Starting phenix.real_space_refine on Mon Mar 11 09:01:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7spa_25370/03_2024/7spa_25370.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7spa_25370/03_2024/7spa_25370.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7spa_25370/03_2024/7spa_25370.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7spa_25370/03_2024/7spa_25370.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7spa_25370/03_2024/7spa_25370.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7spa_25370/03_2024/7spa_25370.pdb" } resolution = 2.8 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= -0.001 sd= 0.807 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1816 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 35 5.16 5 C 3898 2.51 5 N 985 2.21 5 O 1098 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 83": "OD1" <-> "OD2" Residue "C ASP 32": "OD1" <-> "OD2" Residue "C ASP 102": "OD1" <-> "OD2" Residue "A PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 548": "OE1" <-> "OE2" 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: 6017 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 944 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "C" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 918 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 2, 'TRANS': 114} Chain breaks: 2 Chain: "A" Number of atoms: 4155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 4155 Unusual residues: {'3PE': 1, 'NAG': 1, 'Y01': 1} Classifications: {'peptide': 497, 'undetermined': 3} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 483, None: 3} Not linked: pdbres="HIS A 552 " pdbres="NAG A 901 " Not linked: pdbres="NAG A 901 " pdbres="Y01 A 902 " Not linked: pdbres="Y01 A 902 " pdbres="3PE A 903 " Chain breaks: 1 Time building chain proxies: 3.96, per 1000 atoms: 0.66 Number of scatterers: 6017 At special positions: 0 Unit cell: (70.2, 73.44, 153.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 35 16.00 P 1 15.00 O 1098 8.00 N 985 7.00 C 3898 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 95 " 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: 2.43 Conformation dependent library (CDL) restraints added in 1.2 seconds 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1366 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 7 sheets defined 47.8% alpha, 19.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'B' and resid 28 through 32 removed outlier: 3.682A pdb=" N THR B 31 " --> pdb=" O ALA B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 90 Processing helix chain 'B' and resid 107 through 111 removed outlier: 3.575A pdb=" N TYR B 111 " --> pdb=" O THR B 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 113 Processing helix chain 'A' and resid 39 through 74 removed outlier: 3.598A pdb=" N LEU A 74 " --> pdb=" O ASP A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 107 Processing helix chain 'A' and resid 127 through 138 removed outlier: 3.895A pdb=" N ALA A 131 " --> pdb=" O ASP A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 152 Processing helix chain 'A' and resid 156 through 160 removed outlier: 3.558A pdb=" N THR A 159 " --> pdb=" O ASN A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 190 Processing helix chain 'A' and resid 209 through 221 Proline residue: A 217 - end of helix removed outlier: 3.744A pdb=" N CYS A 220 " --> pdb=" O TYR A 216 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ASP A 221 " --> pdb=" O PRO A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 262 removed outlier: 4.005A pdb=" N ARG A 256 " --> pdb=" O PHE A 252 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLY A 257 " --> pdb=" O ASN A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 290 removed outlier: 5.261A pdb=" N ASP A 285 " --> pdb=" O ASN A 281 " (cutoff:3.500A) Proline residue: A 286 - end of helix Processing helix chain 'A' and resid 301 through 312 removed outlier: 3.802A pdb=" N LEU A 305 " --> pdb=" O ASP A 301 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG A 312 " --> pdb=" O GLU A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 358 Processing helix chain 'A' and resid 364 through 392 removed outlier: 4.388A pdb=" N ALA A 368 " --> pdb=" O GLY A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 420 removed outlier: 3.533A pdb=" N GLN A 397 " --> pdb=" O