Starting phenix.real_space_refine (version: 1.21rc1) on Tue Oct 3 18:48:09 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sp9_25369/10_2023/7sp9_25369.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sp9_25369/10_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_25369/10_2023/7sp9_25369.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sp9_25369/10_2023/7sp9_25369.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sp9_25369/10_2023/7sp9_25369.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sp9_25369/10_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-1.21rc1-5097/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: 3.82, per 1000 atoms: 0.64 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: 2.41 Conformation dependent library (CDL) restraints added in 1.1 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: 0.61 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: 1.77 Time building geometry restraints manager: 2.55 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: 3264 16.23 - 32.47: 201 32.47 - 48.70: 46 48.70 - 64.93: 9 64.93 - 81.16: 5 Dihedral angle restraints: 3525 sinusoidal: 1379 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 3522 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: 1.060 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: 0.000 Extract box with map and model: 3.860 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 20.380 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 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:11.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.500 ------------------------------------------------------------------------------- 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 : 11.907 81.163 2156 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 *********************** 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 : 0.725 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 1.0195 time to fit residues: 133.7019 Evaluate side-chains 87 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.618 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8281 ------------------------------------------------------------------------------- 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: 0.8114 moved from start: 0.3578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 6116 Z= 0.353 Angle : 0.687 9.229 8302 Z= 0.359 Chirality : 0.047 0.155 907 Planarity : 0.005 0.039 1026 Dihedral : 5.532 56.200 835 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.90 % Favored : 96.97 % Rotamer: Outliers : 3.03 % Allowed : 11.94 % Favored : 85.03 % 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: 1.04 (0.30), residues: 725 helix: 1.81 (0.29), residues: 311 sheet: 0.94 (0.42), residues: 152 loop : -0.83 (0.34), residues: 262 *********************** 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 117 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 98 time to evaluate : 0.718 Fit side-chains outliers start: 19 outliers final: 11 residues processed: 107 average time/residue: 1.0672 time to fit residues: 120.3822 Evaluate side-chains 85 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 74 time to evaluate : 0.731 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 7 residues processed: 4 average time/residue: 0.5068 time to fit residues: 3.1239 ------------------------------------------------------------------------------- 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: 3.9990 chunk 20 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 18 optimal weight: 0.4980 chunk 65 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 58 optimal weight: 0.6980 chunk 64 optimal weight: 6.9990 chunk 22 optimal weight: 0.3980 chunk 52 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 ** 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: 0.8075 moved from start: 0.3643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6116 Z= 0.159 Angle : 0.489 6.260 8302 Z= 0.262 Chirality : 0.040 0.137 907 Planarity : 0.003 0.030 1026 Dihedral : 5.063 59.168 835 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.34 % Favored : 97.52 % 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: 1.31 (0.31), residues: 725 helix: 2.14 (0.29), residues: 311 sheet: 0.97 (0.42), residues: 152 loop : -0.77 (0.35), residues: 262 *********************** 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 104 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 81 time to evaluate : 0.733 Fit side-chains outliers start: 23 outliers final: 10 residues processed: 93 average time/residue: 1.1428 time to fit residues: 111.8891 Evaluate side-chains 81 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 71 time to evaluate : 0.641 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 8 residues processed: 2 average time/residue: 0.0739 time to fit residues: 1.1327 ------------------------------------------------------------------------------- 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: 0.9980 chunk 49 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- 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: 0.8136 moved from start: 0.4054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6116 Z= 0.231 Angle : 0.532 7.078 8302 Z= 0.283 Chirality : 0.042 0.150 907 Planarity : 0.004 0.041 1026 Dihedral : 5.033 55.905 835 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.76 % Favored : 97.10 % Rotamer: Outliers : 3.98 % Allowed : 15.61 % Favored : 80.41 % 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: 