Starting phenix.real_space_refine on Sun Mar 10 19:28:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dkw_27492/03_2024/8dkw_27492.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dkw_27492/03_2024/8dkw_27492.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dkw_27492/03_2024/8dkw_27492.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dkw_27492/03_2024/8dkw_27492.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dkw_27492/03_2024/8dkw_27492.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dkw_27492/03_2024/8dkw_27492.pdb" } resolution = 3.09 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= 0.004 sd= 0.082 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 15 5.16 5 C 2863 2.51 5 N 704 2.21 5 O 788 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 46": "OE1" <-> "OE2" Residue "A ASP 63": "OD1" <-> "OD2" Residue "A ASP 74": "OD1" <-> "OD2" Residue "A TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 81": "OE1" <-> "OE2" Residue "B ASP 82": "OD1" <-> "OD2" Residue "P PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 74": "OD1" <-> "OD2" Residue "P TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 332": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 4370 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 876 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 3, 'TRANS': 109} Chain: "B" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 814 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "P" Number of atoms: 2680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2680 Classifications: {'peptide': 334} Incomplete info: {'n_c_alpha_c_only': 1} Link IDs: {'PTRANS': 15, 'TRANS': 318} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Time building chain proxies: 2.99, per 1000 atoms: 0.68 Number of scatterers: 4370 At special positions: 0 Unit cell: (78.85, 63.91, 122.01, 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 15 16.00 O 788 8.00 N 704 7.00 C 2863 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 97 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.90 Conformation dependent library (CDL) restraints added in 831.7 milliseconds 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1020 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 8 sheets defined 38.0% alpha, 20.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 28 through 32 removed outlier: 3.940A pdb=" N TYR A 32 " --> pdb=" O PHE A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 92 removed outlier: 3.658A pdb=" N ASP A 91 " --> pdb=" O ARG A 88 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N THR A 92 " --> pdb=" O SER A 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 88 through 92' Processing helix chain 'B' and resid 79 through 83 removed outlier: 4.313A pdb=" N ILE B 83 " --> pdb=" O PRO B 80 " (cutoff:3.500A) Processing helix chain 'P' and resid 120 through 139 removed outlier: 3.902A pdb=" N SER P 124 " --> pdb=" O SER P 120 " (cutoff:3.500A) Processing helix chain 'P' and resid 141 through 152 removed outlier: 3.891A pdb=" N GLN P 145 " --> pdb=" O SER P 141 " (cutoff:3.500A) Processing helix chain 'P' and resid 159 through 182 removed outlier: 3.629A pdb=" N THR P 168 " --> pdb=" O ALA P 164 " (cutoff:3.500A) Processing helix chain 'P' and resid 183 through 194 Processing helix chain 'P' and resid 202 through 226 removed outlier: 3.500A pdb=" N TYR P 226 " --> pdb=" O GLN P 222 " (cutoff:3.500A) Processing helix chain 'P' and resid 234 through 258 Processing helix chain 'P' and resid 263 through 290 removed outlier: 3.531A pdb=" N VAL P 276 " --> pdb=" O ILE P 272 " (cutoff:3.500A) Proline residue: P 283 - end of helix Processing helix chain 'P' and resid 298 through 323 removed outlier: 4.093A pdb=" N LEU P 303 " --> pdb=" O ILE P 299 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU P 313 " --> pdb=" O GLY P 309 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASN P 