delta sigma weight residual 1.336 1.505 -0.169 2.00e-02 2.50e+03 7.12e+01 bond pdb=" C09AX4Q J 401 " pdb=" C13AX4Q J 401 " ideal model delta sigma weight residual 1.651 1.553 0.098 2.00e-02 2.50e+03 2.38e+01 ... (remaining 5250 not shown) Histogram of bond angle deviations from ideal: 98.27 - 105.41: 125 105.41 - 112.55: 2698 112.55 - 119.68: 1748 119.68 - 126.82: 2467 126.82 - 133.96: 75 Bond angle restraints: 7113 Sorted by residual: angle pdb=" C14AX4Q J 401 " pdb=" C07AX4Q J 401 " pdb=" N08AX4Q J 401 " ideal model delta sigma weight residual 104.61 121.25 -16.64 3.00e+00 1.11e-01 3.08e+01 angle pdb=" N06AX4Q J 401 " pdb=" C07AX4Q J 401 " pdb=" N08AX4Q J 401 " ideal model delta sigma weight residual 133.78 118.89 14.89 3.00e+00 1.11e-01 2.46e+01 angle pdb=" C14BX4Q J 401 " pdb=" C07BX4Q J 401 " pdb=" N08BX4Q J 401 " ideal model delta sigma weight residual 104.61 118.92 -14.31 3.00e+00 1.11e-01 2.28e+01 angle pdb=" N06BX4Q J 401 " pdb=" C07BX4Q J 401 " pdb=" N08BX4Q J 401 " ideal model delta sigma weight residual 133.78 121.08 12.70 3.00e+00 1.11e-01 1.79e+01 angle pdb=" CA MET I 237 " pdb=" CB MET I 237 " pdb=" CG MET I 237 " ideal model delta sigma weight residual 114.10 121.72 -7.62 2.00e+00 2.50e-01 1.45e+01 ... (remaining 7108 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.15: 2912 25.15 - 50.30: 212 50.30 - 75.45: 33 75.45 - 100.59: 6 100.59 - 125.74: 2 Dihedral angle restraints: 3165 sinusoidal: 1318 harmonic: 1847 Sorted by residual: dihedral pdb=" C15BX4Q J 401 " pdb=" C17BX4Q J 401 " pdb=" N16BX4Q J 401 " pdb=" C18BX4Q J 401 " ideal model delta sinusoidal sigma weight residual 178.27 52.53 125.74 1 3.00e+01 1.11e-03 1.69e+01 dihedral pdb=" C15AX4Q J 401 " pdb=" C17AX4Q J 401 " pdb=" N16AX4Q J 401 " pdb=" C18AX4Q J 401 " ideal model delta sinusoidal sigma weight residual 178.27 52.57 125.70 1 3.00e+01 1.11e-03 1.69e+01 dihedral pdb=" CA TYR I 91 " pdb=" C TYR I 91 " pdb=" N LEU I 92 " pdb=" CA LEU I 92 " ideal model delta harmonic sigma weight residual 180.00 163.23 16.77 0 5.00e+00 4.00e-02 1.13e+01 ... (remaining 3162 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 474 0.029 - 0.058: 196 0.058 - 0.087: 59 0.087 - 0.116: 37 0.116 - 0.145: 11 Chirality restraints: 777 Sorted by residual: chirality pdb=" CA TYR I 91 " pdb=" N TYR I 91 " pdb=" C TYR I 91 " pdb=" CB TYR I 91 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.23e-01 chirality pdb=" CA PRO J 238 " pdb=" N PRO J 238 " pdb=" C PRO J 238 " pdb=" CB PRO J 238 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.15e-01 chirality pdb=" CA PRO J 140 " pdb=" N PRO J 140 " pdb=" C PRO J 140 " pdb=" CB PRO J 140 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.12 2.00e-01 2.50e+01 3.90e-01 ... (remaining 774 not shown) Planarity restraints: 905 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET I 237 " -0.009 2.00e-02 2.50e+03 1.76e-02 3.10e+00 pdb=" C MET I 237 " 0.030 2.00e-02 2.50e+03 pdb=" O MET I 237 " -0.011 2.00e-02 2.50e+03 pdb=" N LEU I 238 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU I 49 " 0.027 5.00e-02 4.00e+02 4.13e-02 2.74e+00 pdb=" N PRO I 50 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO I 50 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO I 50 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS J 139 " 0.025 5.00e-02 4.00e+02 3.81e-02 2.32e+00 pdb=" N PRO J 140 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO J 140 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO J 140 " 0.021 5.00e-02 4.00e+02 ... (remaining 902 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 545 2.74 - 3.28: 5525 3.28 - 3.82: 10054 3.82 - 4.36: 12052 4.36 - 4.90: 19422 Nonbonded interactions: 47598 Sorted by model distance: nonbonded pdb=" O GLY H 285 " pdb=" O HOH H 401 " model vdw 2.202 2.440 nonbonded pdb=" O ARG I 9 " pdb=" O HOH I 401 " model vdw 2.208 2.440 nonbonded pdb=" O LEU I 144 " pdb=" O HOH I 402 " model vdw 2.222 2.440 nonbonded pdb=" OD1 ASP J 104 " pdb=" OG SER J 106 " model vdw 2.232 2.440 nonbonded pdb=" OE2 GLU J 62 " pdb=" O HOH J 501 " model vdw 2.235 2.440 ... (remaining 47593 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.19 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 12.300 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 19.880 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 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 : 0.007 0.218 5255 Z= 0.416 Angle : 0.716 16.637 7113 Z= 0.321 Chirality : 0.040 0.145 777 Planarity : 0.005 0.041 905 Dihedral : 17.434 125.743 1969 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.29 % Favored : 98.54 % Rotamer: Outliers : 0.90 % Allowed : 16.43 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 1.67 (0.34), residues: 618 helix: 1.97 (0.29), residues: 334 sheet: 0.84 (1.05), residues: 15 loop : 0.08 (0.38), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP I 11 HIS 0.003 0.001 HIS J 131 PHE 0.016 0.002 PHE I 30 TYR 0.020 0.002 TYR I 231 ARG 0.006 0.000 ARG I 63 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 90 time to evaluate : 0.609 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 95 average time/residue: 1.5175 time to fit residues: 149.1440 Evaluate side-chains 92 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 88 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 279 SER Chi-restraints excluded: chain I residue 78 SER Chi-restraints excluded: chain I residue 254 SER Chi-restraints excluded: chain J residue 96 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 5.9990 chunk 46 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 36 optimal weight: 6.9990 chunk 56 optimal weight: 7.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 236 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.0259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5255 Z= 0.218 Angle : 0.549 6.444 7113 Z= 0.279 Chirality : 0.040 0.145 777 Planarity : 0.005 0.043 905 Dihedral : 10.653 125.178 711 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.13 % Favored : 98.71 % Rotamer: Outliers : 1.81 % Allowed : 15.52 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 1.61 (0.34), residues: 618 helix: 1.92 (0.29), residues: 328 sheet: 0.75 (1.06), residues: 15 loop : 0.12 (0.39), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP I 11 HIS 0.003 0.001 HIS J 131 PHE 0.018 0.002 PHE I 30 TYR 0.018 0.002 TYR I 91 ARG 0.003 0.000 ARG I 23 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 94 time to evaluate : 0.602 Fit side-chains REVERT: H 249 GLN cc_start: 0.7144 (OUTLIER) cc_final: 0.6937 (mm-40) outliers start: 10 outliers final: 4 residues processed: 99 average time/residue: 1.5469 time to fit residues: 158.4099 Evaluate side-chains 96 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 91 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 249 GLN Chi-restraints excluded: chain H residue 282 ASP Chi-restraints excluded: chain I residue 12 THR Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain J residue 96 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 31 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 chunk 50 optimal weight: 7.9990 chunk 55 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 18 GLN J 236 GLN J 297 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.0534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 5255 Z= 0.287 Angle : 0.608 7.667 7113 Z= 0.309 Chirality : 0.042 0.151 777 Planarity : 0.005 0.046 905 Dihedral : 10.676 125.501 708 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.62 % Favored : 98.22 % Rotamer: Outliers : 2.71 % Allowed : 14.62 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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 (0.34), residues: 618 helix: 1.52 (0.28), residues: 334 sheet: 0.74 (1.12), residues: 15 loop : -0.05 (0.39), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP I 11 HIS 0.004 0.001 HIS J 131 PHE 0.018 0.002 PHE I 30 TYR 0.018 0.002 TYR I 91 ARG 0.004 0.000 ARG I 23 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 94 time to evaluate : 0.598 Fit side-chains REVERT: H 268 ARG cc_start: 0.6154 (OUTLIER) cc_final: 0.5606 (mtm-85) outliers start: 15 outliers final: 6 residues processed: 104 average time/residue: 1.4909 time to fit residues: 160.5981 Evaluate side-chains 98 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 91 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 268 ARG Chi-restraints excluded: chain H residue 282 ASP Chi-restraints excluded: chain I residue 12 THR Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain J residue 250 LYS Chi-restraints excluded: chain J residue 251 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 55 optimal weight: 7.9990 chunk 42 optimal weight: 5.9990 chunk 29 optimal weight: 0.3980 chunk 6 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 37 optimal weight: 0.5980 chunk 56 optimal weight: 0.8980 chunk 59 optimal weight: 0.0970 chunk 53 optimal weight: 0.5980 chunk 16 optimal weight: 3.9990 chunk 49 optimal weight: 0.5980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 236 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.0561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 5255 Z= 0.133 Angle : 0.482 