Starting phenix.real_space_refine on Fri Dec 8 08:03:28 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sp6_25366/12_2023/7sp6_25366.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sp6_25366/12_2023/7sp6_25366.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sp6_25366/12_2023/7sp6_25366.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sp6_25366/12_2023/7sp6_25366.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sp6_25366/12_2023/7sp6_25366.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sp6_25366/12_2023/7sp6_25366.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.032 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 1808 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: 6 Type Number sf(0) Gaussians Mn 1 7.51 5 P 1 5.49 5 S 35 5.16 5 C 3858 2.51 5 N 977 2.21 5 O 1085 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 62": "OE1" <-> "OE2" Residue "A GLU 125": "OE1" <-> "OE2" Residue "A PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 46": "OE1" <-> "OE2" Residue "B GLU 55": "OE1" <-> "OE2" Residue "B TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 94": "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: 5957 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 4013 Classifications: {'peptide': 493} Link IDs: {'PTRANS': 13, 'TRANS': 479} Chain breaks: 1 Chain: "B" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 941 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "C" Number of atoms: 916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 916 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 3, 'TRANS': 113} Chain breaks: 1 Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 36 Unusual residues: {' MN': 1, 'Y01': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.92, per 1000 atoms: 0.66 Number of scatterers: 5957 At special positions: 0 Unit cell: (72.36, 76.68, 155.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Mn 1 24.99 S 35 16.00 P 1 15.00 O 1085 8.00 N 977 7.00 C 3858 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 95 " distance=2.03 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: 2.48 Conformation dependent library (CDL) restraints added in 1.6 seconds 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1358 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 7 sheets defined 46.8% alpha, 16.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 38 through 74 removed outlier: 3.646A pdb=" N LEU A 74 " --> pdb=" O ASP A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 108 Processing helix chain 'A' and resid 124 through 126 No H-bonds generated for 'chain 'A' and resid 124 through 126' Processing helix chain 'A' and resid 127 through 138 removed outlier: 3.946A pdb=" N ALA A 131 " --> pdb=" O ASP A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 160 removed outlier: 3.539A pdb=" N ILE A 160 " --> pdb=" O GLY A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 190 removed outlier: 3.594A pdb=" N SER A 180 " --> pdb=" O GLY A 176 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR A 182 " --> pdb=" O ARG A 178 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR A 183 " --> pdb=" O GLU A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 221 Proline residue: A 217 - end of helix removed outlier: 3.683A pdb=" N CYS A 220 " --> pdb=" O TYR A 216 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASP A 221 " --> pdb=" O PRO A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 262 removed outlier: 3.938A pdb=" N ARG A 256 " --> pdb=" O PHE A 252 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N GLY A 257 " --> pdb=" O ASN A 253 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N TRP A 262 " --> pdb=" O ALA A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 290 removed outlier: 5.236A pdb=" N ASP A 285 " --> pdb=" O ASN A 281 " (cutoff:3.500A) Proline residue: A 286 - end of helix removed outlier: 3.621A pdb=" N GLN A 290 " --> pdb=" O PRO A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 312 removed outlier: 3.967A pdb=" N ARG A 312 " --> pdb=" O GLU A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 360 removed outlier: 4.485A pdb=" N TRP A 351 " --> pdb=" O CYS A 347 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N TYR A 352 " --> pdb=" O ARG A 348 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU A 354 " --> pdb=" O ILE A 350 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N GLY A 355 " --> pdb=" O TRP A 351 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER A 356 " --> pdb=" O TYR A 352 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA A 357 " --> pdb=" O THR A 353 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS A 359 " --> pdb=" O GLY A 355 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N HIS A 360 " --> pdb=" O SER A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 392 removed outlier: 3.757A pdb=" N ILE A 375 " --> pdb=" O CYS A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 420 Processing helix chain 'A' and resid 421 through 428 removed outlier: 3.808A pdb=" N ALA A 424 " --> pdb=" O ASN A 421 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE A 425 " --> pdb=" O LEU A 422 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL A 428 " --> pdb=" O PHE A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 449 removed outlier: 3.878A pdb=" N VAL A 433 " --> pdb=" O LEU A 429 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ILE A 439 " --> pdb=" O PHE A 435 " (cutoff:3.500A) Proline residue: A 440 - end of helix Processing helix chain 'A' and resid 476 through 497 Processing helix chain 'A' and resid 504 through 535 removed outlier: 3.590A pdb=" N ILE A 533 " --> pdb=" O LEU A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 551 removed outlier: 3.566A pdb=" N LYS A 543 " --> pdb=" O THR A 539 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLU A 544 " --> pdb=" O PRO A 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 90 Processing helix chain 'B' and resid 107 through 111 removed outlier: 3.704A pdb=" N TYR B 111 " --> pdb=" O THR B 108 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 169 through 171 removed outlier: 8.089A pdb=" N ILE A 170 " --> pdb=" O LEU A 116 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N CYS A 118 " --> pdb=" O ILE A 170 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N VAL A 84 " --> pdb=" O ARG A 115 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N ILE A 117 " --> pdb=" O VAL A 84 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N VAL A 86 " --> pdb=" O ILE A 117 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N VAL A 119 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ILE A 88 " --> pdb=" O VAL A 119 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA A 89 " --> pdb=" O ILE A 200 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL A 227 " --> pdb=" O ALA A 274 " (cutoff:3.500A) removed outlier: 8.352A pdb=" N LYS A 225 " --> pdb=" O THR A 276 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N ILE A 224 " --> pdb=" O ILE A 316 " (cutoff:3.500A) removed outlier: 10.234A pdb=" N TYR A 318 " --> pdb=" O ILE A 224 " (cutoff:3.500A) removed outlier: 10.478A pdb=" N ALA A 226 " --> pdb=" O TYR A 318 " (cutoff:3.500A) removed outlier: 10.227A pdb=" N ALA A 228 " --> pdb=" O PRO A 320 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ALA A 322 " --> pdb=" O ALA A 228 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 500 through 501 removed outlier: 6.387A pdb=" N PHE A 500 " --> pdb=" O GLY B 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 3 through 8 removed outlier: 3.974A pdb=" N GLN B 3 " --> pdb=" O SER B 25 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER B 25 " --> pdb=" O GLN B 3 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL B 78 " --> pdb=" O CYS B 22 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR B 77 " --> pdb=" O ASP B 72 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N THR B 68 " --> pdb=" O GLN B 81 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 11 through 12 removed outlier: 7.457A pdb=" N THR B 121 " --> pdb=" O VAL B 12 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 57 through 59 removed outlier: 5.825A pdb=" N PHE B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ARG B 38 " --> pdb=" O PHE B 47 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER B 49 " --> pdb=" O TRP B 36 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 3 through 7 removed outlier: 3.767A pdb=" N GLN C 3 " --> pdb=" O SER C 25 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER C 7 " --> pdb=" O ALA C 21 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ALA C 21 " --> pdb=" O SER C 7 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU C 18 " --> pdb=" O MET C 82 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU C 81 " --> pdb=" O THR C 68 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 58 through 59 removed outlier: 4.336A pdb=" N ALA C 49 " --> pdb=" O TRP C 36 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU C 34 " --> pdb=" O SER C 51 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR C 33 " --> pdb=" O ARG C 98 " (cutoff:3.500A) 287 hydrogen bonds defined for protein. 