Starting phenix.real_space_refine on Sun Mar 10 14:33:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yj5_10816/03_2024/6yj5_10816_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yj5_10816/03_2024/6yj5_10816.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yj5_10816/03_2024/6yj5_10816.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yj5_10816/03_2024/6yj5_10816.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yj5_10816/03_2024/6yj5_10816_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yj5_10816/03_2024/6yj5_10816_neut.pdb" } resolution = 3.5 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= 0.004 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 Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 5 5.16 5 C 1308 2.51 5 N 352 2.21 5 O 396 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "q ARG 13": "NH1" <-> "NH2" Residue "q TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ARG 102": "NH1" <-> "NH2" Residue "q GLU 122": "OE1" <-> "OE2" Residue "q TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ARG 281": "NH1" <-> "NH2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 2061 Number of models: 1 Model: "" Number of chains: 1 Chain: "q" Number of atoms: 2061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2061 Classifications: {'peptide': 306} Incomplete info: {'truncation_to_alanine': 93} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 280} Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 336 Unresolved non-hydrogen angles: 425 Unresolved non-hydrogen dihedrals: 288 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 5, 'TYR:plan': 2, 'ASN:plan1': 4, 'TRP:plan': 2, 'HIS:plan': 3, 'PHE:plan': 3, 'GLU:plan': 10, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 168 Time building chain proxies: 1.79, per 1000 atoms: 0.87 Number of scatterers: 2061 At special positions: 0 Unit cell: (55.915, 72.795, 61.19, 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 5 16.00 O 396 8.00 N 352 7.00 C 1308 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: 0.84 Conformation dependent library (CDL) restraints added in 426.6 milliseconds 608 Ramachandran restraints generated. 304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 564 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 2 sheets defined 34.3% alpha, 5.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'q' and resid 6 through 15 removed outlier: 3.583A pdb=" N LEU q 10 " --> pdb=" O SER q 6 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA q 11 " --> pdb=" O PRO q 7 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LYS q 12 " --> pdb=" O ALA q 8 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N SER q 15 " --> pdb=" O ALA q 11 " (cutoff:3.500A) Processing helix chain 'q' and resid 38 through 43 removed outlier: 3.566A pdb=" N MET q 43 " --> pdb=" O TYR q 39 " (cutoff:3.500A) Processing helix chain 'q' and resid 54 through 59 removed outlier: 3.924A pdb=" N ASN q 59 " --> pdb=" O ILE q 55 " (cutoff:3.500A) Processing helix chain 'q' and resid 74 through 79 Processing helix chain 'q' and resid 100 through 110 removed outlier: 3.763A pdb=" N VAL q 104 " --> pdb=" O GLY q 100 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE q 110 " --> pdb=" O THR q 106 " (cutoff:3.500A) Processing helix chain 'q' and resid 120 through 126 removed outlier: 3.619A pdb=" N TYR q 124 " --> pdb=" O GLY q 120 " (cutoff:3.500A) Processing helix chain 'q' and resid 169 through 175 Processing helix chain 'q' and resid 176 through 179 Processing helix chain 'q' and resid 181 through 185 removed outlier: 3.547A pdb=" N GLY q 184 " --> pdb=" O ASN q 181 " (cutoff:3.500A) Processing helix chain 'q' and resid 186 through 191 removed outlier: 3.526A pdb=" N VAL q 191 " --> pdb=" O ILE q 187 " (cutoff:3.500A) Processing helix chain 'q' and resid 237 through 247 Processing helix chain 'q' and resid 260 through 264 removed outlier: 3.504A pdb=" N VAL q 264 " --> pdb=" O GLY q 261 " (cutoff:3.500A) Processing helix chain 'q' and resid 265 