8.790 7113 Z= 0.245 Chirality : 0.038 0.138 777 Planarity : 0.004 0.041 905 Dihedral : 9.771 119.621 708 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.13 % Favored : 98.71 % Rotamer: Outliers : 1.26 % Allowed : 16.79 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 1.69 (0.34), residues: 618 helix: 1.93 (0.29), residues: 340 sheet: 0.91 (1.02), residues: 15 loop : 0.13 (0.39), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 11 HIS 0.003 0.001 HIS I 161 PHE 0.014 0.001 PHE I 30 TYR 0.015 0.001 TYR I 60 ARG 0.003 0.000 ARG I 63 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 95 time to evaluate : 0.627 Fit side-chains REVERT: H 268 ARG cc_start: 0.6073 (OUTLIER) cc_final: 0.5607 (mtm-85) REVERT: I 77 ARG cc_start: 0.6930 (OUTLIER) cc_final: 0.6177 (ptp-170) REVERT: I 228 MET cc_start: 0.8025 (ptm) cc_final: 0.7766 (ptm) outliers start: 7 outliers final: 3 residues processed: 99 average time/residue: 1.5268 time to fit residues: 156.4464 Evaluate side-chains 94 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 89 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 268 ARG Chi-restraints excluded: chain I residue 77 ARG Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain J residue 251 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 34 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 51 optimal weight: 5.9990 chunk 41 optimal weight: 8.9990 chunk 30 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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: 0.7829 moved from start: 0.0594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 5255 Z= 0.281 Angle : 0.604 9.319 7113 Z= 0.306 Chirality : 0.042 0.147 777 Planarity : 0.005 0.044 905 Dihedral : 10.250 125.490 708 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.62 % Favored : 98.22 % Rotamer: Outliers : 2.35 % Allowed : 14.80 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 1.29 (0.34), residues: 618 helix: 1.59 (0.28), residues: 334 sheet: 0.91 (1.15), residues: 15 loop : -0.01 (0.39), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP J 197 HIS 0.004 0.001 HIS J 131 PHE 0.019 0.002 PHE I 30 TYR 0.019 0.002 TYR I 91 ARG 0.004 0.001 ARG I 23 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 91 time to evaluate : 0.640 Fit side-chains REVERT: H 268 ARG cc_start: 0.6137 (OUTLIER) cc_final: 0.5613 (mtm-85) REVERT: I 77 ARG cc_start: 0.6974 (OUTLIER) cc_final: 0.6200 (ptp-170) REVERT: J 250 LYS cc_start: 0.6170 (OUTLIER) cc_final: 0.5797 (mtmm) outliers start: 13 outliers final: 5 residues processed: 99 average time/residue: 1.6272 time to fit residues: 166.9309 Evaluate side-chains 100 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 92 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 268 ARG Chi-restraints excluded: chain H residue 282 ASP Chi-restraints excluded: chain I residue 77 ARG Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain J residue 70 SER Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain J residue 250 LYS Chi-restraints excluded: chain J residue 251 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 35 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 59 optimal weight: 0.6980 chunk 49 optimal weight: 0.0980 chunk 27 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 6 optimal weight: 5.9990 chunk 34 optimal weight: 0.8980 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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: 0.7784 moved from start: 0.0522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5255 Z= 0.166 Angle : 0.531 10.554 7113 Z= 0.264 Chirality : 0.039 0.141 777 Planarity : 0.005 0.042 905 Dihedral : 9.826 121.412 708 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.29 % Favored : 98.54 % Rotamer: Outliers : 1.44 % Allowed : 16.97 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 1.59 (0.34), residues: 618 helix: 1.83 (0.29), residues: 340 sheet: 0.96 (1.05), residues: 15 loop : 0.10 (0.39), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 11 HIS 0.003 0.001 HIS I 161 PHE 0.015 0.001 PHE I 30 TYR 0.016 0.002 TYR I 91 ARG 0.004 0.000 ARG I 63 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 96 time to evaluate : 0.622 Fit side-chains REVERT: H 268 ARG cc_start: 0.6067 (OUTLIER) cc_final: 0.5569 (mtm-85) REVERT: I 77 ARG cc_start: 0.6935 (OUTLIER) cc_final: 0.6184 (ptp-170) REVERT: I 260 LYS cc_start: 0.7273 (OUTLIER) cc_final: 0.6866 (ttmt) outliers start: 8 outliers final: 3 residues processed: 100 average time/residue: 1.5556 time to fit residues: 160.9208 Evaluate side-chains 95 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 