323 " --> pdb=" O GLN P 319 " (cutoff:3.500A) Processing helix chain 'P' and resid 334 through 356 removed outlier: 3.567A pdb=" N LEU P 338 " --> pdb=" O THR P 334 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 7 Processing sheet with id=AA2, first strand: chain 'A' and resid 59 through 60 removed outlier: 6.604A pdb=" N TRP A 36 " --> pdb=" O VAL A 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 5 through 6 removed outlier: 12.172A pdb=" N CYS B 23 " --> pdb=" O ALA B 74 " (cutoff:3.500A) removed outlier: 11.336A pdb=" N ALA B 74 " --> pdb=" O CYS B 23 " (cutoff:3.500A) removed outlier: 11.467A pdb=" N ALA B 25 " --> pdb=" O THR B 72 " (cutoff:3.500A) removed outlier: 11.318A pdb=" N THR B 72 " --> pdb=" O ALA B 25 " (cutoff:3.500A) removed outlier: 10.826A pdb=" N GLN B 27 " --> pdb=" O ASP B 70 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ASP B 70 " --> pdb=" O GLN B 27 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.436A pdb=" N LEU B 11 " --> pdb=" O GLU B 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 44 through 48 removed outlier: 6.356A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'P' and resid 26 through 27 Processing sheet with id=AA7, first strand: chain 'P' and resid 31 through 35 removed outlier: 6.934A pdb=" N VAL P 32 " --> pdb=" O LEU P 116 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N ILE P 118 " --> pdb=" O VAL P 32 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LEU P 34 " --> pdb=" O ILE P 118 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N THR P 98 " --> pdb=" O THR P 61 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'P' and resid 39 through 43 removed outlier: 3.596A pdb=" N THR P 90 " --> pdb=" O GLU P 71 " (cutoff:3.500A) 211 hydrogen bonds defined for protein. 597 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: 1.48 Time building geometry restraints manager: 2.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1336 1.34 - 1.46: 932 1.46 - 1.57: 2200 1.57 - 1.69: 0 1.69 - 1.81: 22 Bond restraints: 4490 Sorted by residual: bond pdb=" N ILE P 260 " pdb=" CA ILE P 260 " ideal model delta sigma weight residual 1.461 1.496 -0.036 1.19e-02 7.06e+03 9.00e+00 bond pdb=" N VAL P 259 " pdb=" CA VAL P 259 " ideal model delta sigma weight residual 1.456 1.495 -0.039 1.41e-02 5.03e+03 7.52e+00 bond pdb=" N TRP P 262 " pdb=" CA TRP P 262 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.37e-02 5.33e+03 6.84e+00 bond pdb=" N THR P 261 " pdb=" CA THR P 261 " ideal model delta sigma weight residual 1.460 1.500 -0.040 1.83e-02 2.99e+03 4.73e+00 bond pdb=" N GLY P 258 " pdb=" CA GLY P 258 " ideal model delta sigma weight residual 1.449 1.480 -0.031 1.45e-02 4.76e+03 4.53e+00 ... (remaining 4485 not shown) Histogram of bond angle deviations from ideal: 99.66 - 106.59: 116 106.59 - 113.51: 2437 113.51 - 120.43: 1755 120.43 - 127.35: 1758 127.35 - 134.27: 56 Bond angle restraints: 6122 Sorted by residual: angle pdb=" CA ILE P 260 " pdb=" C ILE P 260 " pdb=" O ILE P 260 " ideal model delta sigma weight residual 120.95 116.30 4.65 1.04e+00 9.25e-01 2.00e+01 angle pdb=" C THR P 261 " pdb=" CA THR P 261 " pdb=" CB THR P 261 " ideal model delta sigma weight residual 110.04 115.18 -5.14 1.51e+00 4.39e-01 1.16e+01 angle pdb=" C PRO P 195 " pdb=" N ASN P 196 " pdb=" CA ASN P 196 " ideal model delta sigma weight residual 121.54 127.50 -5.96 1.91e+00 2.74e-01 9.73e+00 angle pdb=" C ILE P 133 " pdb=" N TYR P 134 " pdb=" CA TYR P 134 " ideal model delta sigma weight residual 121.14 115.90 5.24 1.75e+00 3.27e-01 8.96e+00 angle pdb=" C ILE P 260 " pdb=" CA ILE P 260 " pdb=" CB ILE P 260 " ideal model delta sigma weight residual 112.14 115.64 -3.50 1.35e+00 5.49e-01 6.74e+00 ... (remaining 6117 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 2316 17.84 - 35.68: 230 35.68 - 53.52: 32 53.52 - 71.36: 2 71.36 - 89.20: 3 Dihedral angle restraints: 2583 sinusoidal: 986 harmonic: 