through 266 No H-bonds generated for 'chain 'q' and resid 265 through 266' Processing helix chain 'q' and resid 267 through 277 removed outlier: 4.961A pdb=" N LEU q 273 " --> pdb=" O ILE q 269 " (cutoff:3.500A) Processing helix chain 'q' and resid 290 through 297 Processing sheet with id=AA1, first strand: chain 'q' and resid 3 through 5 removed outlier: 3.556A pdb=" N LYS q 3 " --> pdb=" O VAL q 115 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ILE q 89 " --> pdb=" O GLN q 116 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N LEU q 118 " --> pdb=" O ILE q 89 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N VAL q 91 " --> pdb=" O LEU q 118 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'q' and resid 192 through 193 removed outlier: 6.281A pdb=" N THR q 192 " --> pdb=" O ILE q 257 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ILE q 256 " --> pdb=" O ALA q 285 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 44 hydrogen bonds defined for protein. 120 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.49 Time building geometry restraints manager: 0.92 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: 698 1.34 - 1.46: 450 1.46 - 1.57: 950 1.57 - 1.69: 0 1.69 - 1.81: 8 Bond restraints: 2106 Sorted by residual: bond pdb=" CA GLY q 140 " pdb=" C GLY q 140 " ideal model delta sigma weight residual 1.516 1.498 0.019 1.31e-02 5.83e+03 2.04e+00 bond pdb=" C MET q 43 " pdb=" N LYS q 44 " ideal model delta sigma weight residual 1.333 1.312 0.020 1.52e-02 4.33e+03 1.81e+00 bond pdb=" CB PRO q 69 " pdb=" CG PRO q 69 " ideal model delta sigma weight residual 1.492 1.428 0.064 5.00e-02 4.00e+02 1.66e+00 bond pdb=" CG PRO q 48 " pdb=" CD PRO q 48 " ideal model delta sigma weight residual 1.503 1.461 0.042 3.40e-02 8.65e+02 1.53e+00 bond pdb=" CG LEU q 51 " pdb=" CD1 LEU q 51 " ideal model delta sigma weight residual 1.521 1.486 0.035 3.30e-02 9.18e+02 1.15e+00 ... (remaining 2101 not shown) Histogram of bond angle deviations from ideal: 99.95 - 106.76: 80 106.76 - 113.56: 1115 113.56 - 120.36: 784 120.36 - 127.16: 886 127.16 - 133.96: 24 Bond angle restraints: 2889 Sorted by residual: angle pdb=" N GLY q 140 " pdb=" CA GLY q 140 " pdb=" C GLY q 140 " ideal model delta sigma weight residual 114.25 110.04 4.21 1.30e+00 5.92e-01 1.05e+01 angle pdb=" N PHE q 226 " pdb=" CA PHE q 226 " pdb=" CB PHE q 226 " ideal model delta sigma weight residual 110.39 107.68 2.71 9.50e-01 1.11e+00 8.15e+00 angle pdb=" N LEU q 14 " pdb=" CA LEU q 14 " pdb=" C LEU q 14 " ideal model delta sigma weight residual 111.36 114.40 -3.04 1.09e+00 8.42e-01 7.78e+00 angle pdb=" N ASN q 232 " pdb=" CA ASN q 232 " pdb=" C ASN q 232 " ideal model delta sigma weight residual 110.80 116.16 -5.36 2.13e+00 2.20e-01 6.33e+00 angle pdb=" C GLU q 231 " pdb=" N ASN q 232 " pdb=" CA ASN q 232 " ideal model delta sigma weight residual 121.54 125.72 -4.18 1.91e+00 2.74e-01 4.80e+00 ... (remaining 2884 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 1145 17.95 - 35.91: 74 35.91 - 53.86: 11 53.86 - 71.81: 2 71.81 - 89.77: 1 Dihedral angle restraints: 1233 sinusoidal: 355 harmonic: 878 Sorted by residual: dihedral pdb=" CA GLN q 72 " pdb=" C GLN q 72 " pdb=" N THR q 73 " pdb=" CA THR q 73 " ideal model delta harmonic sigma weight residual 180.00 152.20 27.80 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" CA ILE q 269 " pdb=" C ILE q 269 " pdb=" N ASP q 270 " pdb=" CA ASP q 270 " ideal model delta harmonic sigma weight residual 180.00 156.19 23.81 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" CA THR q 138 " pdb=" C THR q 138 " pdb=" N TRP q 139 " pdb=" CA TRP q 139 " ideal model delta harmonic sigma weight residual 180.00 158.78 21.22 0 5.00e+00 4.00e-02 1.80e+01 ... (remaining 1230 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 163 0.030 - 0.060: 107 0.060 - 0.089: 40 0.089 - 0.119: 18 0.119 - 0.148: 6 Chirality restraints: 334 Sorted by residual: chirality pdb=" CA ILE q 130 " pdb=" N ILE q 130 " pdb=" C ILE q 130 " pdb=" CB ILE q 130 