Starting phenix.real_space_refine on Sun Mar 10 17:43:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n8i_24237/03_2024/7n8i_24237.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n8i_24237/03_2024/7n8i_24237.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n8i_24237/03_2024/7n8i_24237.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n8i_24237/03_2024/7n8i_24237.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n8i_24237/03_2024/7n8i_24237.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n8i_24237/03_2024/7n8i_24237.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.053 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 13 5.16 5 C 2315 2.51 5 N 581 2.21 5 O 691 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "L TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 1": "OE1" <-> "OE2" Residue "H PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 46": "OE1" <-> "OE2" Residue "H TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 87": "NH1" <-> "NH2" Residue "H TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 101": "OD1" <-> "OD2" Residue "H TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 237": "NH1" <-> "NH2" Residue "A PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 3600 Number of models: 1 Model: "" Number of chains: 3 Chain: "L" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 823 Classifications: {'peptide': 106} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 98} Chain: "H" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 948 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "A" Number of atoms: 1829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1829 Unusual residues: {'NAG': 5} Classifications: {'peptide': 218, 'undetermined': 5} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 206, None: 5} Not linked: pdbres="PHE A 306 " pdbres="NAG A1301 " Not linked: pdbres="NAG A1301 " pdbres="NAG A1302 " Not linked: pdbres="NAG A1302 " pdbres="NAG A1303 " Not linked: pdbres="NAG A1303 " pdbres="NAG A1304 " Not linked: pdbres="NAG A1304 " pdbres="NAG A1305 " Chain breaks: 4 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 2.47, per 1000 atoms: 0.69 Number of scatterers: 3600 At special positions: 0 Unit cell: (56.481, 85.143, 75.87, 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 13 16.00 O 691 8.00 N 581 7.00 C 2315 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.02 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 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 Links applied NAG-ASN " NAG A1301 " - " ASN A 122 " " NAG A1302 " - " ASN A 61 " " NAG A1303 " - " ASN A 234 " " NAG A1304 " - " ASN A 165 " " NAG A1305 " - " ASN A 282 " Time building additional restraints: 1.26 Conformation dependent library (CDL) restraints added in 796.8 milliseconds 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 826 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 9 sheets defined 5.6% alpha, 47.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.867A pdb=" N ILE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'A' and resid 294 through 303 Processing sheet with id=AA1, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.910A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER L 67 " --> pdb=" O ASP L 70 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.381A pdb=" N LEU L 33 " --> pdb=" O SER L 49 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N SER L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.609A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.625A pdb=" N MET H 34 " --> pdb=" O PHE H 50 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N PHE H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 10 through 12 Processing sheet with id=AA7, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.944A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 47 through 55 removed outlier: 7.356A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.090A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N VAL A 126 " --> pdb=" O TYR A 170 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N TYR A 170 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE A 128 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASN A 164 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) 154 hydrogen bonds defined for protein. 