822 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: 1.79 Time building geometry restraints manager: 2.70 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: 1024 1.33 - 1.45: 1741 1.45 - 1.57: 3268 1.57 - 1.69: 18 1.69 - 1.82: 53 Bond restraints: 6104 Sorted by residual: bond pdb=" CBD Y01 A 601 " pdb=" CBG Y01 A 601 " ideal model delta sigma weight residual 1.520 1.643 -0.123 2.00e-02 2.50e+03 3.77e+01 bond pdb=" CAV Y01 A 601 " pdb=" CAZ Y01 A 601 " ideal model delta sigma weight residual 1.507 1.609 -0.102 2.00e-02 2.50e+03 2.61e+01 bond pdb=" CAY Y01 A 601 " pdb=" OAW Y01 A 601 " ideal model delta sigma weight residual 1.332 1.425 -0.093 2.00e-02 2.50e+03 2.16e+01 bond pdb=" CAV Y01 A 601 " pdb=" CBC Y01 A 601 " ideal model delta sigma weight residual 1.523 1.613 -0.090 2.00e-02 2.50e+03 2.03e+01 bond pdb=" CBF Y01 A 601 " pdb=" CBH Y01 A 601 " ideal model delta sigma weight residual 1.550 1.639 -0.089 2.00e-02 2.50e+03 1.97e+01 ... (remaining 6099 not shown) Histogram of bond angle deviations from ideal: 99.04 - 106.03: 98 106.03 - 113.03: 3208 113.03 - 120.03: 2101 120.03 - 127.03: 2796 127.03 - 134.03: 71 Bond angle restraints: 8274 Sorted by residual: angle pdb=" CAM Y01 A 601 " pdb=" CAY Y01 A 601 " pdb=" OAW Y01 A 601 " ideal model delta sigma weight residual 111.19 124.33 -13.14 3.00e+00 1.11e-01 1.92e+01 angle pdb=" CAI Y01 A 601 " pdb=" CAZ Y01 A 601 " pdb=" CAV Y01 A 601 " ideal model delta sigma weight residual 120.03 131.73 -11.70 3.00e+00 1.11e-01 1.52e+01 angle pdb=" CAZ Y01 A 601 " pdb=" CAV Y01 A 601 " pdb=" CBC Y01 A 601 " ideal model delta sigma weight residual 111.19 122.29 -11.10 3.00e+00 1.11e-01 1.37e+01 angle pdb=" C ASN A 253 " pdb=" N VAL A 254 " pdb=" CA VAL A 254 " ideal model delta sigma weight residual 122.97 120.27 2.70 9.80e-01 1.04e+00 7.60e+00 angle pdb=" CAV Y01 A 601 " pdb=" CAZ Y01 A 601 " pdb=" CBH Y01 A 601 " ideal model delta sigma weight residual 116.96 108.83 8.13 3.00e+00 1.11e-01 7.34e+00 ... (remaining 8269 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 3265 17.95 - 35.89: 266 35.89 - 53.84: 63 53.84 - 71.78: 13 71.78 - 89.73: 7 Dihedral angle restraints: 3614 sinusoidal: 1479 harmonic: 2135 Sorted by residual: dihedral pdb=" CB CYS B 22 " pdb=" SG CYS B 22 " pdb=" SG CYS B 95 " pdb=" CB CYS B 95 " ideal model delta sinusoidal sigma weight residual 93.00 55.78 37.22 1 1.00e+01 1.00e-02 1.96e+01 dihedral pdb=" CA ASP A 77 " pdb=" CB ASP A 77 " pdb=" CG ASP A 77 " pdb=" OD1 ASP A 77 " ideal model delta sinusoidal sigma weight residual -30.00 -87.74 57.74 1 2.00e+01 2.50e-03 1.12e+01 dihedral pdb=" CA ASP A 121 " pdb=" CB ASP A 121 " pdb=" CG ASP A 121 " pdb=" OD1 ASP A 121 " ideal model delta sinusoidal sigma weight residual -30.00 -83.41 53.41 1 2.00e+01 2.50e-03 9.69e+00 ... (remaining 3611 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 837 0.080 - 0.159: 56 0.159 - 0.239: 1 0.239 - 0.318: 1 0.318 - 0.398: 3 Chirality restraints: 898 Sorted by residual: chirality pdb=" CBG Y01 A 601 " pdb=" CAQ Y01 A 601 " pdb=" CBD Y01 A 601 " pdb=" CBI Y01 A 601 " both_signs ideal model delta sigma weight residual False -2.33 -2.73 0.40 2.00e-01 2.50e+01 3.96e+00 chirality pdb=" CBE Y01 A 601 " pdb=" CAP Y01 A 601 " pdb=" CBB Y01 A 601 " pdb=" CBI Y01 A 601 " both_signs ideal model delta sigma weight residual False 2.57 2.93 -0.36 2.00e-01 2.50e+01 3.31e+00 chirality pdb=" CBI Y01 A 601 " pdb=" CAU Y01 A 601 " pdb=" CBE Y01 A 601 " pdb=" CBG Y01 A 601 " both_signs ideal model delta sigma weight residual False 2.94 2.61 0.33 2.00e-01 2.50e+01 2.75e+00 ... (remaining 895 not shown) Planarity restraints: 1020 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 319 " -0.020 5.00e-02 4.00e+02 3.06e-02 1.50e+00 pdb=" N PRO A 320 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 320 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 320 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 144 " 0.014 5.00e-02 4.00e+02 2.13e-02 7.25e-01 pdb=" N PRO A 145 " -0.037 5.00e-02 4.00e+02 pdb=" CA PRO A 145 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO A 145 " 0.012 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN C 76 " 0.004 2.00e-02 2.50e+03 7.24e-03 5.24e-01 pdb=" C ASN C 76 " -0.013 2.00e-02 2.50e+03 pdb=" O ASN C 76 " 0.005 2.00e-02 2.50e+03 pdb=" N THR C 77 " 0.004 2.00e-02 2.50e+03 ... (remaining 1017 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 1826 2.83 - 3.34: 5483 3.34 - 3.86: 9524 3.86 - 4.38: 10524 4.38 - 4.90: 18554 Nonbonded interactions: 45911 Sorted by model distance: nonbonded pdb=" O TRP A 234 " pdb=" OG1 THR A 539 " model vdw 2.308 2.440 nonbonded pdb=" O TYR A 499 " pdb=" OH TYR A 507 " model vdw 2.355 2.440 nonbonded pdb=" OG SER C 51 " pdb=" O GLY C 56 " model vdw 2.358 2.440 nonbonded pdb=" ND2 ASN A 139 " pdb=" O LYS A 166 " model vdw 2.377 2.520 nonbonded pdb=" OE1 GLN A 172 " pdb=" OG1 THR A 183 " model vdw 2.379 2.440 ... (remaining 45906 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.000 Extract box with map and model: 3.840 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 22.060 Find NCS groups from input