Starting phenix.real_space_refine on Fri Dec 8 08:10:17 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sp9_25369/12_2023/7sp9_25369.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sp9_25369/12_2023/7sp9_25369.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sp9_25369/12_2023/7sp9_25369.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sp9_25369/12_2023/7sp9_25369.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sp9_25369/12_2023/7sp9_25369.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sp9_25369/12_2023/7sp9_25369.pdb" } resolution = 2.9 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= 0.828 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: 4 Type Number sf(0) Gaussians S 35 5.16 5 C 3857 2.51 5 N 984 2.21 5 O 1090 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 102": "OD1" <-> "OD2" Residue "C TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 5966 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: 4104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 499, 4104 Unusual residues: {'NAG': 1, 'Y01': 1} Classifications: {'peptide': 497, 'undetermined': 2} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 483, None: 2} Not linked: pdbres="HIS A 552 " pdbres="NAG A 901 " Not linked: pdbres="NAG A 901 " pdbres="Y01 A 902 " Chain breaks: 1 Time building chain proxies: 3.64, per 1000 atoms: 0.61 Number of scatterers: 5966 At special positions: 0 Unit cell: (70.2, 71.28, 154.44, 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 35 16.00 O 1090 8.00 N 984 7.00 C 3857 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: 2.03 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: 24 helices and 7 sheets defined 48.8% alpha, 19.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'B' and resid 28 through 32 removed outlier: 3.889A pdb=" N THR B 31 " --> pdb=" O ALA B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 65 removed outlier: 3.616A pdb=" N GLY B 65 " --> pdb=" O SER B 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 62 through 65' Processing helix chain 'B' and resid 86 through 90 Processing helix chain 'B' and resid 107 through 111 removed outlier: 3.541A pdb=" N TYR B 111 " --> pdb=" O THR B 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 90 removed outlier: 3.620A pdb=" N THR C 90 " --> pdb=" O PRO C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 113 Processing helix chain 'A' and resid 39 through 74 removed outlier: 3.625A 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: 3.970A 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: 3.559A 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: 3.899A pdb=" N CYS A 220 " --> pdb=" O TYR A 216 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP A 221 " --> pdb=" O PRO A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 262 removed outlier: 4.044A pdb=" N ARG A 256 " --> pdb=" O PHE A 252 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLY A 257 " --> pdb=" O ASN A 253 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TRP A 262 " --> pdb=" O ALA A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 290 removed outlier: 5.259A pdb=" N ASP A 285 " --> pdb=" O ASN A 281 " (cutoff:3.500A) Proline residue: A 286 - end of helix removed outlier: 3.514A pdb=" N GLN A 290 " --> pdb=" O PRO A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 312 removed outlier: 3.804A pdb=" N LEU A 305 " --> pdb=" O ASP A 301 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N THR A 306 " --> pdb=" O ASN A 302 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ARG A 312 " --> pdb=" O GLU A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 356 removed outlier: 5.267A pdb=" N TRP A 351 " --> pdb=" O CYS A 347 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N TYR A 352 " --> pdb=" O ARG A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 392 removed outlier: 4.068A pdb=" N ALA A 368 " --> pdb=" O GLY A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 420 Processing helix chain 'A' and resid 421 through 428 removed outlier: 3.616A pdb=" N ALA A 424 " --> pdb=" O ASN A 421 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE A 425 " --> pdb=" O LEU A 422 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL A 428 " --> pdb=" O PHE A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 449 removed outlier: 3.834A pdb=" N VAL A 433 " --> pdb=" O LEU A 429 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ILE A 439 " --> pdb=" O PHE A 435 " (cutoff:3.500A) Proline residue: A 440 - end of helix removed outlier: 3.519A pdb=" N MET A 449 " --> pdb=" O ALA A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 497 Processing helix chain 'A' and resid 504 through 535 removed outlier: 3.708A pdb=" N ILE A 533 " --> pdb=" O LEU A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 552 Processing sheet with id=AA1, first