369 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: 1.28 Time building geometry restraints manager: 1.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 593 1.31 - 1.44: 1076 1.44 - 1.57: 1999 1.57 - 1.69: 6 1.69 - 1.82: 17 Bond restraints: 3691 Sorted by residual: bond pdb=" CA SER A 31 " pdb=" CB SER A 31 " ideal model delta sigma weight residual 1.530 1.477 0.053 1.69e-02 3.50e+03 9.89e+00 bond pdb=" C5 NAG A1304 " pdb=" O5 NAG A1304 " ideal model delta sigma weight residual 1.413 1.470 -0.057 2.00e-02 2.50e+03 8.23e+00 bond pdb=" N VAL A 159 " pdb=" CA VAL A 159 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.32e-02 5.74e+03 7.45e+00 bond pdb=" C5 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.413 1.468 -0.055 2.00e-02 2.50e+03 7.45e+00 bond pdb=" CB LEU A 176 " pdb=" CG LEU A 176 " ideal model delta sigma weight residual 1.530 1.585 -0.055 2.00e-02 2.50e+03 7.43e+00 ... (remaining 3686 not shown) Histogram of bond angle deviations from ideal: 100.74 - 107.39: 118 107.39 - 114.05: 1964 114.05 - 120.70: 1621 120.70 - 127.36: 1285 127.36 - 134.01: 23 Bond angle restraints: 5011 Sorted by residual: angle pdb=" C ASN A 81 " pdb=" N PRO A 82 " pdb=" CA PRO A 82 " ideal model delta sigma weight residual 120.03 127.12 -7.09 9.90e-01 1.02e+00 5.13e+01 angle pdb=" C GLY L 99 " pdb=" N PRO L 100 " pdb=" CA PRO L 100 " ideal model delta sigma weight residual 119.32 127.42 -8.10 1.14e+00 7.69e-01 5.05e+01 angle pdb=" C TYR A 38 " pdb=" N PRO A 39 " pdb=" CA PRO A 39 " ideal model delta sigma weight residual 119.56 126.33 -6.77 1.01e+00 9.80e-01 4.49e+01 angle pdb=" C LEU A 216 " pdb=" N PRO A 217 " pdb=" CA PRO A 217 " ideal model delta sigma weight residual 119.85 126.54 -6.69 1.01e+00 9.80e-01 4.39e+01 angle pdb=" C ALA L 43 " pdb=" N PRO L 44 " pdb=" CA PRO L 44 " ideal model delta sigma weight residual 119.76 126.55 -6.79 1.03e+00 9.43e-01 4.35e+01 ... (remaining 5006 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.43: 2112 16.43 - 32.86: 78 32.86 - 49.29: 13 49.29 - 65.72: 10 65.72 - 82.14: 4 Dihedral angle restraints: 2217 sinusoidal: 925 harmonic: 1292 Sorted by residual: dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " pdb=" CB CYS H 96 " ideal model delta sinusoidal sigma weight residual 93.00 52.69 40.31 1 1.00e+01 1.00e-02 2.28e+01 dihedral pdb=" CA ASN A 165 " pdb=" CB ASN A 165 " pdb=" CG ASN A 165 " pdb=" OD1 ASN A 165 " ideal model delta sinusoidal sigma weight residual 120.00 -168.17 -71.83 2 2.00e+01 2.50e-03 1.08e+01 dihedral pdb=" CA HIS H 35 " pdb=" C HIS H 35 " pdb=" N TRP H 36 " pdb=" CA TRP H 36 " ideal model delta harmonic sigma weight residual 180.00 164.29 15.71 0 5.00e+00 4.00e-02 9.87e+00 ... (remaining 2214 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 397 0.064 - 0.127: 121 0.127 - 0.190: 27 0.190 - 0.254: 10 0.254 - 0.317: 6 Chirality restraints: 561 Sorted by residual: chirality pdb=" C2 NAG A1303 " pdb=" C1 NAG A1303 " pdb=" C3 NAG A1303 " pdb=" N2 NAG A1303 " both_signs ideal model delta sigma weight residual False -2.49 -2.81 0.32 2.00e-01 2.50e+01 2.52e+00 chirality pdb=" C2 NAG A1305 " pdb=" C1 NAG A1305 " pdb=" C3 NAG A1305 " pdb=" N2 NAG A1305 " both_signs ideal model delta sigma weight residual False -2.49 -2.79 0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" C2 NAG A1301 " pdb=" C1 NAG A1301 " pdb=" C3 NAG A1301 " pdb=" N2 NAG A1301 " both_signs ideal model delta sigma weight residual False -2.49 -2.79 0.30 2.00e-01 2.50e+01 2.26e+00 ... (remaining 558 not shown) Planarity restraints: 636 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 165 " 0.026 2.00e-02 2.50e+03 2.66e-02 8.86e+00 pdb=" CG ASN A 165 " -0.013 2.00e-02 2.50e+03 pdb=" OD1 ASN