1597 Sorted by residual: dihedral pdb=" C THR P 261 " pdb=" N THR P 261 " pdb=" CA THR P 261 " pdb=" CB THR P 261 " ideal model delta harmonic sigma weight residual -122.00 -142.14 20.14 0 2.50e+00 1.60e-01 6.49e+01 dihedral pdb=" N THR P 261 " pdb=" C THR P 261 " pdb=" CA THR P 261 " pdb=" CB THR P 261 " ideal model delta harmonic sigma weight residual 123.40 142.24 -18.84 0 2.50e+00 1.60e-01 5.68e+01 dihedral pdb=" CA ARG P 112 " pdb=" C ARG P 112 " pdb=" N ILE P 113 " pdb=" CA ILE P 113 " ideal model delta harmonic sigma weight residual 180.00 159.10 20.90 0 5.00e+00 4.00e-02 1.75e+01 ... (remaining 2580 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.161: 688 0.161 - 0.321: 4 0.321 - 0.482: 0 0.482 - 0.642: 0 0.642 - 0.803: 1 Chirality restraints: 693 Sorted by residual: chirality pdb=" CA THR P 261 " pdb=" N THR P 261 " pdb=" C THR P 261 " pdb=" CB THR P 261 " both_signs ideal model delta sigma weight residual False 2.53 1.72 0.80 2.00e-01 2.50e+01 1.61e+01 chirality pdb=" CB THR P 261 " pdb=" CA THR P 261 " pdb=" OG1 THR P 261 " pdb=" CG2 THR P 261 " both_signs ideal model delta sigma weight residual False 2.55 2.24 0.32 2.00e-01 2.50e+01 2.48e+00 chirality pdb=" CB VAL P 259 " pdb=" CA VAL P 259 " pdb=" CG1 VAL P 259 " pdb=" CG2 VAL P 259 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.57e+00 ... (remaining 690 not shown) Planarity restraints: 764 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP P 235 " 0.028 5.00e-02 4.00e+02 4.29e-02 2.95e+00 pdb=" N PRO P 236 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO P 236 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO P 236 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG P 47 " -0.021 5.00e-02 4.00e+02 3.21e-02 1.65e+00 pdb=" N PRO P 48 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO P 48 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO P 48 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE P 269 " 0.007 2.00e-02 2.50e+03 9.62e-03 1.62e+00 pdb=" CG PHE P 269 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 PHE P 269 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE P 269 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE P 269 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE P 269 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE P 269 " -0.001 2.00e-02 2.50e+03 ... (remaining 761 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 77 2.66 - 3.22: 4170 3.22 - 3.78: 6492 3.78 - 4.34: 9068 4.34 - 4.90: 15515 Nonbonded interactions: 35322 Sorted by model distance: nonbonded pdb=" OH TYR P 134 " pdb=" OD1 ASP P 205 " model vdw 2.097 2.440 nonbonded pdb=" OE1 GLN B 6 " pdb=" OG1 THR B 102 " model vdw 2.169 2.440 nonbonded pdb=" NH2 ARG A 68 " pdb=" OD2 ASP A 91 " model vdw 2.181 2.520 nonbonded pdb=" OG1 THR A 40 " pdb=" O GLU A 42 " model vdw 2.183 2.440 nonbonded pdb=" OG1 THR A 28 " pdb=" OD1 ASN A 31 " model vdw 2.234 2.440 ... (remaining 35317 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.110 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: 5.690 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 17.000 Find NCS groups from input model: 0.120 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: 0.010 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 26.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 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 : 0.006 0.045 4490 Z= 0.380 Angle : 0.711 7.709 6122 Z= 0.405 Chirality : 0.058 0.803 693 Planarity : 0.004 0.043 764 Dihedral : 13.839 89.198 1557 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 0.41 % Allowed : 7.47 % Favored : 92.12 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 4.17 % 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: -2.92 (0.31), residues: 547 helix: -0.87 (0.31), residues: 199 sheet: -2.01 (0.38), residues: 149 loop : -2.84 (0.38), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP P 132 HIS 0.007 