strand: chain 'B' and resid 3 through 7 removed outlier: 3.572A pdb=" N SER B 21 " --> pdb=" O SER B 7 " (cutoff:3.500A) removed outlier: 3.734A 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: 5.557A pdb=" N GLY B 10 " --> pdb=" O THR B 121 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N SER B 49 " --> pdb=" O TRP B 36 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ARG B 38 " --> pdb=" O PHE B 47 " (cutoff:3.500A) removed outlier: 6.236A 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: 5.557A pdb=" N GLY B 10 " --> pdb=" O THR B 121 " (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: 3.744A pdb=" N LEU C 18 " --> pdb=" O MET C 82 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU C 20 " --> pdb=" O LEU C 80 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 47 through 52 removed outlier: 4.005A pdb=" N ALA C 49 " --> pdb=" O TRP C 36 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU C 34 " --> pdb=" O SER C 51 " (cutoff:3.500A) removed outlier: 3.836A 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: 8.625A pdb=" N ILE A 168 " --> pdb=" O ALA A 114 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N LEU A 116 " --> pdb=" O ILE A 168 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N ILE A 170 " --> pdb=" O LEU A 116 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N CYS A 118 " --> pdb=" O ILE A 170 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N GLN A 172 " --> pdb=" O CYS A 118 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N ILE A 120 " --> pdb=" O GLN A 172 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N VAL A 84 " --> pdb=" O VAL A 113 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ARG A 115 " --> pdb=" O VAL A 84 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLY A 90 " --> pdb=" O VAL A 119 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASP A 121 " --> pdb=" O GLY A 90 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ALA A 85 " --> pdb=" O VAL A 198 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N ILE A 200 " --> pdb=" O ALA A 85 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ILE A 87 " --> pdb=" O ILE A 200 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N LEU A 272 " --> pdb=" O GLY A 229 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N LYS A 225 " --> pdb=" O THR A 276 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N ILE A 224 " --> pdb=" O ILE A 316 " (cutoff:3.500A) removed outlier: 10.398A pdb=" N TYR A 318 " --> pdb=" O ILE A 224 " (cutoff:3.500A) removed outlier: 10.615A pdb=" N ALA A 226 " --> pdb=" O TYR A 318 " (cutoff:3.500A) removed outlier: 10.219A pdb=" N ALA A 228 " --> pdb=" O PRO A 320 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ALA A 322 " --> pdb=" O ALA A 228 " (cutoff:3.500A) 316 hydrogen bonds defined for protein. 873 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: 1.76 Time building geometry restraints manager: 2.23 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: 1071 1.33 - 1.45: 1716 1.45 - 1.57: 3260 1.57 - 1.69: 16 1.69 - 1.81: 53 Bond restraints: 6116 Sorted by residual: bond pdb=" CBD Y01 A 902 " pdb=" CBG Y01 A 902 " ideal model delta sigma weight residual 1.520 1.643 -0.123 2.00e-02 2.50e+03 3.81e+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 2.73e+01 bond pdb=" CAV Y01 A 902 " pdb=" CBC Y01 A 902 " ideal model delta sigma weight residual 1.523 1.616 -0.093 2.00e-02 2.50e+03 2.17e+01 bond pdb=" CAY Y01 A 902 " pdb=" OAW Y01 A 902 " ideal model delta sigma weight residual 1.332 1.423 -0.091 2.00e-02 2.50e+03 2.06e+01 bond pdb=" CBF Y01 A 902 " pdb=" CBH Y01 A 902 " ideal model delta sigma weight residual 1.550 1.638 -0.088 2.00e-02 2.50e+03 1.95e+01 ... (remaining 6111 not shown) Histogram of bond angle deviations from ideal: 99.01 - 106.01: 87 106.01 - 113.01: 3212 113.01 - 120.01: 2152 120.01 - 127.01: 2780 127.01 - 134.00: 71 Bond angle restraints: 8302 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 111.19 124.30 -13.11 3.00e+00 1.11e-01 1.91e+01 angle pdb=" CAI Y01 A 902 " pdb=" CAZ Y01 A 902 " pdb=" CAV Y01 A 902 " ideal model delta sigma weight residual 120.03 131.83 -11.80 3.00e+00 1.11e-01 1.55e+01 angle pdb=" CAZ Y01 A 902 " pdb=" CAV Y01 A 902 " pdb=" CBC Y01 A 902 " ideal model delta sigma weight residual 111.19 122.91 -11.72 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 116.96 108.74 8.22 3.00e+00 1.11e-01 7.50e+00 angle pdb=" C VAL A 254 " pdb=" N GLU A 255 " pdb=" CA GLU A 255 " ideal model delta sigma weight residual 120.44 116.76 3.68 1.36e+00 5.41e-01 7.31e+00 ... (remaining 8297 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.23: 3334 16.23 - 32.47: 207 32.47 - 48.70: 48 48.70 - 64.93: 13 64.93 - 81.16: 5 Dihedral angle restraints: 3607 sinusoidal: 1461 harmonic: 2146 Sorted by residual: dihedral pdb=" CB MET A 382 " pdb=" CG MET A 382 " pdb=" SD MET A 382 " pdb=" CE MET A 382 " ideal model delta sinusoidal sigma weight residual -60.00 -111.24 51.24 3 1.50e+01 4.44e-03 8.99e+00 dihedral pdb=" CA LEU A 293 " pdb=" CB LEU A 293 " pdb=" CG LEU A 293 " pdb=" CD1 LEU A 293 " ideal model delta sinusoidal sigma weight residual 60.00 104.68 -44.68 3 1.50e+01 4.44e-03 8.04e+00 dihedral pdb=" CA ARG A 334 " pdb=" CB ARG A 334 " pdb=" CG ARG A 334 " pdb=" CD ARG A 334 " ideal model delta sinusoidal sigma weight residual -180.00 -137.28 -42.72 3 1.50e+01 4.44e-03 7.67e+00 ... (remaining 3604 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 838 0.080 - 0.159: 63 0.159 - 0.239: 2 0.239 - 0.319: 1 0.319 - 0.398: 3 Chirality restraints: 907 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 3.97e+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 2.93 -0.36 2.00e-01 2.50e+01 3.29e+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 2.61 0.33 2.00e-01 2.50e+01 2.67e+00 ... (remaining 904 not shown) Planarity restraints: 1026 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 94 " 0.019 5.00e-02 4.00e+02 2.90e-02 1.35e+00 pdb=" N PRO A 95 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO A 95 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 95 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 346 " -0.009 2.00e-02 2.50e+03 7.12e-03 1.27e+00 pdb=" CG TRP A 346 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 TRP A 346 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TRP A 346 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 346 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 346 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 346 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 346 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 346 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 346 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 447 " -0.006 2.00e-02 2.50e+03 8.45e-03 1.25e+00 pdb=" CG PHE A 447 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 PHE A 447 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE A 447 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE A 447 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 447 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 447 " 0.000 2.00e-02 2.50e+03 ... (remaining 1023 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1081 2.78 - 3.31: 5704 3.31 - 3.84: 9815 3.84 - 4.37: 11047 4.37 - 4.90: 19773 Nonbonded interactions: 47420 Sorted by model distance: nonbonded pdb=" O TYR A 499 " pdb=" OH TYR A 507 " model vdw 2.245 2.440 nonbonded pdb=" OH TYR A 46 " pdb=" OAG Y01 A 902 " model vdw 2.291 2.440 nonbonded pdb=" OG SER C 51 " pdb=" O GLY C 56 " model vdw 2.311 2.440 nonbonded pdb=" O THR A 82 " pdb=" OH TYR A 110 " model vdw 2.322 2.440 nonbonded pdb=" NH2 ARG A 67 " pdb=" O SER A 260 " model vdw 2.323 2.520 ... (remaining 47415 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: 0.790 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: 3.860 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 19.920 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 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 0.123 6116 Z= 0.291 Angle : 0.568 13.110 8302 Z= 0.260 Chirality : 0.046 0.398 907 Planarity : 0.003 0.029 1026 Dihedral : 12.065 81.163 2238 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % 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: 1.62 (0.31), residues: 725 helix: 2.16 (0.29), residues: 315 sheet: 1.47 (0.44), residues: 150 loop : -0.55 (0.36), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 346 HIS 0.003 0.001 HIS A 552 PHE 0.019 0.001 PHE A 447 TYR 0.013 0.001 TYR A 414 ARG 0.005 0.000 ARG A 67 *********************** 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 124 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 0.701 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.9801 time to fit residues: 128.6413 Evaluate side-chains 87 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.727 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 60 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 56 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 GLN ** A 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.3235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 6116 Z= 0.360 Angle : 0.645 8.643 8302 Z= 0.341 Chirality : 0.045 0.143 907 Planarity : 0.004 0.042 1026 Dihedral : 5.729 53.062 917 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.76 % Favored : 97.10 % Rotamer: Outliers : 2.87 % Allowed : 11.78 % Favored : 85.35 % 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: 1.17 (0.30), residues: 725 helix: 1.92 (0.29), residues: 311 sheet: 1.04 (0.42), residues: 152 loop : -0.79 (0.34), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 262 HIS 0.001 0.001 HIS A 195 PHE 0.020 0.002 PHE A 98 TYR 