A 165 " -0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN A 165 " -0.040 2.00e-02 2.50e+03 pdb=" C1 NAG A1304 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP L 28 " -0.014 2.00e-02 2.50e+03 2.88e-02 8.27e+00 pdb=" C ASP L 28 " 0.050 2.00e-02 2.50e+03 pdb=" O ASP L 28 " -0.019 2.00e-02 2.50e+03 pdb=" N ILE L 29 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER L 7 " -0.014 2.00e-02 2.50e+03 2.64e-02 6.97e+00 pdb=" C SER L 7 " 0.046 2.00e-02 2.50e+03 pdb=" O SER L 7 " -0.016 2.00e-02 2.50e+03 pdb=" N PRO L 8 " -0.015 2.00e-02 2.50e+03 ... (remaining 633 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 1070 2.83 - 3.35: 2861 3.35 - 3.86: 5945 3.86 - 4.38: 7279 4.38 - 4.90: 12391 Nonbonded interactions: 29546 Sorted by model distance: nonbonded pdb=" O SER A 31 " pdb=" OG SER A 31 " model vdw 2.309 2.440 nonbonded pdb=" OD2 ASP H 73 " pdb=" NZ LYS H 76 " model vdw 2.532 2.520 nonbonded pdb=" N ASP H 54 " pdb=" N GLY H 55 " model vdw 2.566 2.560 nonbonded pdb=" OD1 ASN A 165 " pdb=" O5 NAG A1304 " model vdw 2.597 3.040 nonbonded pdb=" OG1 THR A 108 " pdb=" N THR A 109 " model vdw 2.610 2.520 ... (remaining 29541 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: 16.210 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: 26.080 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.050 Find NCS groups from input model: 0.100 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:12.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.057 3691 Z= 0.694 Angle : 1.232 8.102 5011 Z= 0.830 Chirality : 0.074 0.317 561 Planarity : 0.006 0.029 631 Dihedral : 10.639 82.143 1379 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 0.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 0.26 % Allowed : 0.52 % Favored : 99.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.04 (0.40), residues: 431 helix: -1.13 (1.30), residues: 17 sheet: 1.05 (0.35), residues: 206 loop : 0.62 (0.44), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.005 TRP A 64 HIS 0.002 0.001 HIS A 66 PHE 0.015 0.003 PHE A 55 TYR 0.028 0.004 TYR H 104 ARG 0.003 0.001 ARG H 67 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 80 time to evaluate : 0.395 Fit side-chains REVERT: L 30 ARG cc_start: 0.8259 (mmm-85) cc_final: 0.8047 (mtm180) REVERT: L 81 GLU cc_start: 0.7524 (pm20) cc_final: 0.7197 (pm20) REVERT: H 34 MET cc_start: 0.9008 (mmm) cc_final: 0.8508 (mmm) outliers start: 1 outliers final: 0 residues processed: 80 average time/residue: 0.9768 time to fit residues: 80.9743 Evaluate side-chains 52 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 37 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 18 optimal weight: 0.1980 chunk 11 optimal weight: 1.9990 chunk 22 optimal weight: 0.0570 chunk 17 optimal weight: 0.0170 chunk 34 optimal weight: 0.1980 chunk 13 optimal weight: 0.0980 chunk 20 optimal weight: 0.3980 chunk 25 optimal weight: 0.6980 chunk 39 optimal weight: 0.1980 overall best weight: 0.1136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 57 ASN A 115 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 3691 Z= 0.141 Angle : 0.502 4.411 5011 Z= 0.267 Chirality : 0.044 0.160 561 Planarity : 0.004 0.033 631 Dihedral : 4.893 46.498 588 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.29 % Allowed : 9.54 % Favored : 89.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.45 (0.41), residues: 431 helix: 3.19 (1.68), residues: 11 sheet: 1.22 (0.35), residues: 212 loop : 0.70 (0.45), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 64 HIS 0.002 0.001 HIS H 35 PHE 0.009 0.001 PHE A 55 TYR 0.011 0.001 TYR A 170 ARG 0.002 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 62 time to evaluate : 0.413 Fit side-chains REVERT: L 30 ARG cc_start: 0.8280 (mmm-85) cc_final: 0.8054 (mtm180) REVERT: L 81 GLU cc_start: 0.7618 (pm20) cc_final: 0.7252 (pm20) REVERT: H 17 SER cc_start: 0.8858 (p) cc_final: 0.8592 (m) REVERT: A 129 LYS cc_start: 0.8445 (mtpp) cc_final: 0.8193 (mtmt) REVERT: A 190 ARG cc_start: 0.7972 (OUTLIER) cc_final: 0.7521 (mtm110) REVERT: A 304 LYS cc_start: 0.8401 (mmmt) cc_final: 0.8159 (mttt) outliers start: 5 outliers final: 3 residues processed: 65 average time/residue: 1.1205 time to fit residues: 75.3704 Evaluate side-chains 54 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 50 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 190 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 22 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 33 optimal weight: 0.0010 chunk 27 optimal weight: 0.9990 chunk 11 optimal weight: 0.0670 chunk 40 optimal weight: 0.2980 chunk 43 optimal weight: 0.4980 chunk 35 optimal weight: 0.9990 chunk 39 optimal weight: 0.0870 chunk 13 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 overall best weight: 0.1902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 38 GLN H 57 ASN A 115 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3691 Z= 0.176 Angle : 0.509 5.907 5011 Z= 0.264 Chirality : 0.044 0.144 561 Planarity : 0.003 0.032 631 Dihedral : 4.625 40.557 588 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.06 % Allowed : 9.28 % Favored : 88.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.52 (0.42), residues: 431 helix: 3.39 (1.74), residues: 11 sheet: 1.28 (0.35), residues: 212 loop : 0.70 (0.47), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 64 HIS 0.002 0.001 HIS A 49 PHE 0.010 0.001 PHE A 133 TYR 0.011 0.001 TYR H 95 ARG 0.002 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 60 time to evaluate : 0.362 Fit side-chains REVERT: L 30 ARG cc_start: 0.8285 (mmm-85) cc_final: 0.8045 (mtm180) REVERT: L 42 LYS cc_start: 0.8522 (mptt) cc_final: 0.8279 (mmtm) REVERT: H 17 SER cc_start: 0.8885 (p) cc_final: 0.8633 (m) REVERT: A 129 LYS cc_start: 0.8610 (mtpp) cc_final: 0.8267 (mtmt) REVERT: A 190 ARG cc_start: 0.7980 (OUTLIER) cc_final: 0.7539 (mtm110) REVERT: A 205 SER cc_start: 0.8833 (p) cc_final: 0.8592 (t) REVERT: A 287 ASP cc_start: 0.8393 (OUTLIER) cc_final: 0.8107 (t0) outliers start: 8 outliers final: 3 residues processed: 64 average time/residue: 1.2323 time to fit residues: 81.3152 Evaluate side-chains 59 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 54 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 287 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 39 optimal weight: 0.6980 chunk 30 optimal weight: 0.1980 chunk 20 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 26 optimal weight: 0.0970 chunk 40 optimal weight: 0.5980 chunk 42 optimal weight: 0.3980 chunk 38 optimal weight: 0.0050 chunk 11 optimal weight: 0.0370 chunk 35 optimal weight: 0.9980 overall best weight: 0.1470 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A 188 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 3691 Z= 0.144 Angle : 0.471 5.760 5011 Z= 0.245 Chirality : 0.043 0.135 561 Planarity : 0.003 0.034 631 Dihedral : 4.365 36.205 588 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.55 % Allowed : 10.05 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.58 (0.42), residues: 431 helix: 3.25 (1.72), residues: 11 sheet: 1.46 (0.35), residues: 207 loop : 0.61 (0.46), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 64 HIS 0.002 0.001 HIS H 35 PHE 0.009 0.001 PHE A 133 TYR 0.011 0.001 TYR A 170 ARG 0.001 0.000 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 53 time to evaluate : 0.396 Fit side-chains REVERT: L 30 ARG cc_start: 0.8294 (mmm-85) cc_final: 0.8036 (mtm180) REVERT: H 17 SER cc_start: 0.8852 (p) cc_final: 0.8605 (m) REVERT: A 102 ARG cc_start: 0.7681 (mtm110) cc_final: 0.7430 (mtp85) REVERT: A 129 LYS cc_start: 0.8591 (mtpp) cc_final: 0.8232 (mtmt) REVERT: A 190 ARG cc_start: 0.7958 (OUTLIER) cc_final: 0.7529 (mtm110) REVERT: A 304 LYS cc_start: 0.8430 (mmmt) cc_final: 0.8227 (mttt) outliers start: 6 outliers final: 4 residues processed: 56 average time/residue: 1.2363 time to fit residues: 71.4897 Evaluate side-chains 55 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 50 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 