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.48e-01 chirality pdb=" CA PRO q 101 " pdb=" N PRO q 101 " pdb=" C PRO q 101 " pdb=" CB PRO q 101 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.82e-01 chirality pdb=" CA ILE q 257 " pdb=" N ILE q 257 " pdb=" C ILE q 257 " pdb=" CB ILE q 257 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.44e-01 ... (remaining 331 not shown) Planarity restraints: 387 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG q 197 " 0.029 5.00e-02 4.00e+02 4.29e-02 2.95e+00 pdb=" N PRO q 198 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO q 198 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO q 198 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY q 100 " 0.026 5.00e-02 4.00e+02 4.00e-02 2.56e+00 pdb=" N PRO q 101 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO q 101 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO q 101 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE q 74 " -0.013 2.00e-02 2.50e+03 1.09e-02 2.07e+00 pdb=" CG PHE q 74 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 PHE q 74 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE q 74 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE q 74 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE q 74 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE q 74 " -0.006 2.00e-02 2.50e+03 ... (remaining 384 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 168 2.73 - 3.27: 2199 3.27 - 3.81: 3086 3.81 - 4.36: 3655 4.36 - 4.90: 6026 Nonbonded interactions: 15134 Sorted by model distance: nonbonded pdb=" NZ LYS q 108 " pdb=" OE2 GLU q 274 " model vdw 2.183 2.520 nonbonded pdb=" N SER q 2 " pdb=" OE1 GLU q 274 " model vdw 2.206 2.520 nonbonded pdb=" O ARG q 102 " pdb=" OG1 THR q 106 " model vdw 2.246 2.440 nonbonded pdb=" NH2 ARG q 102 " pdb=" OD2 ASP q 288 " model vdw 2.261 2.520 nonbonded pdb=" N GLU q 9 " pdb=" OE1 GLU q 9 " model vdw 2.321 2.520 ... (remaining 15129 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.980 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: 18.750 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.390 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5928 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 0.064 2106 Z= 0.492 Angle : 0.874 5.754 2889 Z= 0.505 Chirality : 0.048 0.148 334 Planarity : 0.005 0.043 387 Dihedral : 13.190 89.768 669 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.50 % Favored : 87.50 % Rotamer: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -5.13 (0.38), residues: 304 helix: -4.08 (0.28), residues: 88 sheet: -2.97 (0.77), residues: 28 loop : -3.29 (0.40), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP q 142 HIS 0.001 0.001 HIS q 112 PHE 0.024 0.002 PHE q 74 TYR 0.008 0.002 TYR q 124 ARG 0.006 0.001 ARG q 163 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 608 Ramachandran restraints generated. 304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 608 Ramachandran restraints generated. 304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 0.256 Fit side-chains revert: symmetry clash REVERT: q 4 LEU cc_start: 0.6754 (pp) cc_final: 0.6549 (pp) REVERT: q 6 SER cc_start: 0.7911 (m) cc_final: 0.7182 (p) REVERT: q 89 ILE cc_start: 0.8145 (pt) cc_final: 0.7855 (mt) REVERT: q 114 ASN cc_start: 0.6728 (m110) cc_final: 0.6156 (m110) REVERT: q 117 PHE cc_start: 0.8105 (t80) cc_final: 0.7728 (t80) REVERT: q 163 ARG cc_start: 0.6876 (ptp90) cc_final: 0.6622 (ptp90) outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 0.1596 time to fit residues: 7.9632 Evaluate side-chains 32 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 0.232 ------------------------------------------------------------------------------- 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: 3.9990 chunk 22 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 27 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 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: 0.6075 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2106 Z= 0.197 Angle : 0.606 4.811 2889 Z= 0.323 Chirality : 0.050 0.141 334 Planarity : 0.005 0.043 387 Dihedral : 5.670 20.792 320 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.54 % Favored : 90.46 % Rotamer: Outliers : 2.45 % Allowed : 7.98 % Favored : 89.