model: 0.220 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: 0.010 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 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 6104 Z= 0.294 Angle : 0.577 13.136 8274 Z= 0.253 Chirality : 0.045 0.398 898 Planarity : 0.002 0.031 1020 Dihedral : 14.433 89.727 2250 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.31), residues: 723 helix: 2.49 (0.30), residues: 302 sheet: 1.88 (0.45), residues: 135 loop : -0.78 (0.33), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP C 53 HIS 0.000 0.000 HIS A 360 PHE 0.005 0.001 PHE C 37 TYR 0.011 0.001 TYR A 480 ARG 0.001 0.000 ARG B 66 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 0.771 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.1910 time to fit residues: 31.2023 Evaluate side-chains 95 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 0.772 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1816 ------------------------------------------------------------------------------- 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: 4.9990 chunk 30 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6104 Z= 0.197 Angle : 0.487 5.263 8274 Z= 0.256 Chirality : 0.040 0.156 898 Planarity : 0.003 0.027 1020 Dihedral : 5.979 57.855 939 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.64 % Allowed : 8.97 % Favored : 90.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.31), residues: 723 helix: 2.49 (0.29), residues: 313 sheet: 1.51 (0.44), residues: 133 loop : -1.19 (0.33), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 53 HIS 0.001 0.001 HIS A 552 PHE 0.020 0.001 PHE A 185 TYR 0.019 0.001 TYR A 46 ARG 0.002 0.000 ARG A 178 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 110 time to evaluate : 0.825 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 111 average time/residue: 0.1516 time to fit residues: 23.4595 Evaluate side-chains 94 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 92 time to evaluate : 0.714 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2132 time to fit residues: 1.5172 ------------------------------------------------------------------------------- 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: 1.9990 chunk 20 optimal weight: 0.7980 chunk 54 optimal weight: 3.9990 chunk 44 optimal weight: 0.5980 chunk 18 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 70 optimal weight: 6.9990 chunk 58 optimal weight: 4.9990 chunk 64 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 GLN B 13 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6104 Z= 0.235 Angle : 0.503 6.608 8274 Z= 0.269 Chirality : 0.041 0.162 898 Planarity : 0.003 0.025 1020 Dihedral : 5.792 49.779 939 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.76 % Allowed : 15.54 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.31), residues: 723 helix: 2.45 (0.29), residues: 312 sheet: 1.18 (0.41), residues: 140 loop : -1.25 (0.34), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 472 HIS 0.003 0.001 HIS A 552 PHE 0.012 0.002 PHE A 520 TYR 0.014 0.002 TYR A 550 ARG 0.004 0.000 ARG C 101 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 100 time to evaluate : 0.733 Fit side-chains outliers start: 11 outliers final: 5 residues processed: 107 average time/residue: 0.1773 time to fit residues: 25.2910 Evaluate side-chains 95 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 90 time to evaluate : 0.699 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0652 time to fit residues: 1.5082 ------------------------------------------------------------------------------- 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: 5.9990 chunk 49 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 62 optimal weight: 0.7980 chunk 18 optimal weight: 0.0980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.3729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6104 Z= 0.202 Angle : 0.493 6.197 8274 Z= 0.262 Chirality : 0.040 0.165 898 Planarity : 0.003 0.027 1020 Dihedral : 5.608 42.204 939 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.76 % Allowed : 17.79 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.31), residues: 723 helix: 2.42 (0.29), residues: 312 sheet: 1.00 (0.41), residues: 140 loop : -1.30 (0.34), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 246 HIS 0.001 0.001 HIS A 360 PHE 0.012 0.001 PHE A 427 TYR 0.015 0.002 TYR C 105 ARG 0.006 0.000 ARG B 27 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 98 time to evaluate : 0.728 Fit side-chains outliers start: 11 outliers final: 6 residues processed: 103 average time/residue: 0.2134 time to fit residues: 28.2881 Evaluate side-chains 97 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 91 time to evaluate : 0.655 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1098 