89 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 268 ARG Chi-restraints excluded: chain I residue 77 ARG Chi-restraints excluded: chain I residue 260 LYS Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain J residue 251 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 43 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 50 optimal weight: 10.0000 chunk 59 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 297 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.0583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5255 Z= 0.286 Angle : 0.619 9.811 7113 Z= 0.311 Chirality : 0.042 0.147 777 Planarity : 0.005 0.045 905 Dihedral : 10.210 125.555 708 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.46 % Favored : 98.38 % Rotamer: Outliers : 1.81 % Allowed : 15.88 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 1.25 (0.34), residues: 618 helix: 1.56 (0.28), residues: 334 sheet: 0.87 (1.15), residues: 15 loop : -0.02 (0.39), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP I 11 HIS 0.004 0.001 HIS J 131 PHE 0.018 0.002 PHE I 30 TYR 0.021 0.002 TYR I 231 ARG 0.004 0.001 ARG I 23 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 89 time to evaluate : 0.610 Fit side-chains REVERT: H 268 ARG cc_start: 0.6142 (OUTLIER) cc_final: 0.5607 (mtm-85) REVERT: I 77 ARG cc_start: 0.6977 (OUTLIER) cc_final: 0.6203 (ptp-170) REVERT: I 260 LYS cc_start: 0.7320 (OUTLIER) cc_final: 0.6810 (ttmt) outliers start: 10 outliers final: 5 residues processed: 95 average time/residue: 1.5779 time to fit residues: 155.1097 Evaluate side-chains 98 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 90 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 268 ARG Chi-restraints excluded: chain H residue 282 ASP Chi-restraints excluded: chain I residue 77 ARG Chi-restraints excluded: chain I residue 260 LYS Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain J residue 70 SER Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain J residue 251 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 11 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 46 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 52 optimal weight: 0.9980 chunk 55 optimal weight: 0.7980 chunk 33 optimal weight: 8.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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: 0.7795 moved from start: 0.0480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5255 Z= 0.172 Angle : 0.538 9.814 7113 Z= 0.270 Chirality : 0.039 0.144 777 Planarity : 0.005 0.043 905 Dihedral : 9.919 122.485 708 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.29 % Favored : 98.54 % Rotamer: Outliers : 1.44 % Allowed : 16.43 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 1.59 (0.34), residues: 618 helix: 1.86 (0.29), residues: 334 sheet: 0.85 (1.05), residues: 15 loop : 0.11 (0.39), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP I 11 HIS 0.003 0.001 HIS I 161 PHE 0.016 0.002 PHE I 30 TYR 0.016 0.002 TYR I 91 ARG 0.005 0.000 ARG I 63 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 91 time to evaluate : 0.663 Fit side-chains REVERT: H 268 ARG cc_start: 0.6091 (OUTLIER) cc_final: 0.5587 (mtm-85) REVERT: I 77 ARG cc_start: 0.6944 (OUTLIER) cc_final: 0.6182 (ptp-170) REVERT: I 260 LYS cc_start: 0.7282 (OUTLIER) cc_final: 0.6836 (ttmt) outliers start: 8 outliers final: 4 residues processed: 96 average time/residue: 1.5450 time to fit residues: 153.6635 Evaluate side-chains 96 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 89 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 268 ARG Chi-restraints excluded: chain I residue 77 ARG Chi-restraints excluded: chain I residue 260 LYS Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain J residue 70 SER Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain J residue 251 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 24 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 chunk 36 optimal weight: 7.9990 chunk 58 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- 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: 0.7804 moved from start: 0.0466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 5255 Z= 0.208 Angle : 0.566 10.468 7113 Z= 0.281 Chirality : 0.040 0.143 777 Planarity : 0.005 0.044 905 Dihedral : 9.921 123.459 708 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.46 % Favored : 98.38 % Rotamer: Outliers : 1.62 % Allowed : 16.06 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 1.53 (0.34), residues: 618 helix: 1.79 (0.29), residues: 334 sheet: 0.81 (1.10), residues: 15 