206 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 0.9990 chunk 0 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 36 optimal weight: 0.0970 chunk 29 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.086 3691 Z= 0.551 Angle : 0.695 10.438 5011 Z= 0.349 Chirality : 0.052 0.163 561 Planarity : 0.005 0.036 631 Dihedral : 5.729 40.917 588 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.32 % Allowed : 11.60 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.20 (0.41), residues: 431 helix: 3.30 (1.78), residues: 11 sheet: 1.33 (0.36), residues: 199 loop : 0.23 (0.42), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP H 47 HIS 0.003 0.002 HIS A 49 PHE 0.017 0.003 PHE A 133 TYR 0.017 0.002 TYR A 279 ARG 0.003 0.001 ARG H 67 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 54 time to evaluate : 0.401 Fit side-chains REVERT: L 30 ARG cc_start: 0.8347 (mmm-85) cc_final: 0.8089 (mtm180) REVERT: L 93 ASN cc_start: 0.8589 (p0) cc_final: 0.8308 (p0) REVERT: H 13 GLN cc_start: 0.8322 (mm110) cc_final: 0.8103 (mm110) REVERT: H 17 SER cc_start: 0.8887 (p) cc_final: 0.8677 (m) REVERT: H 114 GLN cc_start: 0.8153 (OUTLIER) cc_final: 0.7356 (pm20) REVERT: A 102 ARG cc_start: 0.7895 (mtm110) cc_final: 0.7650 (mtp85) REVERT: A 129 LYS cc_start: 0.8597 (mtpp) cc_final: 0.8268 (mtmt) REVERT: A 134 GLN cc_start: 0.8737 (tp40) cc_final: 0.8530 (tp-100) outliers start: 9 outliers final: 5 residues processed: 58 average time/residue: 1.2432 time to fit residues: 74.4760 Evaluate side-chains 56 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 50 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain H residue 114 GLN Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 206 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 0.2980 chunk 10 optimal weight: 0.9980 chunk 42 optimal weight: 0.2980 chunk 35 optimal weight: 0.0980 chunk 19 optimal weight: 0.2980 chunk 3 optimal weight: 0.0970 chunk 14 optimal weight: 0.3980 chunk 22 optimal weight: 0.5980 chunk 41 optimal weight: 0.1980 chunk 4 optimal weight: 0.0970 chunk 31 optimal weight: 0.0870 overall best weight: 0.1154 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 3691 Z= 0.128 Angle : 0.468 6.238 5011 Z= 0.243 Chirality : 0.043 0.131 561 Planarity : 0.004 0.034 631 Dihedral : 4.537 35.843 588 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.55 % Allowed : 12.37 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.31 (0.42), residues: 431 helix: 3.08 (1.70), residues: 11 sheet: 1.34 (0.36), residues: 207 loop : 0.35 (0.46), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 64 HIS 0.002 0.001 HIS H 35 PHE 0.009 0.001 PHE A 133 TYR 0.011 0.001 TYR A 170 ARG 0.001 0.000 ARG A 190 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 54 time to evaluate : 0.413 Fit side-chains REVERT: L 30 ARG cc_start: 0.8303 (mmm-85) cc_final: 0.8058 (mtm180) REVERT: H 17 SER cc_start: 0.8819 (p) cc_final: 0.8597 (m) REVERT: H 114 GLN cc_start: 0.8084 (OUTLIER) cc_final: 0.7359 (pm20) REVERT: A 129 LYS cc_start: 0.8538 (mtpp) cc_final: 0.8207 (mtmt) REVERT: A 190 ARG cc_start: 0.7875 (OUTLIER) cc_final: 0.7520 (mtm110) outliers start: 6 outliers final: 3 residues processed: 56 average time/residue: 1.2513 time to fit residues: 72.3273 Evaluate side-chains 58 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 53 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain H residue 114 GLN Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 206 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 chunk 26 optimal weight: 0.0670 chunk 25 optimal weight: 0.0770 chunk 19 optimal weight: 0.9990 chunk 16 optimal weight: 0.0010 chunk 12 optimal weight: 0.4980 chunk 8 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 overall best weight: 0.2482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 57 ASN A 115 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3691 Z= 0.211 Angle : 0.510 7.180 5011 Z= 0.262 Chirality : 0.045 0.139 561 Planarity : 0.004 0.035 631 Dihedral : 4.606 