0.013 0.002 TYR A 528 ARG 0.005 0.001 ARG B 98 *********************** 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 114 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 96 time to evaluate : 0.670 Fit side-chains outliers start: 18 outliers final: 13 residues processed: 105 average time/residue: 1.0582 time to fit residues: 117.2393 Evaluate side-chains 88 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 75 time to evaluate : 0.674 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 8 residues processed: 5 average time/residue: 0.4619 time to fit residues: 3.5154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 36 optimal weight: 0.7980 chunk 20 optimal weight: 4.9990 chunk 54 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 64 optimal weight: 10.0000 chunk 22 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 GLN B 116 GLN A 253 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6116 Z= 0.183 Angle : 0.499 6.377 8302 Z= 0.266 Chirality : 0.041 0.143 907 Planarity : 0.003 0.030 1026 Dihedral : 5.337 53.217 917 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.21 % Favored : 97.66 % Rotamer: Outliers : 3.66 % Allowed : 15.29 % Favored : 81.05 % 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: 1.29 (0.30), residues: 725 helix: 2.12 (0.29), residues: 311 sheet: 1.01 (0.42), residues: 152 loop : -0.82 (0.34), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 262 HIS 0.001 0.000 HIS A 195 PHE 0.013 0.001 PHE A 49 TYR 0.012 0.001 TYR C 115 ARG 0.008 0.001 ARG C 75 *********************** 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 103 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 80 time to evaluate : 0.703 Fit side-chains outliers start: 23 outliers final: 12 residues processed: 92 average time/residue: 1.1728 time to fit residues: 113.3216 Evaluate side-chains 86 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 74 time to evaluate : 0.688 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 8 residues processed: 4 average time/residue: 0.4793 time to fit residues: 2.9977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 64 optimal weight: 0.0010 chunk 49 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 69 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 overall best weight: 0.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 GLN A 253 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.3765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6116 Z= 0.171 Angle : 0.490 6.363 8302 Z= 0.263 Chirality : 0.040 0.142 907 Planarity : 0.003 0.039 1026 Dihedral : 5.041 52.715 917 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.76 % Favored : 97.10 % Rotamer: Outliers : 3.66 % Allowed : 16.24 % Favored : 80.10 % 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: 1.27 (0.31), residues: 725 helix: 2.08 (0.29), residues: 312 sheet: 0.98 (0.42), residues: 152 loop : -0.78 (0.34), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 246 HIS 0.001 0.000 HIS A 195 PHE 0.013 0.001 PHE A 49 TYR 0.012 0.001 TYR A 430 ARG 0.008 0.001 ARG C 75 *********************** 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 100 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 77 time to evaluate : 0.679 Fit side-chains outliers start: 23 outliers final: 14 residues processed: 92 average time/residue: 1.1621 time to fit residues: 112.3377 Evaluate side-chains 87 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 73 time to evaluate : 0.614 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 11 residues processed: 3 average time/residue: 0.6428 time to fit residues: 2.9344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 57 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 48 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 GLN C 73 ASN A 253 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.4404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 6116 Z= 0.308 Angle : 0.580 7.452 8302 Z= 0.312 Chirality : 0.044 0.160 907 Planarity : 0.004 0.039 1026 Dihedral : 5.079 36.087 917 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.76 % Favored : 97.10 % Rotamer: Outliers : 3.98 % Allowed : 16.24 % Favored : 79.78 % 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: 1.04 (0.31), residues: 725 helix: 1.88 (0.29), residues: 317 sheet: 0.97 (0.43), residues: 145 loop : -0.97 (0.34), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 246 HIS 0.002 0.001 HIS A 195 PHE 0.019 0.002 PHE B 47 TYR 0.016 0.002 TYR C 115 ARG 0.007 0.001 ARG C 75 *********************** 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 101 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 76 time to evaluate : 0.732 Fit side-chains outliers start: 25 outliers final: 15 residues processed: 92 average time/residue: 1.1629 time to fit residues: 112.5345 Evaluate side-chains 84 