0.001 HIS B 55 PHE 0.022 0.001 PHE P 269 TYR 0.013 0.001 TYR A 100 ARG 0.006 0.001 ARG P 112 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 61 time to evaluate : 0.496 Fit side-chains TARDY: cannot create tardy model for: "ASP B 30 " (corrupted residue). Skipping it. REVERT: A 19 LYS cc_start: 0.8201 (tttp) cc_final: 0.7871 (tttm) REVERT: B 79 GLN cc_start: 0.8490 (mm-40) cc_final: 0.8218 (mt0) REVERT: P 140 ILE cc_start: 0.7610 (tt) cc_final: 0.7170 (tp) REVERT: P 223 CYS cc_start: 0.7044 (p) cc_final: 0.6765 (p) outliers start: 2 outliers final: 0 residues processed: 63 average time/residue: 0.1748 time to fit residues: 14.0255 Evaluate side-chains 56 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 0.5980 chunk 40 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 42 optimal weight: 0.5980 chunk 16 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 49 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 3 GLN B 28 ASN P 222 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.0904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4490 Z= 0.211 Angle : 0.565 6.557 6122 Z= 0.294 Chirality : 0.045 0.168 693 Planarity : 0.004 0.038 764 Dihedral : 4.845 18.837 596 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 2.07 % Allowed : 13.28 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -1.55 (0.34), residues: 547 helix: 0.83 (0.35), residues: 197 sheet: -1.59 (0.42), residues: 140 loop : -2.40 (0.37), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP P 262 HIS 0.002 0.001 HIS B 55 PHE 0.017 0.001 PHE P 269 TYR 0.018 0.001 TYR P 134 ARG 0.006 0.001 ARG A 66 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 58 time to evaluate : 0.494 Fit side-chains TARDY: cannot create tardy model for: "ASP B 30 " (corrupted residue). Skipping it. REVERT: A 19 LYS cc_start: 0.8156 (tttp) cc_final: 0.7907 (tttm) REVERT: B 79 GLN cc_start: 0.8366 (mm-40) cc_final: 0.8153 (mt0) REVERT: P 140 ILE cc_start: 0.7564 (tt) cc_final: 0.7130 (tp) REVERT: P 223 CYS cc_start: 0.6956 (p) cc_final: 0.6598 (p) REVERT: P 269 PHE cc_start: 0.7196 (OUTLIER) cc_final: 0.6711 (m-80) outliers start: 10 outliers final: 6 residues processed: 64 average time/residue: 0.1633 time to fit residues: 13.4017 Evaluate side-chains 62 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 55 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 68 ARG Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 134 TYR Chi-restraints excluded: chain P residue 201 VAL Chi-restraints excluded: chain P residue 269 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 27 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 13 optimal weight: 0.0970 chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 chunk 16 optimal weight: 0.0270 chunk 39 optimal weight: 0.5980 overall best weight: 0.4436 ------------------------------------------------------------------------------- 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: 0.7832 moved from start: 0.1268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4490 Z= 0.173 Angle : 0.534 5.915 6122 Z= 0.277 Chirality : 0.044 0.145 693 Planarity : 0.003 0.034 764 Dihedral : 4.645 18.458 596 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 2.49 % Allowed : 16.39 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.35), residues: 547 helix: 1.48 (0.36), residues: 197 sheet: -1.22 (0.44), residues: 136 loop : -2.10 (0.38), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP P 132 HIS 0.001 0.000 HIS B 55 PHE 0.017 0.001 PHE A 69 TYR 0.015 0.001 TYR P 134 ARG 0.004 0.000 ARG A 66 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 55 time to evaluate : 0.507 Fit side-chains TARDY: cannot create tardy model for: "ASP B 30 " (corrupted residue). Skipping it. REVERT: A 19 LYS cc_start: 0.8187 (tttp) cc_final: 0.7980 (tttm) REVERT: P 140 ILE cc_start: 0.7564 (tt) cc_final: 0.7127 (tp) REVERT: P 269 PHE cc_start: 0.7180 (OUTLIER) cc_final: 0.6754 (m-80) outliers start: 12 outliers final: 7 residues processed: 62 average time/residue: 0.1710 time to fit residues: 13.8243 Evaluate side-chains 61 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 53 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 68 ARG Chi-restraints excluded: chain B residue 42 ASP Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 134 TYR Chi-restraints excluded: chain P residue 201 VAL Chi-restraints excluded: chain P residue 269 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 48 optimal weight: 8.9990 chunk 36 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 49 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.1191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 4490 Z= 0.307 Angle : 0.592 7.275 6122 Z= 0.304 Chirality : 0.046 0.153 693 Planarity : 0.004 0.033 764 Dihedral : 4.847 18.938 596 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 3.32 % Allowed : 16.39 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.36), residues: 547 helix: 1.50 (0.36), residues: 197 sheet: -1.34 (0.41), residues: 157 loop : -2.04 (0.41), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP P 132 HIS 0.002 0.001 HIS B 55 PHE 0.021 0.001 PHE A 69 TYR 0.019 0.001 TYR P 134 ARG 0.005 0.000 ARG A 66 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 52 time to evaluate : 0.492 Fit side-chains TARDY: cannot create tardy model for: "ASP B 30 " (corrupted residue). Skipping it. REVERT: P 140 ILE cc_start: 0.7525 (tt) cc_final: 0.7107 (tp) REVERT: P 269 PHE cc_start: 0.7421 (OUTLIER) cc_final: 0.6795 (m-80) outliers start: 16 outliers final: 10 residues processed: 63 average time/residue: 0.1626 time to fit residues: 13.3189 Evaluate side-chains 62 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 51 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 68 ARG Chi-restraints excluded: chain B residue 42 ASP Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 69 ILE Chi-restraints excluded: chain P residue 134 TYR Chi-restraints excluded: chain P residue 201 VAL Chi-restraints excluded: chain P residue 269 PHE Chi-restraints excluded: chain P residue 282 PHE Chi-restraints excluded: chain P residue 330 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 44 optimal weight: 0.6980 chunk 36 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 46 optimal weight: 0.6980 chunk 13 optimal weight: 0.3980 chunk 17 optimal weight: 0.6980 chunk 47 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 3 GLN B 5 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4490 Z= 0.204 Angle : 0.547 8.244 6122 Z= 0.280 Chirality : 0.044 0.146 693 Planarity : 0.003 0.032 764 Dihedral : 4.687 18.743 596 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 3.73 % Allowed : 16.60 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.36), residues: 547 helix: 1.73 (0.36), residues: 197 sheet: -1.11 (0.45), residues: 137 loop : -1.82 (0.39), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP P 132 HIS 0.002 0.001 HIS B 55 PHE 0.016 0.001 PHE A 69 TYR 0.015 0.001 TYR P 134 ARG 0.005 0.000 ARG A 66 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 54 time to evaluate : 0.500 Fit side-chains TARDY: cannot create tardy model for: "ASP B 30 " (corrupted residue). Skipping it. REVERT: A 19 LYS cc_start: 0.8292 (tttp) cc_final: 0.7969 (tttm) REVERT: P 140 ILE cc_start: 0.7505 (tt) cc_final: 0.7063 (tp) REVERT: P 180 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.7851 (mp) REVERT: P 269 PHE cc_start: 0.7210 (OUTLIER) cc_final: 0.6736 (m-80) outliers start: 18 outliers final: 9 residues processed: 67 average time/residue: 0.1652 time to fit residues: 14.2639 Evaluate side-chains 63 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 52 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 69 ILE Chi-restraints excluded: chain P residue 82 VAL Chi-restraints excluded: chain P residue 134 TYR Chi-restraints