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -3.54 (0.44), residues: 304 helix: -2.73 (0.40), residues: 94 sheet: -1.22 (0.83), residues: 27 loop : -2.40 (0.46), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP q 291 HIS 0.003 0.002 HIS q 112 PHE 0.014 0.001 PHE q 74 TYR 0.013 0.002 TYR q 52 ARG 0.002 0.001 ARG q 102 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 608 Ramachandran restraints generated. 304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 608 Ramachandran restraints generated. 304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 36 time to evaluate : 0.255 Fit side-chains REVERT: q 18 GLU cc_start: 0.7173 (mp0) cc_final: 0.6957 (mp0) REVERT: q 39 TYR cc_start: 0.7422 (t80) cc_final: 0.7145 (t80) REVERT: q 46 ARG cc_start: 0.7863 (ptt-90) cc_final: 0.7621 (ptt-90) REVERT: q 52 TYR cc_start: 0.8151 (t80) cc_final: 0.7930 (t80) REVERT: q 114 ASN cc_start: 0.6732 (m110) cc_final: 0.6515 (m110) outliers start: 4 outliers final: 2 residues processed: 37 average time/residue: 0.1362 time to fit residues: 6.1498 Evaluate side-chains 31 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 29 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain q residue 113 ASP Chi-restraints excluded: chain q residue 259 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 22 optimal weight: 0.0060 chunk 18 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 29 optimal weight: 8.9990 chunk 24 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 21 optimal weight: 8.9990 chunk 26 optimal weight: 1.9990 chunk 20 optimal weight: 0.4980 chunk 14 optimal weight: 2.9990 overall best weight: 1.1000 ------------------------------------------------------------------------------- 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: 0.6174 moved from start: 0.3903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 2106 Z= 0.250 Angle : 0.611 4.529 2889 Z= 0.326 Chirality : 0.050 0.143 334 Planarity : 0.006 0.047 387 Dihedral : 5.632 19.855 320 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.51 % Favored : 88.49 % Rotamer: Outliers : 2.45 % Allowed : 12.88 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -2.96 (0.46), residues: 304 helix: -2.32 (0.43), residues: 100 sheet: -0.67 (0.94), residues: 28 loop : -2.00 (0.48), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP q 105 HIS 0.004 0.003 HIS q 112 PHE 0.015 0.002 PHE q 74 TYR 0.008 0.002 TYR q 157 ARG 0.004 0.001 ARG q 133 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 608 Ramachandran restraints generated. 304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 608 Ramachandran restraints generated. 304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 36 time to evaluate : 0.232 Fit side-chains REVERT: q 9 GLU cc_start: 0.5872 (mp0) cc_final: 0.5586 (mp0) REVERT: q 17 LYS cc_start: 0.5331 (mmpt) cc_final: 0.4877 (mtmt) REVERT: q 72 GLN cc_start: 0.7420 (mt0) cc_final: 0.6556 (mp10) outliers start: 4 outliers final: 1 residues processed: 38 average time/residue: 0.1084 time to fit residues: 5.1271 Evaluate side-chains 28 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 27 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain q residue 113 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 3 optimal weight: 5.9990 chunk 13 optimal weight: 0.0870 chunk 18 optimal weight: 4.9990 chunk 27 optimal weight: 0.2980 chunk 28 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 overall best weight: 1.2162 ------------------------------------------------------------------------------- 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: 0.6206 moved from start: 0.4521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 2106 Z= 0.259 Angle : 0.582 4.553 2889 Z= 0.308 Chirality : 0.049 