2.07 (0.29), residues: 311 sheet: 0.91 (0.42), residues: 152 loop : -0.83 (0.34), residues: 262 *********************** 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 101 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 76 time to evaluate : 0.690 Fit side-chains outliers start: 25 outliers final: 17 residues processed: 94 average time/residue: 1.1450 time to fit residues: 113.3515 Evaluate side-chains 86 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 69 time to evaluate : 0.748 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 14 residues processed: 3 average time/residue: 0.1383 time to fit residues: 1.4836 ------------------------------------------------------------------------------- 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: 0.3980 chunk 39 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 59 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 62 optimal weight: 0.4980 chunk 17 optimal weight: 4.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- 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: 0.8116 moved from start: 0.4090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6116 Z= 0.165 Angle : 0.498 7.122 8302 Z= 0.264 Chirality : 0.040 0.149 907 Planarity : 0.003 0.041 1026 Dihedral : 4.884 58.169 835 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.62 % Favored : 97.24 % Rotamer: Outliers : 3.98 % Allowed : 16.40 % Favored : 79.62 % 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: 1.28 (0.31), residues: 725 helix: 2.15 (0.29), residues: 311 sheet: 0.92 (0.43), residues: 152 loop : -0.82 (0.34), residues: 262 *********************** 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: 25 poor density : 74 time to evaluate : 0.700 Fit side-chains outliers start: 25 outliers final: 16 residues processed: 92 average time/residue: 1.1553 time to fit residues: 111.9132 Evaluate side-chains 86 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 70 time to evaluate : 0.685 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 14 residues processed: 2 average time/residue: 0.1034 time to fit residues: 1.2218 ------------------------------------------------------------------------------- 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: 0.7980 chunk 13 optimal weight: 7.9990 chunk 40 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 chunk 36 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- 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 78 ASN A 253 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.4547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 6116 Z= 0.300 Angle : 0.578 7.279 8302 Z= 0.310 Chirality : 0.043 0.173 907 Planarity : 0.004 0.046 1026 Dihedral : 4.911 44.423 835 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.90 % Favored : 96.97 % Rotamer: Outliers : 3.98 % Allowed : 15.45 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.31), residues: 725 helix: 1.88 (0.29), residues: 317 sheet: 0.69 (0.42), residues: 153 loop : -0.96 (0.35), residues: 255 *********************** 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 101 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 76 time to evaluate : 0.698 Fit side-chains outliers start: 25 outliers final: 15 residues processed: 94 average time/residue: 1.1462 time to fit residues: 113.3893 Evaluate side-chains 85 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 70 time to evaluate : 0.634 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 13 residues processed: 2 average time/residue: 0.1009 time to fit residues: 1.1891 ------------------------------------------------------------------------------- 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: 1.9990 chunk 39 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 38 optimal weight: 0.0030 chunk 69 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 27 optimal weight: 0.0370 chunk 41 optimal weight: 0.9980 overall best weight: 0.5268 ------------------------------------------------------------------------------- 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: 0.8132 moved from start: 0.4440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 6116 Z= 0.149 Angle : 0.520 7.699 8302 Z= 0.273 Chirality : 0.040 0.157 907 Planarity : 0.004 0.046 1026 Dihedral : 4.479 35.947 835 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.48 % Favored : 97.38 % Rotamer: Outliers : 3.66 % Allowed : 17.36 % 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: 1.15 (0.31), residues: 725 helix: 2.07 (0.29), residues: 316 sheet: 0.92 (0.43), residues: 143 loop : -0.97 (0.34), residues: 266 *********************** 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 103 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 80 time to evaluate : 0.763 Fit side-chains outliers start: 23 outliers final: 14 residues processed: 96 average time/residue: 1.1207 time to fit residues: 113.5119 Evaluate side-chains 86 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 72 time to evaluate : 0.680 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 12 residues processed: 2 average time/residue: 0.2014 time to fit residues: 1.3931 ------------------------------------------------------------------------------- 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: 0.3980 chunk 13 optimal weight: 0.1980 chunk 44 optimal weight: 3.9990 chunk 47 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 54 optimal weight: 6.9990 chunk 63 optimal weight: 0.8980 chunk 66 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- 