excluded: chain P residue 180 LEU Chi-restraints excluded: chain P residue 201 VAL Chi-restraints excluded: chain P residue 269 PHE Chi-restraints excluded: chain P residue 282 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 10 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 chunk 43 optimal weight: 0.4980 chunk 24 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 17 optimal weight: 7.9990 chunk 27 optimal weight: 0.3980 chunk 50 optimal weight: 0.9980 chunk 5 optimal weight: 0.2980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 3 GLN B 5 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4490 Z= 0.203 Angle : 0.546 8.640 6122 Z= 0.279 Chirality : 0.044 0.146 693 Planarity : 0.003 0.031 764 Dihedral : 4.653 18.704 596 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 3.32 % Allowed : 17.84 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.36), residues: 547 helix: 1.81 (0.37), residues: 197 sheet: -1.23 (0.44), residues: 146 loop : -1.67 (0.41), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP P 235 HIS 0.001 0.000 HIS B 55 PHE 0.035 0.001 PHE A 69 TYR 0.016 0.001 TYR P 134 ARG 0.005 0.000 ARG A 66 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 54 time to evaluate : 0.457 Fit side-chains TARDY: cannot create tardy model for: "ASP B 30 " (corrupted residue). Skipping it. REVERT: A 19 LYS cc_start: 0.8323 (tttp) cc_final: 0.8022 (tttm) REVERT: B 3 GLN cc_start: 0.7624 (OUTLIER) cc_final: 0.6675 (tm130) REVERT: P 140 ILE cc_start: 0.7511 (tt) cc_final: 0.7065 (tp) REVERT: P 180 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.7884 (mp) REVERT: P 269 PHE cc_start: 0.7216 (OUTLIER) cc_final: 0.6743 (m-80) outliers start: 16 outliers final: 9 residues processed: 67 average time/residue: 0.1538 time to fit residues: 13.5678 Evaluate side-chains 64 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 52 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 69 ILE Chi-restraints excluded: chain P residue 82 VAL Chi-restraints excluded: chain P residue 134 TYR Chi-restraints excluded: chain P residue 180 LEU Chi-restraints excluded: chain P residue 201 VAL Chi-restraints excluded: chain P residue 269 PHE Chi-restraints excluded: chain P residue 282 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 52 optimal weight: 0.9990 chunk 32 optimal weight: 0.1980 chunk 31 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 3 GLN B 5 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 4490 Z= 0.237 Angle : 0.559 9.113 6122 Z= 0.286 Chirality : 0.044 0.147 693 Planarity : 0.003 0.030 764 Dihedral : 4.713 18.835 596 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 3.32 % Allowed : 19.50 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.36), residues: 547 helix: 1.74 (0.36), residues: 199 sheet: -1.26 (0.44), residues: 146 loop : -1.63 (0.42), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP P 235 HIS 0.001 0.001 HIS B 55 PHE 0.020 0.001 PHE A 69 TYR 0.016 0.001 TYR P 134 ARG 0.005 0.000 ARG A 66 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 54 time to evaluate : 0.534 Fit side-chains TARDY: cannot create tardy model for: "ASP B 30 " (corrupted residue). Skipping it. REVERT: A 19 LYS cc_start: 0.8342 (tttp) cc_final: 0.8035 (tttm) REVERT: P 140 ILE cc_start: 0.7521 (tt) cc_final: 0.7076 (tp) REVERT: P 180 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.7875 (mp) REVERT: P 269 PHE cc_start: 0.7264 (OUTLIER) cc_final: 0.6745 (m-80) outliers start: 16 outliers final: 10 residues processed: 65 average time/residue: 0.1551 time to fit residues: 13.2591 Evaluate side-chains 65 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 53 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain B residue 5 ASN Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 69 ILE Chi-restraints excluded: chain P residue 82 VAL Chi-restraints excluded: chain P residue 134 TYR Chi-restraints excluded: chain P residue 180 LEU Chi-restraints excluded: chain P residue 201 VAL Chi-restraints excluded: chain P residue 269 PHE Chi-restraints excluded: chain P residue 282 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 35 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 chunk 47 optimal weight: 8.9990 chunk 49 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 29 optimal weight: 0.0020 chunk 21 optimal weight: 0.2980 chunk 38 optimal weight: 0.4980 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 5 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4490 Z= 0.186 Angle : 0.540 9.655 6122 Z= 0.276 Chirality : 0.043 0.145 693 Planarity : 0.003 0.029 764 Dihedral : 4.649 18.766 596 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 2.90 % Allowed : 20.12 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.36), residues: 547 helix: 1.84 (0.36), residues: 199 sheet: -1.17 (0.44), residues: 142 loop : -1.63 (0.41), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP P 235 HIS 0.001 0.000 HIS B 55 PHE 0.016 0.001 PHE A 69 TYR 0.015 0.001 TYR P 134 ARG 0.004 0.000 ARG A 66 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 55 time to evaluate : 0.518 Fit side-chains TARDY: cannot create tardy model for: "ASP B 30 " (corrupted residue). Skipping it. REVERT: A 19 LYS cc_start: 0.8372 (tttp) cc_final: 0.8034 (tttm) REVERT: P 67 ILE cc_start: 0.7569 (OUTLIER) cc_final: 0.6947 (tp) REVERT: P 140 ILE cc_start: 0.7490 (tt) cc_final: 0.7040 (tp) REVERT: P 180 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.7865 (mp) REVERT: P 269 PHE cc_start: 0.7183 (OUTLIER) cc_final: 0.6732 (m-80) outliers start: 14 outliers final: 10 residues processed: 65 average time/residue: 0.1549 time to fit residues: 13.3322 Evaluate side-chains 67 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 54 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain B residue 5 ASN Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 67 ILE Chi-restraints excluded: chain P residue 69 ILE Chi-restraints excluded: chain P residue 82 VAL Chi-restraints excluded: chain P residue 134 TYR Chi-restraints excluded: chain P residue 180 LEU Chi-restraints excluded: chain P residue 201 VAL Chi-restraints excluded: chain P residue 269 PHE Chi-restraints excluded: chain P residue 282 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 14 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 48 optimal weight: 8.9990 chunk 31 optimal weight: 1.9990 chunk 51 optimal weight: 0.0270 chunk 24 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 chunk 49 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 5 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4490 Z= 0.205 Angle : 0.554 10.122 6122 Z= 0.283 Chirality : 0.044 0.145 693 Planarity : 0.003 0.029 764 Dihedral : 4.622 18.734 596 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 2.90 % Allowed : 20.12 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.36), residues: 547 helix: 1.85 (0.36), residues: 199 sheet: -1.21 (0.44), residues: 142 loop : -1.59 (0.42), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP P 235 HIS 0.001 0.000 HIS B 55 PHE 0.018 0.001 PHE A 69 TYR 0.015 0.001 TYR P 134 ARG 0.003 0.000 ARG A 66 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 53 time to evaluate : 0.500 Fit side-chains TARDY: cannot create tardy model for: "ASP B 30 " (corrupted residue). Skipping it. REVERT: A 19 LYS cc_start: 0.8409 (tttp) cc_final: 0.8091 (tttm) REVERT: P 67 ILE cc_start: 0.7554 (OUTLIER) cc_final: 0.6944 (tp) REVERT: P 140 ILE cc_start: 0.7492 (tt) cc_final: 0.7042 (tp) REVERT: P 180 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.7882 (mp) REVERT: P 269 PHE cc_start: 0.7213 (OUTLIER) cc_final: 0.6739 (m-80) outliers start: 14 outliers final: 10 residues processed: 63 average time/residue: 0.1502 time to fit residues: 12.4541 Evaluate side-chains 66 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 