ASP A 393 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA A 399 " --> pdb=" O ARG A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 428 removed outlier: 3.714A pdb=" N ALA A 424 " --> pdb=" O ASN A 421 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE A 425 " --> pdb=" O LEU A 422 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL A 428 " --> pdb=" O PHE A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 449 removed outlier: 3.873A pdb=" N VAL A 433 " --> pdb=" O LEU A 429 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ILE A 439 " --> pdb=" O PHE A 435 " (cutoff:3.500A) Proline residue: A 440 - end of helix Processing helix chain 'A' and resid 476 through 497 Processing helix chain 'A' and resid 504 through 534 Processing helix chain 'A' and resid 539 through 552 removed outlier: 3.540A pdb=" N GLU A 544 " --> pdb=" O PRO A 540 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 3 through 8 removed outlier: 3.503A pdb=" N GLN B 3 " --> pdb=" O SER B 25 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL B 20 " --> pdb=" O LEU B 80 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 10 through 12 removed outlier: 5.794A pdb=" N GLY B 10 " --> pdb=" O THR B 121 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N SER B 49 " --> pdb=" O TRP B 36 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N ARG B 38 " --> pdb=" O PHE B 47 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N PHE B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 10 through 12 removed outlier: 5.794A pdb=" N GLY B 10 " --> pdb=" O THR B 121 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA B 97 " --> pdb=" O TYR B 113 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 101 Processing sheet with id=AA5, first strand: chain 'C' and resid 4 through 7 removed outlier: 3.629A pdb=" N LEU C 18 " --> pdb=" O MET C 82 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 47 through 52 removed outlier: 3.757A pdb=" N ALA C 49 " --> pdb=" O TRP C 36 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU C 34 " --> pdb=" O SER C 51 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU C 97 " --> pdb=" O TYR C 115 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N TYR C 115 " --> pdb=" O LEU C 97 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 142 through 143 removed outlier: 8.760A pdb=" N ILE A 168 " --> pdb=" O ALA A 114 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LEU A 116 " --> pdb=" O ILE A 168 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N ILE A 170 " --> pdb=" O LEU A 116 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N CYS A 118 " --> pdb=" O ILE A 170 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N GLN A 172 " --> pdb=" O CYS A 118 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ILE A 120 " --> pdb=" O GLN A 172 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL A 84 " --> pdb=" O VAL A 113 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ARG A 115 " --> pdb=" O VAL A 84 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY A 90 " --> pdb=" O VAL A 119 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASP A 121 " --> pdb=" O GLY A 90 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ALA A 85 " --> pdb=" O VAL A 198 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N ILE A 200 " --> pdb=" O ALA A 85 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ILE A 87 " --> pdb=" O ILE A 200 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N LEU A 272 " --> pdb=" O GLY A 229 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N LYS A 225 " --> pdb=" O THR A 276 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N ILE A 224 " --> pdb=" O ILE A 316 " (cutoff:3.500A) removed outlier: 10.395A pdb=" N TYR A 318 " --> pdb=" O ILE A 224 " (cutoff:3.500A) removed outlier: 10.587A pdb=" N ALA A 226 " --> pdb=" O TYR A 318 " (cutoff:3.500A) removed outlier: 10.220A pdb=" N ALA A 228 " --> pdb=" O PRO A 320 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ALA A 322 " --> pdb=" O ALA A 228 " (cutoff:3.500A) 319 hydrogen bonds defined for protein. 885 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: 1.81 Time building geometry restraints manager: 2.