0.135 334 Planarity : 0.006 0.052 387 Dihedral : 5.483 18.771 320 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.54 % Favored : 90.46 % Rotamer: Outliers : 4.29 % Allowed : 12.27 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -2.81 (0.45), residues: 304 helix: -2.13 (0.45), residues: 100 sheet: -0.53 (0.99), residues: 28 loop : -1.96 (0.46), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP q 291 HIS 0.004 0.002 HIS q 112 PHE 0.016 0.002 PHE q 74 TYR 0.008 0.001 TYR q 92 ARG 0.003 0.001 ARG q 133 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 608 Ramachandran restraints generated. 304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 608 Ramachandran restraints generated. 304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 30 time to evaluate : 0.240 Fit side-chains REVERT: q 9 GLU cc_start: 0.5876 (mp0) cc_final: 0.5576 (mp0) REVERT: q 17 LYS cc_start: 0.5468 (mmpt) cc_final: 0.4854 (mtmt) REVERT: q 72 GLN cc_start: 0.7462 (mt0) cc_final: 0.6629 (mp10) REVERT: q 89 ILE cc_start: 0.8095 (OUTLIER) cc_final: 0.7772 (mt) REVERT: q 95 GLN cc_start: 0.6481 (mt0) cc_final: 0.6231 (mp10) REVERT: q 269 ILE cc_start: 0.7139 (OUTLIER) cc_final: 0.6772 (pt) outliers start: 7 outliers final: 3 residues processed: 35 average time/residue: 0.0977 time to fit residues: 4.4163 Evaluate side-chains 31 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 26 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain q residue 51 LEU Chi-restraints excluded: chain q residue 89 ILE Chi-restraints excluded: chain q residue 106 THR Chi-restraints excluded: chain q residue 113 ASP Chi-restraints excluded: chain q residue 269 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 21 optimal weight: 20.0000 chunk 11 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 7 optimal weight: 0.1980 chunk 9 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 17 optimal weight: 7.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6205 moved from start: 0.4754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2106 Z= 0.224 Angle : 0.553 4.344 2889 Z= 0.292 Chirality : 0.048 0.117 334 Planarity : 0.006 0.055 387 Dihedral : 5.297 19.216 320 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.20 % Favored : 89.80 % Rotamer: Outliers : 4.29 % Allowed : 12.27 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -2.59 (0.46), residues: 304 helix: -1.86 (0.48), residues: 100 sheet: -0.60 (0.99), residues: 28 loop : -1.85 (0.47), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP q 291 HIS 0.004 0.002 HIS q 112 PHE 0.014 0.002 PHE q 74 TYR 0.006 0.001 TYR q 157 ARG 0.002 0.001 ARG q 133 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 608 Ramachandran restraints generated. 304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 608 Ramachandran restraints generated. 304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 26 time to evaluate : 0.231 Fit side-chains REVERT: q 9 GLU cc_start: 0.5883 (mp0) cc_final: 0.5626 (mp0) REVERT: q 17 LYS cc_start: 0.5672 (mmpt) cc_final: 0.5127 (ptpt) REVERT: q 72 GLN cc_start: 0.7394 (mt0) cc_final: 0.6610 (mp10) REVERT: q 89 ILE cc_start: 0.8060 (OUTLIER) cc_final: 0.7680 (mt) REVERT: q 95 GLN cc_start: 0.6339 (mt0) cc_final: 0.6041 (mp10) outliers start: 7 outliers final: 4 residues processed: 31 average time/residue: 0.1431 time to fit residues: 5.3180 Evaluate side-chains 28 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 23 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain q residue 51 LEU Chi-restraints excluded: chain q residue 89 ILE Chi-restraints excluded: chain q residue 106 THR Chi-restraints excluded: chain q residue 113 ASP Chi-restraints excluded: chain q residue 118 LEU 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: 1.9990 chunk 24 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 21 optimal weight: 20.0000 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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: 0.6242 moved from start: 