34.945 588 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.55 % Allowed : 12.37 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.29 (0.42), residues: 431 helix: 3.31 (1.74), residues: 11 sheet: 1.39 (0.37), residues: 195 loop : 0.32 (0.44), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 64 HIS 0.002 0.001 HIS A 49 PHE 0.011 0.001 PHE A 133 TYR 0.012 0.001 TYR H 95 ARG 0.001 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 55 time to evaluate : 0.368 Fit side-chains REVERT: L 30 ARG cc_start: 0.8310 (mmm-85) cc_final: 0.8034 (mtm180) REVERT: L 93 ASN cc_start: 0.8513 (p0) cc_final: 0.8237 (p0) REVERT: H 17 SER cc_start: 0.8831 (p) cc_final: 0.8614 (m) REVERT: H 114 GLN cc_start: 0.8113 (OUTLIER) cc_final: 0.7401 (pm20) REVERT: A 129 LYS cc_start: 0.8541 (mtpp) cc_final: 0.8219 (mtmt) outliers start: 6 outliers final: 4 residues processed: 58 average time/residue: 1.2349 time to fit residues: 74.0587 Evaluate side-chains 60 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 55 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain H residue 114 GLN Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 206 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 20 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 33 optimal weight: 0.0870 chunk 38 optimal weight: 0.7980 chunk 40 optimal weight: 0.3980 chunk 37 optimal weight: 1.9990 chunk 39 optimal weight: 0.4980 chunk 23 optimal weight: 0.1980 chunk 17 optimal weight: 0.9980 chunk 31 optimal weight: 0.3980 chunk 12 optimal weight: 0.5980 overall best weight: 0.3158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 57 ASN A 115 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3691 Z= 0.255 Angle : 0.539 7.374 5011 Z= 0.275 Chirality : 0.045 0.142 561 Planarity : 0.004 0.036 631 Dihedral : 4.766 34.808 588 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.55 % Allowed : 12.89 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.23 (0.42), residues: 431 helix: 3.34 (1.75), residues: 11 sheet: 1.37 (0.37), residues: 195 loop : 0.24 (0.44), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 47 HIS 0.002 0.001 HIS A 49 PHE 0.013 0.002 PHE A 133 TYR 0.012 0.001 TYR H 95 ARG 0.001 0.000 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 55 time to evaluate : 0.420 Fit side-chains REVERT: L 30 ARG cc_start: 0.8317 (mmm-85) cc_final: 0.8041 (mtm180) REVERT: L 93 ASN cc_start: 0.8528 (p0) cc_final: 0.8272 (p0) REVERT: H 17 SER cc_start: 0.8855 (p) cc_final: 0.8637 (m) REVERT: H 114 GLN cc_start: 0.8128 (OUTLIER) cc_final: 0.7382 (pm20) REVERT: A 129 LYS cc_start: 0.8545 (mtpp) cc_final: 0.8233 (mtmt) outliers start: 6 outliers final: 4 residues processed: 58 average time/residue: 1.2796 time to fit residues: 76.7050 Evaluate side-chains 60 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 55 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain H residue 114 GLN Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 206 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 35 optimal weight: 0.9980 chunk 37 optimal weight: 0.0870 chunk 39 optimal weight: 0.7980 chunk 25 optimal weight: 0.0060 chunk 41 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 43 optimal weight: 0.4980 chunk 40 optimal weight: 0.0980 chunk 34 optimal weight: 0.2980 chunk 3 optimal weight: 0.7980 overall best weight: 0.1974 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 57 ASN A 115 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3691 Z= 0.176 Angle : 0.494 6.924 5011 Z= 0.253 Chirality : 0.044 0.135 561 Planarity : 0.004 0.035 631 Dihedral : 4.430 32.156 588 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.29 % Allowed : 13.66 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.24 (0.42), residues: 431 helix: 3.10 (1.70), residues: 11 sheet: 1.37 (0.37), residues: 198 loop : 0.26 (0.44), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 47 HIS 0.002 0.001 HIS H 35 PHE 0.011 0.001 PHE A 133 TYR 0.011 0.001 TYR H 95 ARG 0.001 