time to fit residues: 1.8290 ------------------------------------------------------------------------------- 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: 0.9980 chunk 39 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 51 optimal weight: 0.3980 chunk 28 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 35 optimal weight: 0.8980 chunk 62 optimal weight: 0.0670 chunk 17 optimal weight: 0.8980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 542 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.3873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 6104 Z= 0.153 Angle : 0.465 6.950 8274 Z= 0.246 Chirality : 0.039 0.154 898 Planarity : 0.003 0.034 1020 Dihedral : 5.431 38.190 939 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.44 % Allowed : 17.31 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.31), residues: 723 helix: 2.47 (0.29), residues: 312 sheet: 0.94 (0.41), residues: 140 loop : -1.27 (0.34), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 246 HIS 0.001 0.000 HIS A 360 PHE 0.011 0.001 PHE A 520 TYR 0.011 0.001 TYR A 414 ARG 0.005 0.000 ARG B 27 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 102 time to evaluate : 0.701 Fit side-chains outliers start: 9 outliers final: 6 residues processed: 106 average time/residue: 0.1942 time to fit residues: 26.9335 Evaluate side-chains 100 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 94 time to evaluate : 0.693 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0653 time to fit residues: 1.5890 ------------------------------------------------------------------------------- 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: 0.8980 chunk 62 optimal weight: 0.3980 chunk 13 optimal weight: 0.8980 chunk 40 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 69 optimal weight: 5.9990 chunk 57 optimal weight: 0.9980 chunk 32 optimal weight: 6.9990 chunk 5 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 chunk 67 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: ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.4101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6104 Z= 0.170 Angle : 0.480 7.495 8274 Z= 0.252 Chirality : 0.039 0.152 898 Planarity : 0.003 0.027 1020 Dihedral : 5.397 35.542 939 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.92 % Allowed : 17.79 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.31), residues: 723 helix: 2.44 (0.29), residues: 312 sheet: 0.89 (0.42), residues: 140 loop : -1.30 (0.34), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 246 HIS 0.001 0.000 HIS A 174 PHE 0.016 0.001 PHE B 67 TYR 0.011 0.001 TYR A 414 ARG 0.007 0.000 ARG B 27 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 93 time to evaluate : 0.707 Fit side-chains outliers start: 12 outliers final: 7 residues processed: 99 average time/residue: 0.1974 time to fit residues: 25.7661 Evaluate side-chains 97 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 90 time to evaluate : 0.930 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1027 time to fit residues: 1.8914 ------------------------------------------------------------------------------- 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: 2.9990 chunk 39 optimal weight: 0.5980 chunk 50 optimal weight: 0.5980 chunk 58 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.4230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6104 Z= 0.173 Angle : 0.493 8.139 8274 Z= 0.258 Chirality : 0.039 0.156 898 Planarity : 0.003 0.026 1020 Dihedral : 5.381 35.852 939 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.96 % Allowed : 18.43 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.31), residues: 723 helix: 2.45 (0.29), residues: 312 sheet: 0.86 (0.43), residues: 140 loop : -1.32 (0.34), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 246 HIS 0.001 0.000 HIS A 174 PHE 0.014 0.001 PHE B 67 TYR 0.011 0.001 TYR A 414 ARG 0.006 0.000 ARG B 27 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 96 time to evaluate : 0.720 Fit side-chains outliers start: 6 outliers final: 6 residues processed: 100 average time/residue: 0.2061 time to fit residues: 26.8221 Evaluate side-chains 99 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 93 time to evaluate : 0.766 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0707 time to fit residues: 1.7874 ------------------------------------------------------------------------------- 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: 0.8980 chunk 13 optimal weight: 3.9990 chunk 44 optimal weight: 0.0270 chunk 47 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 63 optimal weight: 0.6980 chunk 66 optimal weight: 0.0040 chunk 60 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 overall best weight: 0.5050 