0.5176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 2106 Z= 0.316 Angle : 0.615 5.506 2889 Z= 0.321 Chirality : 0.050 0.131 334 Planarity : 0.006 0.058 387 Dihedral : 5.700 19.020 320 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.86 % Favored : 89.14 % Rotamer: Outliers : 4.91 % Allowed : 13.50 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.68 (0.45), residues: 304 helix: -2.03 (0.45), residues: 103 sheet: -0.15 (1.03), residues: 25 loop : -1.90 (0.46), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP q 291 HIS 0.006 0.004 HIS q 112 PHE 0.015 0.002 PHE q 74 TYR 0.008 0.001 TYR q 157 ARG 0.003 0.001 ARG q 163 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 608 Ramachandran restraints generated. 304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 608 Ramachandran restraints generated. 304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 28 time to evaluate : 0.230 Fit side-chains REVERT: q 9 GLU cc_start: 0.5938 (mp0) cc_final: 0.5715 (mp0) REVERT: q 17 LYS cc_start: 0.5947 (mmpt) cc_final: 0.5279 (ptpt) REVERT: q 72 GLN cc_start: 0.7496 (mt0) cc_final: 0.6596 (mp10) REVERT: q 89 ILE cc_start: 0.8074 (OUTLIER) cc_final: 0.7750 (mt) REVERT: q 228 GLU cc_start: 0.7043 (mt-10) cc_final: 0.6657 (mt-10) outliers start: 8 outliers final: 5 residues processed: 34 average time/residue: 0.1451 time to fit residues: 5.9297 Evaluate side-chains 33 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 27 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain q residue 51 LEU Chi-restraints excluded: chain q residue 89 ILE Chi-restraints excluded: chain q residue 106 THR Chi-restraints excluded: chain q residue 113 ASP Chi-restraints excluded: chain q residue 118 LEU Chi-restraints excluded: chain q residue 283 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 16 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 18 optimal weight: 9.9990 chunk 17 optimal weight: 7.9990 chunk 13 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 19 optimal weight: 0.0670 chunk 14 optimal weight: 0.0010 overall best weight: 0.5124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: q 116 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6202 moved from start: 0.5253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 2106 Z= 0.164 Angle : 0.520 4.502 2889 Z= 0.272 Chirality : 0.047 0.120 334 Planarity : 0.005 0.060 387 Dihedral : 4.975 18.717 320 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.22 % Favored : 91.78 % Rotamer: Outliers : 3.68 % Allowed : 15.95 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -2.25 (0.47), residues: 304 helix: -1.45 (0.54), residues: 90 sheet: -0.59 (1.01), residues: 26 loop : -1.69 (0.46), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP q 291 HIS 0.003 0.002 HIS q 112 PHE 0.013 0.001 PHE q 74 TYR 0.004 0.001 TYR q 92 ARG 0.001 0.000 ARG q 102 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 608 Ramachandran restraints generated. 304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 608 Ramachandran restraints generated. 304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 28 time to evaluate : 0.239 Fit side-chains REVERT: q 17 LYS cc_start: 0.5826 (mmpt) cc_final: 0.5205 (ptpt) REVERT: q 72 GLN cc_start: 0.7379 (mt0) cc_final: 0.6540 (mp10) REVERT: q 89 ILE cc_start: 0.8224 (OUTLIER) cc_final: 0.7952 (mt) REVERT: q 95 GLN cc_start: 0.6327 (mt0) cc_final: 0.6054 (mp10) REVERT: q 165 GLU cc_start: 0.6857 (mp0) cc_final: 0.6631 (mm-30) REVERT: q 228 GLU cc_start: 0.6912 (mt-10) cc_final: 0.6515 (mt-10) outliers start: 6 outliers final: 3 residues processed: 32 average time/residue: 0.1196 time to fit residues: 4.7496 Evaluate side-chains 29 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 25 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain q residue 89 ILE Chi-restraints excluded: chain q residue 106 THR Chi-restraints excluded: chain q residue 113 ASP Chi-restraints excluded: chain q residue 118 LEU 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: 0.6980 chunk 26 