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1038 1.33 - 1.45: 1756 1.45 - 1.57: 3300 1.57 - 1.69: 19 1.69 - 1.81: 53 Bond restraints: 6166 Sorted by residual: bond pdb=" CBD Y01 A 902 " pdb=" CBG Y01 A 902 " ideal model delta sigma weight residual 1.520 1.642 -0.122 2.00e-02 2.50e+03 3.72e+01 bond pdb=" CAV Y01 A 902 " pdb=" CAZ Y01 A 902 " ideal model delta sigma weight residual 1.507 1.612 -0.105 2.00e-02 2.50e+03 2.75e+01 bond pdb=" CAV Y01 A 902 " pdb=" CBC Y01 A 902 " ideal model delta sigma weight residual 1.523 1.618 -0.095 2.00e-02 2.50e+03 2.25e+01 bond pdb=" CBF Y01 A 902 " pdb=" CBH Y01 A 902 " ideal model delta sigma weight residual 1.550 1.644 -0.094 2.00e-02 2.50e+03 2.21e+01 bond pdb=" CAY Y01 A 902 " pdb=" OAW Y01 A 902 " ideal model delta sigma weight residual 1.332 1.426 -0.094 2.00e-02 2.50e+03 2.21e+01 ... (remaining 6161 not shown) Histogram of bond angle deviations from ideal: 99.01 - 106.00: 89 106.00 - 113.00: 3233 113.00 - 120.00: 2177 120.00 - 127.00: 2785 127.00 - 133.99: 73 Bond angle restraints: 8357 Sorted by residual: angle pdb=" CAM Y01 A 902 " pdb=" CAY Y01 A 902 " pdb=" OAW Y01 A 902 " ideal model delta sigma weight residual 111.19 124.33 -13.14 3.00e+00 1.11e-01 1.92e+01 angle pdb=" CAZ Y01 A 902 " pdb=" CAV Y01 A 902 " pdb=" CBC Y01 A 902 " ideal model delta sigma weight residual 111.19 123.54 -12.35 3.00e+00 1.11e-01 1.69e+01 angle pdb=" CAI Y01 A 902 " pdb=" CAZ Y01 A 902 " pdb=" CAV Y01 A 902 " ideal model delta sigma weight residual 120.03 131.77 -11.74 3.00e+00 1.11e-01 1.53e+01 angle pdb=" CAV Y01 A 902 " pdb=" CAZ Y01 A 902 " pdb=" CBH Y01 A 902 " ideal model delta sigma weight residual 116.96 108.50 8.46 3.00e+00 1.11e-01 7.96e+00 angle pdb=" OAG Y01 A 902 " pdb=" CAY Y01 A 902 " pdb=" OAW Y01 A 902 " ideal model delta sigma weight residual 123.38 115.56 7.82 3.00e+00 1.11e-01 6.80e+00 ... (remaining 8352 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.92: 3367 16.92 - 33.84: 236 33.84 - 50.76: 37 50.76 - 67.68: 11 67.68 - 84.60: 5 Dihedral angle restraints: 3656 sinusoidal: 1510 harmonic: 2146 Sorted by residual: dihedral pdb=" CA TYR A 248 " pdb=" CB TYR A 248 " pdb=" CG TYR A 248 " pdb=" CD1 TYR A 248 " ideal model delta sinusoidal sigma weight residual 90.00 35.42 54.58 2 2.00e+01 2.50e-03 7.97e+00 dihedral pdb=" N LYS A 359 " pdb=" CA LYS A 359 " pdb=" CB LYS A 359 " pdb=" CG LYS A 359 " ideal model delta sinusoidal sigma weight residual -60.00 -103.05 43.05 3 1.50e+01 4.44e-03 7.73e+00 dihedral pdb=" CB MET A 481 " pdb=" CG MET A 481 " pdb=" SD MET A 481 " pdb=" CE MET A 481 " ideal model delta sinusoidal sigma weight residual 60.00 102.32 -42.32 3 1.50e+01 4.44e-03 7.59e+00 ... (remaining 3653 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 845 0.080 - 0.159: 55 0.159 - 0.239: 4 0.239 - 0.318: 1 0.318 - 0.398: 3 Chirality restraints: 908 Sorted by residual: chirality pdb=" CBG Y01 A 902 " pdb=" CAQ Y01 A 902 " pdb=" CBD Y01 A 902 " pdb=" CBI Y01 A 902 " both_signs ideal model delta sigma weight residual False -2.33 -2.73 0.40 2.00e-01 2.50e+01 3.96e+00 chirality pdb=" CBE Y01 A 902 " pdb=" CAP Y01 A 902 " pdb=" CBB Y01 A 902 " pdb=" CBI Y01 A 902 " both_signs ideal model delta sigma weight residual False 2.57 2.92 -0.36 2.00e-01 2.50e+01 3.20e+00 chirality pdb=" CBI Y01 A 902 " pdb=" CAU Y01 A 902 " pdb=" CBE Y01 A 902 " pdb=" CBG Y01 A 902 " both_signs ideal model delta sigma weight residual False 2.94 2.62 0.32 2.00e-01 2.50e+01 2.58e+00 ... (remaining 905 not shown) Planarity restraints: 1028 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 345 " -0.011 2.00e-02 2.50e+03 2.26e-02 5.09e+00 pdb=" C SER A 345 " 0.039 2.00e-02 2.50e+03 pdb=" O SER A 345 " -0.015 2.00e-02 2.50e+03 pdb=" N TRP A 346 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 319 " -0.017 5.00e-02 4.00e+02 2.59e-02 1.07e+00 pdb=" N PRO A 320 " 0.045 5.00e-02 4.00e+02 pdb=" CA PRO A 320 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 320 " -0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 172 " -0.015 5.00e-02 4.00e+02 2.29e-02 8.36e-01 pdb=" N PRO A 173 " 0.040 5.00e-02 4.00e+02 pdb=" CA PRO A 173 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 173 " -0.013 5.00e-02 4.00e+02 ... (remaining 1025 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 1506 2.80 - 3.32: 5630 3.32 - 3.85: 9730 3.85 - 4.37: 11034 4.37 - 4.90: 19557 Nonbonded interactions: 47457 Sorted by model distance: nonbonded pdb=" OG SER A 343 " pdb=" NH1 ARG A 442 " model vdw 2.275 2.520 nonbonded pdb=" OG SER C 51 " pdb=" O GLY C 56 " model vdw 2.298 2.440 nonbonded pdb=" NZ LYS A 391 " pdb=" O ASP A 393 " model vdw 2.333 2.520 nonbonded pdb=" O ASN A 80 " pdb=" ND2 ASN A 112 " model vdw 2.349 2.520 nonbonded pdb=" O TRP A 71 " pdb=" OH TYR A 216 " model vdw 2.350 2.440 ... (remaining 47452 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: 0.