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 69 time to evaluate : 0.688 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 12 residues processed: 3 average time/residue: 0.1416 time to fit residues: 1.8960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 23 optimal weight: 9.9990 chunk 62 optimal weight: 0.0980 chunk 13 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 69 optimal weight: 0.5980 chunk 57 optimal weight: 0.4980 chunk 32 optimal weight: 0.0970 chunk 5 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 GLN A 253 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.4249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6116 Z= 0.143 Angle : 0.511 7.572 8302 Z= 0.267 Chirality : 0.040 0.157 907 Planarity : 0.003 0.041 1026 Dihedral : 4.532 32.367 917 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.48 % Favored : 97.38 % Rotamer: Outliers : 3.82 % Allowed : 16.40 % Favored : 79.78 % 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: 1.23 (0.31), residues: 725 helix: 2.02 (0.29), residues: 317 sheet: 1.09 (0.44), residues: 143 loop : -0.85 (0.35), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 246 HIS 0.001 0.001 HIS A 552 PHE 0.020 0.001 PHE A 447 TYR 0.014 0.001 TYR A 414 ARG 0.011 0.000 ARG C 75 *********************** 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 107 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 83 time to evaluate : 0.775 Fit side-chains outliers start: 24 outliers final: 14 residues processed: 100 average time/residue: 1.2300 time to fit residues: 129.1606 Evaluate side-chains 86 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 72 time to evaluate : 0.696 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 11 residues processed: 3 average time/residue: 0.1865 time to fit residues: 1.7964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 7 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 50 optimal weight: 0.1980 chunk 58 optimal weight: 4.9990 chunk 38 optimal weight: 0.0670 chunk 69 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 overall best weight: 0.6120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 GLN A 253 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.4293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6116 Z= 0.157 Angle : 0.507 7.427 8302 Z= 0.268 Chirality : 0.040 0.154 907 Planarity : 0.004 0.049 1026 Dihedral : 4.388 31.038 917 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.76 % Favored : 97.10 % Rotamer: Outliers : 3.03 % Allowed : 17.99 % 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: 1.26 (0.31), residues: 725 helix: 2.07 (0.29), residues: 317 sheet: 1.10 (0.43), residues: 143 loop : -0.86 (0.35), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 346 HIS 0.001 0.000 HIS A 195 PHE 0.012 0.001 PHE A 49 TYR 0.015 0.001 TYR A 414 ARG 0.012 0.001 ARG C 75 *********************** 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 93 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 74 time to evaluate : 0.676 Fit side-chains outliers start: 19 outliers final: 12 residues processed: 87 average time/residue: 1.1358 time to fit residues: 104.0157 Evaluate side-chains 82 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 70 time to evaluate : 0.676 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 11 residues processed: 1 average time/residue: 0.2137 time to fit residues: 1.1632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 20 optimal weight: 1.9990 chunk 13 optimal weight: 0.0000 chunk 44 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 6 optimal weight: 0.0870 chunk 54 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 overall best weight: 0.7966 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 GLN A 253 ASN ** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.4371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6116 Z= 0.177 Angle : 0.522 7.666 8302 Z= 0.277 Chirality : 0.041 0.169 907 Planarity : 0.004 0.054 1026 Dihedral : 4.338 29.448 917 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.76 % Favored : 97.10 % Rotamer: Outliers : 3.03 % Allowed : 18.31 % 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: 1.26 (0.31), residues: 725 helix: 2.07 (0.29), residues: 317 sheet: 1.12 (0.43), residues: 143 loop : -0.89 (0.35), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 346 HIS 0.001 0.000 HIS A 195 PHE 0.012 0.001 PHE B 47 TYR 0.014 0.001 TYR A 414 ARG 0.013 0.001 ARG C 75 *********************** 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 97 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 78 time to evaluate : 0.714 Fit side-chains outliers start: 19 outliers final: 14 residues processed: 92 average time/residue: 1.1743 time to fit residues: 113.6196 Evaluate side-chains 88 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 74 time to evaluate : 0.727 