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 21 optimal weight: 8.9990 chunk 8 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 17 optimal weight: 0.0770 overall best weight: 0.6738 ------------------------------------------------------------------------------- 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: 0.6199 moved from start: 0.5379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2106 Z= 0.180 Angle : 0.524 4.459 2889 Z= 0.272 Chirality : 0.047 0.118 334 Planarity : 0.005 0.057 387 Dihedral : 4.826 18.639 320 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.55 % Favored : 91.45 % Rotamer: Outliers : 4.29 % Allowed : 15.34 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -2.17 (0.47), residues: 304 helix: -1.32 (0.55), residues: 84 sheet: -0.78 (1.00), residues: 26 loop : -1.64 (0.45), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP q 291 HIS 0.002 0.001 HIS q 112 PHE 0.012 0.001 PHE q 74 TYR 0.005 0.001 TYR q 157 ARG 0.001 0.000 ARG q 102 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 608 Ramachandran restraints generated. 304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 608 Ramachandran restraints generated. 304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 26 time to evaluate : 0.241 Fit side-chains REVERT: q 17 LYS cc_start: 0.5789 (mmpt) cc_final: 0.5263 (ptpt) REVERT: q 72 GLN cc_start: 0.7242 (mt0) cc_final: 0.6431 (mp10) REVERT: q 89 ILE cc_start: 0.8277 (OUTLIER) cc_final: 0.7989 (mt) REVERT: q 95 GLN cc_start: 0.6321 (mt0) cc_final: 0.6084 (mp10) REVERT: q 165 GLU cc_start: 0.6882 (mp0) cc_final: 0.6643 (mm-30) REVERT: q 228 GLU cc_start: 0.6863 (mt-10) cc_final: 0.6448 (mt-10) outliers start: 7 outliers final: 5 residues processed: 30 average time/residue: 0.1207 time to fit residues: 4.5112 Evaluate side-chains 33 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 27 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain q residue 47 ILE Chi-restraints excluded: chain q residue 89 ILE Chi-restraints excluded: chain q residue 106 THR Chi-restraints excluded: chain q residue 113 ASP Chi-restraints excluded: chain q residue 118 LEU Chi-restraints excluded: chain q residue 269 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 28 optimal weight: 7.9990 chunk 17 optimal weight: 1.9990 chunk 13 optimal weight: 0.0270 chunk 19 optimal weight: 4.9990 chunk 29 optimal weight: 0.0980 chunk 27 optimal weight: 0.0870 chunk 23 optimal weight: 0.6980 chunk 2 optimal weight: 0.8980 chunk 18 optimal weight: 5.9990 chunk 14 optimal weight: 0.0670 chunk 25 optimal weight: 0.9990 overall best weight: 0.1954 ------------------------------------------------------------------------------- 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: 0.6147 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 : 0.002 0.018 2106 Z= 0.118 Angle : 0.484 4.448 2889 Z= 0.252 Chirality : 0.046 0.125 334 Planarity : 0.005 0.058 387 Dihedral : 4.310 17.498 320 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 1.84 % Allowed : 17.18 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -1.93 (0.48), residues: 304 helix: -1.12 (0.56), residues: 83 sheet: -1.12 (0.94), residues: 28 loop : -1.41 (0.46), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP q 291 HIS 0.001 0.001 HIS q 112 PHE 0.012 0.001 PHE q 74 TYR 0.004 0.001 TYR q 92 ARG 0.001 0.000 ARG q 46 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 608 Ramachandran restraints generated. 304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 608 Ramachandran restraints generated. 