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 3.880 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 20.970 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:16.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 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 : 0.004 0.122 6166 Z= 0.275 Angle : 0.574 13.143 8357 Z= 0.264 Chirality : 0.046 0.398 908 Planarity : 0.002 0.026 1028 Dihedral : 12.248 84.599 2287 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.31), residues: 725 helix: 2.14 (0.30), residues: 320 sheet: 2.01 (0.44), residues: 140 loop : -0.72 (0.34), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP C 116 HIS 0.000 0.000 HIS A 174 PHE 0.004 0.001 PHE A 252 TYR 0.008 0.001 TYR A 299 ARG 0.002 0.000 ARG A 247 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 0.733 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 1.1550 time to fit residues: 156.3224 Evaluate side-chains 81 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 61 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 37 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 ASN A 253 ASN A 339 GLN A 537 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6166 Z= 0.241 Angle : 0.545 5.787 8357 Z= 0.294 Chirality : 0.042 0.178 908 Planarity : 0.004 0.052 1028 Dihedral : 6.985 72.061 966 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.23 % Allowed : 10.67 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.66 (0.31), residues: 725 helix: 2.28 (0.30), residues: 314 sheet: 1.75 (0.45), residues: 141 loop : -0.72 (0.33), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 262 HIS 0.003 0.001 HIS A 360 PHE 0.021 0.002 PHE A 379 TYR 0.020 0.002 TYR A 377 ARG 0.004 0.001 ARG A 303 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 92 time to evaluate : 0.707 Fit side-chains REVERT: A 382 MET cc_start: 0.8286 (mmm) cc_final: 0.7919 (mmm) outliers start: 14 outliers final: 6 residues processed: 101 average time/residue: 1.1250 time to fit residues: 119.5318 Evaluate side-chains 82 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 76 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 351 TRP Chi-restraints excluded: chain A residue 387 TYR Chi-restraints excluded: chain A residue 516 SER Chi-restraints excluded: chain A residue 518 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 36 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 65 optimal weight: 0.0670 chunk 22 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 overall best weight: 0.9322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.3999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6166 Z= 0.191 Angle : 0.502 5.788 8357 Z= 0.274 Chirality : 0.041 0.178 908 Planarity : 0.003 0.025 1028 Dihedral : 6.615 70.837 966 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.03 % Allowed : 14.65 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.70 (0.31), residues: 725 helix: 2.22 (0.29), residues: 319 sheet: 1.92 (0.45), residues: 141 loop : -0.74 (0.33), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 262 HIS 0.003 0.001 HIS A 195 PHE 0.024 0.001 PHE A 379 TYR 0.012 0.001 TYR A 377 ARG 0.006 0.001 ARG A 303 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 86 time to evaluate : 0.737 Fit side-chains REVERT: B 83 ASP cc_start: 0.6801 (m-30) cc_final: 0.6367 (m-30) REVERT: C 75 ARG cc_start: 0.7522 (mpp80) cc_final: 0.7127 (mpp80) REVERT: A 253 ASN cc_start: 0.7036 (OUTLIER) cc_final: 0.6820 (m-40) REVERT: A 519 VAL cc_start: 0.9080 (t) cc_final: 0.8862 (p) outliers start: 19 outliers final: 10 residues processed: 101 average time/residue: 1.1440 time to fit residues: 121.4762 Evaluate side-chains 92 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 81 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 253 ASN Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 338 GLN Chi-restraints excluded: chain A residue 387 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 65 optimal weight: 0.8980 chunk 49 optimal