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 12 residues processed: 2 average time/residue: 0.1623 time to fit residues: 1.3596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 66 optimal weight: 5.9990 chunk 38 optimal weight: 0.0270 chunk 28 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 58 optimal weight: 0.0030 chunk 61 optimal weight: 3.9990 chunk 64 optimal weight: 0.0040 chunk 42 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 overall best weight: 0.8064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 GLN C 73 ASN A 253 ASN ** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.4433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6116 Z= 0.181 Angle : 0.554 13.375 8302 Z= 0.289 Chirality : 0.041 0.168 907 Planarity : 0.004 0.057 1026 Dihedral : 4.310 28.315 917 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.76 % Favored : 97.10 % Rotamer: Outliers : 2.87 % Allowed : 18.79 % Favored : 78.34 % 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: 1.23 (0.31), residues: 725 helix: 2.04 (0.28), residues: 317 sheet: 1.11 (0.43), residues: 143 loop : -0.91 (0.35), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 346 HIS 0.001 0.000 HIS A 195 PHE 0.012 0.001 PHE B 47 TYR 0.014 0.001 TYR A 414 ARG 0.013 0.001 ARG C 75 *********************** 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 95 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 77 time to evaluate : 0.625 Fit side-chains outliers start: 18 outliers final: 14 residues processed: 91 average time/residue: 1.1297 time to fit residues: 108.5529 Evaluate side-chains 87 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 73 time to evaluate : 0.723 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 13 residues processed: 1 average time/residue: 0.2339 time to fit residues: 1.2141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 32 optimal weight: 0.6980 chunk 47 optimal weight: 0.6980 chunk 71 optimal weight: 0.8980 chunk 66 optimal weight: 5.9990 chunk 57 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 60 optimal weight: 0.6980 chunk 17 optimal weight: 6.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 GLN C 73 ASN A 253 ASN ** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.4467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6116 Z= 0.176 Angle : 0.565 13.374 8302 Z= 0.293 Chirality : 0.041 0.173 907 Planarity : 0.004 0.060 1026 Dihedral : 4.254 27.684 917 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.48 % Favored : 97.38 % Rotamer: Outliers : 2.39 % Allowed : 19.59 % Favored : 78.03 % 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: 1.22 (0.31), residues: 725 helix: 2.01 (0.28), residues: 317 sheet: 1.17 (0.44), residues: 143 loop : -0.92 (0.35), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP A 346 HIS 0.001 0.000 HIS A 195 PHE 0.019 0.001 PHE A 447 TYR 0.014 0.001 TYR A 414 ARG 0.014 0.001 ARG C 75 ********************** 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 90 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 75 time to evaluate : 0.730 Fit side-chains outliers start: 15 outliers final: 14 residues processed: 87 average time/residue: 1.1492 time to fit residues: 105.4290 Evaluate side-chains 86 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 72 time to evaluate : 0.720 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 14 residues processed: 1 average time/residue: 0.2281 time to fit residues: 1.2231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 52 optimal weight: 0.6980 chunk 8 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 23 optimal weight: 8.9990 chunk 58 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 chunk 3 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 GLN C 73 ASN A 253 ASN ** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.098061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.085715 restraints weight = 12498.305| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 2.02 r_work: 0.3122 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.4687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6116 Z= 0.244 Angle : 0.585 12.267 8302 Z= 0.309 Chirality : 0.042 0.172 907 Planarity : 0.004 0.034 1026 Dihedral : 4.476 28.907 917 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.90 % Favored : 96.97 % Rotamer: Outliers : 2.39 % Allowed : 19.59 % Favored : 78.03 % 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: 1.13 (0.31), residues: 725 helix: 1.97 (0.29), residues: 317 sheet: 1.16 (0.44), residues: 143 loop : -1.04 (0.35), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP A 346 HIS 0.001 0.001 HIS A 195 PHE 0.019 0.002 PHE A 447 TYR 0.014 0.001 TYR A 414 ARG 0.007 0.001 ARG B 27 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2514.70 seconds wall clock time: 45 minutes 28.93 seconds (2728.93 seconds total)