304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 31 time to evaluate : 0.243 Fit side-chains REVERT: q 17 LYS cc_start: 0.5719 (mmpt) cc_final: 0.5273 (ptpt) REVERT: q 39 TYR cc_start: 0.7426 (t80) cc_final: 0.6922 (t80) REVERT: q 72 GLN cc_start: 0.7227 (mt0) cc_final: 0.6429 (mp10) REVERT: q 228 GLU cc_start: 0.6823 (mt-10) cc_final: 0.6384 (mt-10) outliers start: 3 outliers final: 1 residues processed: 32 average time/residue: 0.1234 time to fit residues: 4.8505 Evaluate side-chains 29 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 28 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain q residue 106 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 0.6980 chunk 21 optimal weight: 0.2980 chunk 3 optimal weight: 4.9990 chunk 6 optimal weight: 0.0060 chunk 23 optimal weight: 0.5980 chunk 9 optimal weight: 3.9990 chunk 24 optimal weight: 0.3980 chunk 4 optimal weight: 0.2980 chunk 20 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 17 optimal weight: 0.3980 overall best weight: 0.2796 ------------------------------------------------------------------------------- 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: 0.6141 moved from start: 0.5528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 2106 Z= 0.135 Angle : 0.489 4.470 2889 Z= 0.253 Chirality : 0.046 0.120 334 Planarity : 0.005 0.055 387 Dihedral : 4.198 17.928 320 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 0.61 % Allowed : 17.18 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -1.88 (0.47), residues: 304 helix: -1.06 (0.55), residues: 83 sheet: -1.32 (0.91), residues: 28 loop : -1.34 (0.46), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP q 291 HIS 0.000 0.000 HIS q 112 PHE 0.009 0.001 PHE q 74 TYR 0.004 0.001 TYR q 157 ARG 0.002 0.000 ARG q 133 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 608 Ramachandran restraints generated. 304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 608 Ramachandran restraints generated. 304 Oldfield, 0 Emsley, 304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 27 time to evaluate : 0.235 Fit side-chains REVERT: q 17 LYS cc_start: 0.5599 (mmpt) cc_final: 0.5208 (ptpt) REVERT: q 23 ASP cc_start: 0.7067 (t0) cc_final: 0.6744 (t0) REVERT: q 39 TYR cc_start: 0.7422 (t80) cc_final: 0.6907 (t80) REVERT: q 72 GLN cc_start: 0.7138 (mt0) cc_final: 0.6320 (mp10) REVERT: q 228 GLU cc_start: 0.6815 (mt-10) cc_final: 0.6348 (mt-10) REVERT: q 259 MET cc_start: 0.6938 (ptp) cc_final: 0.6252 (ptm) outliers start: 1 outliers final: 1 residues processed: 28 average time/residue: 0.1051 time to fit residues: 3.7666 Evaluate side-chains 28 residues out of total 256 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 27 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain q residue 106 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 0.0970 chunk 16 optimal weight: 0.0370 chunk 20 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 18 optimal weight: 8.9990 chunk 17 optimal weight: 4.9990 chunk 11 optimal weight: 0.5980 chunk 29 optimal weight: 0.0010 chunk 1 optimal weight: 0.1980 chunk 28 optimal weight: 1.9990 overall best weight: 0.1862 ------------------------------------------------------------------------------- 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 = 0.3981 r_free = 0.3981 target = 0.177123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.162549 restraints weight = 2968.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.163831 restraints weight = 2217.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.164417 restraints weight = 1789.910| |-----------------------------------------------------------------------------| r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6889 moved from start: 0.5649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 2106 Z= 0.117 Angle : 0.470 4.437 2889 Z= 0.243 Chirality : 0.045 0.122 334 Planarity : 0.005 0.056 387 Dihedral : 3.920 17.231 320 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 0.00 % Allowed : 17.79 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -1.68 (0.48), residues: 304 helix: -0.89 (0.56), residues: 83 sheet: -1.12 (0.96), residues: 28 loop : -1.23 (0.46), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP q 291 HIS 0.000 0.000 HIS q 112 PHE 0.008 0.001 PHE q 74 TYR 0.004 0.001 TYR q 92 ARG 0.001 0.000 ARG q 46 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1117.30 seconds wall clock time: 20 minutes 29.59 seconds (1229.59 seconds total)