loop : 0.12 (0.39), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP I 11 HIS 0.003 0.001 HIS J 131 PHE 0.017 0.002 PHE I 30 TYR 0.018 0.002 TYR I 91 ARG 0.004 0.000 ARG I 63 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 89 time to evaluate : 0.621 Fit side-chains REVERT: H 268 ARG cc_start: 0.6111 (OUTLIER) cc_final: 0.5603 (mtm-85) REVERT: I 77 ARG cc_start: 0.6943 (OUTLIER) cc_final: 0.6184 (ptp-170) REVERT: I 260 LYS cc_start: 0.7296 (OUTLIER) cc_final: 0.6842 (ttmt) outliers start: 9 outliers final: 4 residues processed: 94 average time/residue: 1.5597 time to fit residues: 152.0535 Evaluate side-chains 96 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 89 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 268 ARG Chi-restraints excluded: chain I residue 77 ARG Chi-restraints excluded: chain I residue 260 LYS Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain J residue 70 SER Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain J residue 251 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 61 optimal weight: 0.0010 chunk 56 optimal weight: 5.9990 chunk 49 optimal weight: 0.7980 chunk 5 optimal weight: 6.9990 chunk 37 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 39 optimal weight: 0.0980 chunk 52 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 overall best weight: 1.1790 ------------------------------------------------------------------------------- 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: 0.7804 moved from start: 0.0485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 5255 Z= 0.210 Angle : 0.569 10.032 7113 Z= 0.283 Chirality : 0.040 0.143 777 Planarity : 0.005 0.043 905 Dihedral : 9.946 123.725 708 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.46 % Favored : 98.38 % Rotamer: Outliers : 1.26 % Allowed : 16.25 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 1.52 (0.34), residues: 618 helix: 1.77 (0.29), residues: 334 sheet: 0.76 (1.09), residues: 15 loop : 0.13 (0.39), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP I 11 HIS 0.003 0.001 HIS J 131 PHE 0.017 0.002 PHE I 30 TYR 0.018 0.002 TYR I 91 ARG 0.004 0.000 ARG I 63 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 89 time to evaluate : 0.623 Fit side-chains REVERT: H 268 ARG cc_start: 0.6112 (OUTLIER) cc_final: 0.5607 (mtm-85) REVERT: I 77 ARG cc_start: 0.6943 (OUTLIER) cc_final: 0.6185 (ptp-170) REVERT: I 260 LYS cc_start: 0.7301 (OUTLIER) cc_final: 0.6832 (ttmt) outliers start: 7 outliers final: 4 residues processed: 93 average time/residue: 1.5579 time to fit residues: 150.0014 Evaluate side-chains 95 residues out of total 554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 88 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 268 ARG Chi-restraints excluded: chain I residue 77 ARG Chi-restraints excluded: chain I residue 260 LYS Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain J residue 70 SER Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain J residue 251 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 13 optimal weight: 0.5980 chunk 49 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 9 optimal weight: 8.9990 chunk 43 optimal weight: 4.9990 chunk 2 optimal weight: 0.3980 chunk 35 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.170265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.142032 restraints weight = 23553.034| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 2.72 r_work: 0.3606 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3505 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3499 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3499 r_free = 0.3499 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3499 r_free = 0.3499 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3499 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.0490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5255 Z= 0.193 Angle : 0.558 10.124 7113 Z= 0.277 Chirality : 0.039 0.144 777 Planarity : 0.005 0.043 905 Dihedral : 9.846 123.256 708 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.29 % Favored : 98.54 % Rotamer: Outliers : 1.62 % Allowed : 16.43 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 1.58 (0.34), residues: 618 helix: 1.83 (0.29), residues: 334 sheet: 0.83 (1.08), residues: 15 loop : 0.14 (0.39), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP I 11 HIS 0.003 0.001 HIS J 131 PHE 0.016 0.002 PHE I 30 TYR 0.018 0.002 TYR I 91 ARG 0.004 0.000 ARG I 63 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3149.33 seconds wall clock time: 56 minutes 47.45 seconds (3407.45 seconds total)