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.4278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6104 Z= 0.147 Angle : 0.501 8.473 8274 Z= 0.260 Chirality : 0.040 0.234 898 Planarity : 0.003 0.027 1020 Dihedral : 5.313 37.728 939 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.64 % Allowed : 18.59 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.31), residues: 723 helix: 2.55 (0.29), residues: 311 sheet: 0.80 (0.43), residues: 140 loop : -1.30 (0.35), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 246 HIS 0.001 0.000 HIS A 174 PHE 0.012 0.001 PHE B 67 TYR 0.015 0.001 TYR C 105 ARG 0.006 0.000 ARG B 27 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 97 time to evaluate : 0.701 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 98 average time/residue: 0.1936 time to fit residues: 25.0376 Evaluate side-chains 95 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 94 time to evaluate : 0.648 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0603 time to fit residues: 0.9775 ------------------------------------------------------------------------------- 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: 4.9990 chunk 38 optimal weight: 4.9990 chunk 28 optimal weight: 0.3980 chunk 50 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 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 0.034 6104 Z= 0.243 Angle : 0.556 8.939 8274 Z= 0.294 Chirality : 0.041 0.218 898 Planarity : 0.003 0.029 1020 Dihedral : 5.677 38.101 939 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.48 % Allowed : 20.35 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.31), residues: 723 helix: 2.46 (0.29), residues: 311 sheet: 0.74 (0.43), residues: 140 loop : -1.47 (0.34), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 246 HIS 0.002 0.001 HIS A 360 PHE 0.020 0.002 PHE B 67 TYR 0.012 0.001 TYR A 414 ARG 0.007 0.000 ARG B 27 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 92 time to evaluate : 0.807 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 94 average time/residue: 0.1912 time to fit residues: 23.4795 Evaluate side-chains 93 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 90 time to evaluate : 0.731 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0579 time to fit residues: 1.3193 ------------------------------------------------------------------------------- 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: 4.9990 chunk 47 optimal weight: 0.2980 chunk 71 optimal weight: 0.6980 chunk 66 optimal weight: 5.9990 chunk 57 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.4682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6104 Z= 0.173 Angle : 0.524 8.903 8274 Z= 0.273 Chirality : 0.040 0.207 898 Planarity : 0.003 0.030 1020 Dihedral : 5.554 38.893 939 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.00 % Allowed : 20.83 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.31), residues: 723 helix: 2.53 (0.28), residues: 311 sheet: 0.65 (0.41), residues: 149 loop : -1.54 (0.34), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 53 HIS 0.001 0.000 HIS A 174 PHE 0.014 0.001 PHE B 67 TYR 0.011 0.001 TYR A 414 ARG 0.007 0.000 ARG B 27 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 0.716 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.1987 time to fit residues: 25.4941 Evaluate side-chains 94 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 0.717 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9516 ------------------------------------------------------------------------------- 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: 0.9990 chunk 15 optimal weight: 0.8980 chunk 57 optimal weight: 0.0870 chunk 23 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 chunk 3 optimal weight: 0.0870 chunk 41 optimal weight: 6.9990 overall best weight: 0.5536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.113962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.096346 restraints weight = 9880.963| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.63 r_work: 0.3154 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.4688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6104 Z= 0.158 Angle : 0.512 8.771 8274 Z= 0.266 Chirality : 0.040 0.202 898 Planarity : 0.003 0.031 1020 Dihedral : 5.434 39.815 939 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.16 % Allowed : 20.83 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.31), residues: 723 helix: 2.60 (0.28), residues: 311 sheet: 0.60 (0.41), residues: 149 loop : -1.56 (0.34), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 53 HIS 0.001 0.000 HIS A 360 PHE 0.014 0.001 PHE B 67 TYR 0.011 0.001 TYR A 414 ARG 0.007 0.000 ARG B 27 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1664.67 seconds wall clock time: 31 minutes 9.75 seconds (1869.75 seconds total)