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: 0.8131 moved from start: 0.4408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6116 Z= 0.158 Angle : 0.517 7.677 8302 Z= 0.274 Chirality : 0.040 0.169 907 Planarity : 0.004 0.054 1026 Dihedral : 4.322 32.365 835 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.62 % Favored : 97.24 % Rotamer: Outliers : 3.03 % Allowed : 18.63 % 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: 1.14 (0.31), residues: 725 helix: 2.06 (0.28), residues: 316 sheet: 0.71 (0.42), residues: 151 loop : -0.87 (0.35), residues: 258 *********************** 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 96 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 77 time to evaluate : 0.730 Fit side-chains outliers start: 19 outliers final: 15 residues processed: 91 average time/residue: 1.1455 time to fit residues: 109.8957 Evaluate side-chains 88 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 73 time to evaluate : 0.667 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 14 residues processed: 1 average time/residue: 0.2189 time to fit residues: 1.1624 ------------------------------------------------------------------------------- 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: 4.9990 chunk 28 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 58 optimal weight: 0.6980 chunk 61 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 41 optimal weight: 0.6980 overall best weight: 1.8786 ------------------------------------------------------------------------------- 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: 0.8208 moved from start: 0.4773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 6116 Z= 0.322 Angle : 0.613 9.670 8302 Z= 0.326 Chirality : 0.044 0.212 907 Planarity : 0.004 0.060 1026 Dihedral : 4.662 29.580 835 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.76 % Favored : 97.10 % Rotamer: Outliers : 3.34 % Allowed : 18.47 % Favored : 78.18 % 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: 0.95 (0.31), residues: 725 helix: 1.91 (0.29), residues: 317 sheet: 0.67 (0.42), residues: 151 loop : -1.05 (0.35), residues: 257 *********************** 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 98 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 77 time to evaluate : 0.715 Fit side-chains outliers start: 21 outliers final: 13 residues processed: 92 average time/residue: 1.1593 time to fit residues: 112.1936 Evaluate side-chains 81 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 68 time to evaluate : 0.647 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 13 residues processed: 0 time to fit residues: 0.8801 ------------------------------------------------------------------------------- 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: 0.9990 chunk 47 optimal weight: 0.1980 chunk 71 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 57 optimal weight: 0.6980 chunk 5 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 60 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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: 0.8153 moved from start: 0.4680 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= 0.172 Angle : 0.576 13.480 8302 Z= 0.299 Chirality : 0.041 0.171 907 Planarity : 0.004 0.058 1026 Dihedral : 4.409 31.055 835 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.62 % Favored : 97.24 % Rotamer: Outliers : 2.39 % Allowed : 19.11 % Favored : 78.50 % 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: 1.06 (0.30), residues: 725 helix: 1.96 (0.28), residues: 317 sheet: 0.95 (0.43), residues: 143 loop : -1.02 (0.35), residues: 265 ********************** 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 91 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 76 time to evaluate : 0.638 Fit side-chains outliers start: 15 outliers final: 13 residues processed: 89 average time/residue: 1.1461 time to fit residues: 107.4410 Evaluate side-chains 86 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 73 time to evaluate : 0.694 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 13 residues processed: 1 average time/residue: 0.2226 time to fit residues: 1.1989 ------------------------------------------------------------------------------- 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: 0.9980 chunk 8 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 57 optimal weight: 0.8980 chunk 23 optimal weight: 9.9990 chunk 58 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 10 optimal weight: 0.2980 chunk 50 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 41 optimal weight: 0.2980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3485 r_free = 0.3485 target = 0.099290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.087522 restraints weight = 12422.870| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 1.94 r_work: 0.3191 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.4619 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= 0.194 Angle : 0.576 11.808 8302 Z= 0.300 Chirality : 0.042 0.172 907 Planarity : 0.004 0.042 1026 Dihedral : 4.363 31.906 835 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.62 % Favored : 97.24 % 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: 1.04 (0.30), residues: 725 helix: 1.95 (0.28), residues: 317 sheet: 0.93 (0.43), residues: 143 loop : -1.03 (0.35), residues: 265 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2432.94 seconds wall clock time: 43 minutes 47.34 seconds (2627.34 seconds total)