53 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain B residue 5 ASN Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 67 ILE Chi-restraints excluded: chain P residue 69 ILE Chi-restraints excluded: chain P residue 82 VAL Chi-restraints excluded: chain P residue 134 TYR Chi-restraints excluded: chain P residue 180 LEU Chi-restraints excluded: chain P residue 201 VAL Chi-restraints excluded: chain P residue 269 PHE Chi-restraints excluded: chain P residue 282 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 4 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 26 optimal weight: 0.2980 chunk 34 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 42 optimal weight: 0.0980 chunk 17 optimal weight: 2.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 5 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4490 Z= 0.199 Angle : 0.552 10.558 6122 Z= 0.281 Chirality : 0.044 0.145 693 Planarity : 0.003 0.029 764 Dihedral : 4.612 18.731 596 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 2.70 % Allowed : 20.54 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.37), residues: 547 helix: 1.89 (0.36), residues: 199 sheet: -1.22 (0.44), residues: 142 loop : -1.53 (0.42), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP P 235 HIS 0.001 0.000 HIS B 55 PHE 0.017 0.001 PHE A 69 TYR 0.015 0.001 TYR P 134 ARG 0.004 0.000 ARG A 66 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1094 Ramachandran restraints generated. 547 Oldfield, 0 Emsley, 547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 53 time to evaluate : 0.533 Fit side-chains TARDY: cannot create tardy model for: "ASP B 30 " (corrupted residue). Skipping it. REVERT: A 19 LYS cc_start: 0.8404 (tttp) cc_final: 0.8069 (tttm) REVERT: P 67 ILE cc_start: 0.7524 (OUTLIER) cc_final: 0.6934 (tp) REVERT: P 140 ILE cc_start: 0.7485 (tt) cc_final: 0.7033 (tp) REVERT: P 180 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.7874 (mp) REVERT: P 269 PHE cc_start: 0.7205 (OUTLIER) cc_final: 0.6740 (m-80) outliers start: 13 outliers final: 10 residues processed: 62 average time/residue: 0.1531 time to fit residues: 12.3675 Evaluate side-chains 66 residues out of total 482 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 53 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain B residue 5 ASN Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 67 ILE Chi-restraints excluded: chain P residue 69 ILE Chi-restraints excluded: chain P residue 82 VAL Chi-restraints excluded: chain P residue 134 TYR Chi-restraints excluded: chain P residue 180 LEU Chi-restraints excluded: chain P residue 201 VAL Chi-restraints excluded: chain P residue 269 PHE Chi-restraints excluded: chain P residue 282 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 44 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 37 optimal weight: 0.2980 chunk 2 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 1 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 5 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.171980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.132905 restraints weight = 4897.125| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 2.31 r_work: 0.3434 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 4490 Z= 0.236 Angle : 0.567 10.951 6122 Z= 0.288 Chirality : 0.045 0.147 693 Planarity : 0.003 0.029 764 Dihedral : 4.645 18.790 596 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 2.70 % Allowed : 20.54 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.36), residues: 547 helix: 1.83 (0.36), residues: 199 sheet: -1.27 (0.43), residues: 142 loop : -1.53 (0.42), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP P 235 HIS 0.001 0.001 HIS B 55 PHE 0.016 0.001 PHE A 69 TYR 0.017 0.001 TYR P 134 ARG 0.004 0.000 ARG A 66 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1349.40 seconds wall clock time: 24 minutes 58.90 seconds (1498.90 seconds total)