weight: 0.0470 chunk 34 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 63 optimal weight: 0.3980 chunk 19 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 overall best weight: 0.8480 ------------------------------------------------------------------------------- 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: 0.8161 moved from start: 0.4463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6166 Z= 0.180 Angle : 0.497 6.773 8357 Z= 0.268 Chirality : 0.041 0.188 908 Planarity : 0.003 0.036 1028 Dihedral : 6.490 69.904 966 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.34 % Allowed : 15.29 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.31), residues: 725 helix: 2.28 (0.30), residues: 314 sheet: 1.94 (0.44), residues: 139 loop : -0.80 (0.33), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 262 HIS 0.002 0.001 HIS A 360 PHE 0.024 0.001 PHE A 379 TYR 0.013 0.001 TYR A 377 ARG 0.007 0.001 ARG A 303 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 82 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 46 GLU cc_start: 0.7050 (pm20) cc_final: 0.6813 (mp0) outliers start: 21 outliers final: 10 residues processed: 95 average time/residue: 1.0767 time to fit residues: 108.0466 Evaluate side-chains 86 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 76 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 60 TYR Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 338 GLN Chi-restraints excluded: chain A residue 387 TYR Chi-restraints excluded: chain A residue 487 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 40 optimal weight: 3.9990 chunk 1 optimal weight: 10.0000 chunk 52 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 36 optimal weight: 0.0980 chunk 63 optimal weight: 0.1980 chunk 17 optimal weight: 6.9990 chunk 23 optimal weight: 20.0000 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 475 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.4991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6166 Z= 0.227 Angle : 0.541 6.979 8357 Z= 0.290 Chirality : 0.042 0.211 908 Planarity : 0.004 0.045 1028 Dihedral : 6.647 68.596 966 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.21 % Favored : 97.66 % Rotamer: Outliers : 3.18 % Allowed : 15.61 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.31), residues: 725 helix: 2.20 (0.30), residues: 314 sheet: 1.76 (0.44), residues: 140 loop : -0.86 (0.33), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 262 HIS 0.003 0.001 HIS A 360 PHE 0.022 0.001 PHE A 447 TYR 0.013 0.001 TYR C 115 ARG 0.011 0.001 ARG A 303 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 79 time to evaluate : 0.696 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 11 residues processed: 92 average time/residue: 1.1676 time to fit residues: 113.0915 Evaluate side-chains 88 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 77 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain C residue 60 TYR Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 338 GLN Chi-restraints excluded: chain A residue 387 TYR Chi-restraints excluded: chain A residue 487 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 63 optimal weight: 0.9990 chunk 13 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 5 optimal weight: 0.0980 chunk 23 optimal weight: 10.0000 chunk 37 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 overall best weight: 1.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS A 475 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.5540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 6166 Z= 0.314 Angle : 0.597 7.759 8357 Z= 0.321 Chirality : 0.044 0.256 908 Planarity : 0.004 0.035 1028 Dihedral : 7.048 68.015 966 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.62 % Favored : 97.24 % Rotamer: Outliers : 3.03 % Allowed : 16.24 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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 (0.31), residues: 725 helix: 1.97 (0.29), residues: 314 sheet: 1.19 (0.42), residues: 157 loop : -0.77 (0.35), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 262 HIS 0.003 0.002 HIS A 360 PHE 0.029 0.002 PHE A 379 TYR 0.017 0.002 TYR C 115 ARG 0.007 0.001 ARG A 303 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 85 time to evaluate : 0.721 Fit side-chains revert: symmetry clash REVERT: A 46 TYR cc_start: 0.5855 (OUTLIER) cc_final: 0.4595 (t80) outliers start: 19 outliers final: 12 residues processed: 98 average time/residue: 1.1427 time to fit residues: 117.7767 Evaluate side-chains 95 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 82 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain C residue 60 TYR Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain A residue 46 TYR Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 338 GLN Chi-restraints excluded: chain A residue 387 TYR Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 516 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 7 optimal weight: 0.0970 chunk 40 optimal weight: 0.0770 chunk 51 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 59 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 overall best weight: 0.5336 ------------------------------------------------------------------------------- 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: 0.8227 moved from start: 0.5422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6166 Z= 0.157 Angle : 0.522 8.196 8357 Z= 0.278 Chirality : 0.040 0.206 908 Planarity : 0.003 0.038 1028 Dihedral : 6.609 65.863 966 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.48 % Favored : 97.38 % Rotamer: Outliers : 2.23 % Allowed : 18.31 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.43 (0.31), residues: 725 helix: 2.12 (0.30), residues: 314 sheet: 1.55 (0.44), residues: 141 loop : -0.84 (0.33), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 262 HIS 0.002 0.001 HIS A 174 PHE 0.025 0.001 PHE A 447 TYR 0.011 0.001 TYR A 414 ARG 0.008 0.000 ARG A 303 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 87 time to evaluate : 0.653 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 TYR cc_start: 0.5720 (OUTLIER) cc_final: 0.4430 (t80) outliers start: 14 outliers final: 7 residues processed: 97 average time/residue: 1.1908 time to fit residues: 121.1119 Evaluate side-chains 89 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 81 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 88 GLU Chi-restraints excluded: chain C residue 60 TYR Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain A residue 46 TYR Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 338 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 42 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 13 optimal weight: 0.0040 chunk 44 optimal weight: 2.9990 chunk 47 optimal weight: 0.2980 chunk 34 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 chunk 55 optimal weight: 4.9990 chunk 64 optimal weight: 0.8980 chunk 67 optimal weight: 5.9990 chunk 61 optimal weight: 0.0020 overall best weight: 0.4000 ------------------------------------------------------------------------------- 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: 0.8204 moved from start: 0.5411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6166 Z= 0.143 Angle : 0.535 8.966 8357 Z= 0.280 Chirality : 0.040 0.202 908 Planarity : 0.003 0.031 1028 Dihedral : 6.397 65.342 966 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.48 % Favored : 97.38 % Rotamer: Outliers : 1.59 % Allowed : 18.95 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.49 (0.31), residues: 725 helix: 2.12 (0.30), residues: 315 sheet: 1.79 (0.44), residues: 137 loop : -0.85 (0.33), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 346 HIS 0.002 0.001 HIS A 360 PHE 0.028 0.001 PHE A 447 TYR 0.011 0.001 TYR A 414 ARG 0.004 0.000 ARG A 256 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 83 time to evaluate : 0.703 Fit side-chains revert: symmetry clash REVERT: A 46 TYR cc_start: 0.5687 (OUTLIER) cc_final: 0.4411 (t80) outliers start: 10 outliers final: 7 residues processed: 89 average time/residue: 1.2583 time to fit residues: 117.4647 Evaluate side-chains 87 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 79 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain C residue 60 TYR Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain A residue 46 TYR Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 338 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 65 optimal weight: 1.9990 chunk 67 optimal weight: 6.9990 chunk 39 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 62 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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: 0.8234 moved from start: 