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 56 time to evaluate : 0.363 Fit side-chains REVERT: L 30 ARG cc_start: 0.8305 (mmm-85) cc_final: 0.8045 (mtm180) REVERT: L 93 ASN cc_start: 0.8514 (p0) cc_final: 0.8281 (p0) REVERT: H 17 SER cc_start: 0.8811 (p) cc_final: 0.8605 (m) REVERT: H 114 GLN cc_start: 0.8089 (OUTLIER) cc_final: 0.7366 (pm20) REVERT: A 129 LYS cc_start: 0.8549 (mtpp) cc_final: 0.8215 (mtmt) outliers start: 5 outliers final: 4 residues processed: 59 average time/residue: 1.1737 time to fit residues: 71.5397 Evaluate side-chains 60 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 55 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain H residue 114 GLN Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 206 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 26 optimal weight: 0.5980 chunk 21 optimal weight: 0.5980 chunk 27 optimal weight: 0.0870 chunk 37 optimal weight: 0.4980 chunk 10 optimal weight: 0.1980 chunk 32 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 9 optimal weight: 0.1980 chunk 34 optimal weight: 0.1980 chunk 14 optimal weight: 0.8980 chunk 35 optimal weight: 0.2980 overall best weight: 0.1958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 57 ASN A 115 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3691 Z= 0.177 Angle : 0.492 7.132 5011 Z= 0.252 Chirality : 0.044 0.137 561 Planarity : 0.004 0.035 631 Dihedral : 4.338 30.446 588 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.29 % Allowed : 13.92 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.28 (0.42), residues: 431 helix: 3.18 (1.72), residues: 11 sheet: 1.41 (0.37), residues: 198 loop : 0.27 (0.45), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 47 HIS 0.002 0.001 HIS H 35 PHE 0.011 0.001 PHE A 133 TYR 0.011 0.001 TYR H 95 ARG 0.001 0.000 ARG A 102 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 55 time to evaluate : 0.394 Fit side-chains REVERT: L 30 ARG cc_start: 0.8333 (mmm-85) cc_final: 0.8048 (mtm180) REVERT: L 42 LYS cc_start: 0.8549 (mptt) cc_final: 0.8168 (mmtm) REVERT: L 93 ASN cc_start: 0.8518 (p0) cc_final: 0.8285 (p0) REVERT: H 17 SER cc_start: 0.8811 (p) cc_final: 0.8603 (m) REVERT: H 114 GLN cc_start: 0.8106 (OUTLIER) cc_final: 0.7373 (pm20) REVERT: A 129 LYS cc_start: 0.8544 (mtpp) cc_final: 0.8214 (mtmt) outliers start: 5 outliers final: 4 residues processed: 58 average time/residue: 1.2444 time to fit residues: 74.5282 Evaluate side-chains 60 residues out of total 390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 55 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain H residue 114 GLN Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 206 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 4 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 40 optimal weight: 0.3980 chunk 23 optimal weight: 0.0670 chunk 29 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 57 ASN A 115 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.104891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.088315 restraints weight = 4261.694| |-----------------------------------------------------------------------------| r_work (start): 0.2848 rms_B_bonded: 1.44 r_work: 0.2740 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2615 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.2615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 3691 Z= 0.362 Angle : 0.585 8.026 5011 Z= 0.295 Chirality : 0.047 0.143 561 Planarity : 0.004 0.036 631 Dihedral : 4.926 32.937 588 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.29 % Allowed : 14.18 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.16 (0.42), residues: 431 helix: 3.37 (1.76), residues: 11 sheet: 1.35 (0.38), residues: 190 loop : 0.20 (0.43), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP H 47 HIS 0.002 0.001 HIS A 49 PHE 0.015 0.002 PHE A 133 TYR 0.013 0.002 TYR A 279 ARG 0.002 0.000 ARG A 102 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2322.82 seconds wall clock time: 41 minutes 50.66 seconds (2510.66 seconds total)