0.5490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6166 Z= 0.179 Angle : 0.537 9.521 8357 Z= 0.284 Chirality : 0.041 0.210 908 Planarity : 0.003 0.031 1028 Dihedral : 6.433 64.987 966 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.62 % Favored : 97.24 % Rotamer: Outliers : 2.55 % Allowed : 18.47 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.46 (0.31), residues: 725 helix: 2.10 (0.30), residues: 314 sheet: 1.66 (0.45), residues: 139 loop : -0.80 (0.33), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 262 HIS 0.002 0.001 HIS A 360 PHE 0.027 0.001 PHE A 447 TYR 0.012 0.001 TYR A 414 ARG 0.002 0.000 ARG B 66 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 78 time to evaluate : 0.780 Fit side-chains revert: symmetry clash REVERT: A 46 TYR cc_start: 0.5675 (OUTLIER) cc_final: 0.4433 (t80) outliers start: 16 outliers final: 9 residues processed: 87 average time/residue: 1.1280 time to fit residues: 103.6333 Evaluate side-chains 88 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 78 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain C residue 60 TYR Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain A residue 46 TYR Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 338 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 32 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 72 optimal weight: 0.6980 chunk 66 optimal weight: 5.9990 chunk 57 optimal weight: 0.7980 chunk 6 optimal weight: 0.4980 chunk 44 optimal weight: 2.9990 chunk 35 optimal weight: 0.2980 chunk 46 optimal weight: 3.9990 chunk 61 optimal weight: 0.0050 chunk 17 optimal weight: 5.9990 overall best weight: 0.4594 ------------------------------------------------------------------------------- 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: 0.8205 moved from start: 0.5481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6166 Z= 0.142 Angle : 0.520 9.511 8357 Z= 0.273 Chirality : 0.040 0.202 908 Planarity : 0.003 0.031 1028 Dihedral : 6.313 63.990 966 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.03 % Favored : 96.83 % Rotamer: Outliers : 1.43 % Allowed : 19.59 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.47 (0.31), residues: 725 helix: 2.16 (0.30), residues: 313 sheet: 1.64 (0.45), residues: 139 loop : -0.84 (0.33), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 346 HIS 0.001 0.000 HIS A 360 PHE 0.028 0.001 PHE A 447 TYR 0.011 0.001 TYR A 414 ARG 0.003 0.000 ARG B 66 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 77 time to evaluate : 0.714 Fit side-chains revert: symmetry clash REVERT: B 46 GLU cc_start: 0.6607 (pm20) cc_final: 0.6329 (pp20) REVERT: A 46 TYR cc_start: 0.5656 (OUTLIER) cc_final: 0.4419 (t80) outliers start: 9 outliers final: 5 residues processed: 83 average time/residue: 1.1567 time to fit residues: 101.1136 Evaluate side-chains 80 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 74 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 60 TYR Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain A residue 46 TYR Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 338 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 53 optimal weight: 4.9990 chunk 8 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 58 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 chunk 7 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.095593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.079312 restraints weight = 12715.362| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 2.05 r_work: 0.3035 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.5747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6166 Z= 0.250 Angle : 0.579 9.796 8357 Z= 0.306 Chirality : 0.043 0.215 908 Planarity : 0.004 0.070 1028 Dihedral : 6.658 63.846 966 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.17 % Favored : 96.69 % Rotamer: Outliers : 1.91 % Allowed : 19.43 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.38 (0.31), residues: 725 helix: 2.00 (0.29), residues: 314 sheet: 1.39 (0.44), residues: 148 loop : -0.74 (0.34), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 262 HIS 0.003 0.001 HIS A 360 PHE 0.028 0.001 PHE A 447 TYR 0.013 0.001 TYR A 430 ARG 0.011 0.001 ARG B 66 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2547.47 seconds wall clock time: 46 minutes 3.18 seconds (2763.18 seconds total)