Starting phenix.real_space_refine (version: dev) on Tue Nov 29 13:09:06 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lz0_30020/11_2022/6lz0_30020_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lz0_30020/11_2022/6lz0_30020.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lz0_30020/11_2022/6lz0_30020.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lz0_30020/11_2022/6lz0_30020.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lz0_30020/11_2022/6lz0_30020_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lz0_30020/11_2022/6lz0_30020_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A TYR 359": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4778/modules/chem_data/mon_lib" Total number of atoms: 4006 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2846 Classifications: {'peptide': 375} Link IDs: {'PTRANS': 17, 'TRANS': 357} Chain breaks: 1 Chain: "B" Number of atoms: 1154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1154 Classifications: {'peptide': 216} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 161} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 205} Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 550 Unresolved non-hydrogen angles: 705 Unresolved non-hydrogen dihedrals: 460 Unresolved non-hydrogen chiralities: 50 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 12, 'TYR:plan': 4, 'ASN:plan1': 7, 'TRP:plan': 4, 'HIS:plan': 3, 'PHE:plan': 5, 'GLU:plan': 16, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 289 Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 6 Unusual residues: {'2OP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.87, per 1000 atoms: 0.72 Number of scatterers: 4006 At special positions: 0 Unit cell: (106.526, 58.698, 118.483, 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 25 16.00 O 698 8.00 N 679 7.00 C 2604 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.64 Conformation dependent library (CDL) restraints added in 709.7 milliseconds 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1054 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 18 helices and 4 sheets defined 59.4% alpha, 14.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 18 through 34 Processing helix chain 'A' and resid 37 through 49 removed outlier: 3.680A pdb=" N THR A 41 " --> pdb=" O PRO A 37 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N VAL A 42 " --> pdb=" O LYS A 38 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N PHE A 43 " --> pdb=" O SER A 39 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N PHE A 44 " --> pdb=" O ILE A 40 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N LYS A 45 " --> pdb=" O THR A 41 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N GLU A 46 " --> pdb=" O VAL A 42 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLY A 49 " --> pdb=" O LYS A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 83 removed outlier: 5.185A pdb=" N ILE A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N SER A 62 " --> pdb=" O VAL A 58 " (cutoff:3.500A) Proline residue: A 74 - end of helix Processing helix chain 'A' and resid 86 through 105 removed outlier: 4.207A pdb=" N PHE A 105 " --> pdb=" O ILE A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 138 removed outlier: 3.895A pdb=" N VAL A 118 " --> pdb=" O VAL A 114 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N ILE A 119 " --> pdb=" O CYS A 115 " (cutoff:3.500A) Proline residue: A 130 - end of helix removed outlier: 3.780A pdb=" N THR A 133 " --> pdb=" O ASN A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 171 removed outlier: 4.808A pdb=" N SER A 154 " --> pdb=" O ALA A 150 " (cutoff:3.500A) Proline residue: A 155 - end of helix removed outlier: 4.510A pdb=" N ALA A 162 " --> pdb=" O LEU A 158 " (cutoff:3.500A) Proline residue: A 163 - end of helix Processing helix chain 'A' and resid 174 through 192 removed outlier: 4.364A pdb=" N GLY A 183 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU A 184 " --> pdb=" O ILE A 180 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N CYS A 189 " --> pdb=" O LEU A 185 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 276 removed outlier: 3.884A pdb=" N ILE A 272 " --> pdb=" O SER A 268 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N PHE A 275 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N GLY A 276 " --> pdb=" O ILE A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 290 removed outlier: 5.655A pdb=" N SER A 285 " --> pdb=" O LEU A 281 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N SER A 286 " --> pdb=" O VAL A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 321 removed outlier: 3.937A pdb=" N VAL A 311 " --> pdb=" O PHE A 307 " (cutoff:3.500A) Proline residue: A 314 - end of helix removed outlier: 3.733A pdb=" N ASN A 321 " --> pdb=" O GLY A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 326 No H-bonds generated for 'chain 'A' and resid 323 through 326' Processing helix chain 'A' and resid 331 through 344 removed outlier: 3.716A pdb=" N ALA A 335 " --> pdb=" O TYR A 331 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N SER A 336 " --> pdb=" O PHE A 332 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL A 337 " --> pdb=" O PHE A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 382 removed outlier: 5.537A pdb=" N VAL A 358 " --> pdb=" O GLY A 355 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N LEU A 374 " --> pdb=" O SER A 371 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N MET A 379 " --> pdb=" O GLU A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 415 removed outlier: 3.738A pdb=" N ILE A 396 " --> pdb=" O GLY A 392 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N VAL A 397 " --> pdb=" O LEU A 393 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLU A 398 " --> pdb=" O VAL A 394 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N CYS A 399 " --> pdb=" O THR A 395 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N CYS A 400 " --> pdb=" O ILE A 396 " (cutoff:3.500A) Proline residue: A 401 - end of helix Proline residue: A 406 - end of helix removed outlier: 4.457A pdb=" N ARG A 411 " --> pdb=" O PRO A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 447 removed outlier: 3.804A pdb=" N VAL A 428 " --> pdb=" O TRP A 424 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N MET A 441 " --> pdb=" O LEU A 437 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N GLY A 442 " --> pdb=" O PHE A 438 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ILE A 443 " --> pdb=" O ILE A 439 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASN A 444 " --> pdb=" O GLY A 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 80 No H-bonds generated for 'chain 'B' and resid 78 through 80' Processing helix chain 'B' and resid 154 through 156 No H-bonds generated for 'chain 'B' and resid 154 through 156' Processing helix chain 'B' and resid 205 through 237 removed outlier: 4.999A pdb=" N TRP B 210 " --> pdb=" O ALA B 207 " (cutoff:3.500A) Proline residue: B 211 - end of helix removed outlier: 3.527A pdb=" N VAL B 221 " --> pdb=" O GLU B 218 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N LYS B 234 " --> pdb=" O LYS B 231 " (cutoff:3.500A) Proline residue: B 235 - end of helix Processing sheet with id= A, first strand: chain 'B' and resid 25 through 33 Processing sheet with id= B, first strand: chain 'B' and resid 95 through 100 removed outlier: 4.067A pdb=" N GLY B 95 " --> pdb=" O PHE B 89 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 113 through 117 removed outlier: 8.600A pdb=" N GLU B 114 " --> pdb=" O ILE B 197 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N THR B 199 " --> pdb=" O GLU B 114 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N ILE B 116 " --> pdb=" O THR B 199 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ARG B 201 " --> pdb=" O ILE B 116 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLY B 192 " --> pdb=" O SER B 189 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N TRP B 139 " --> pdb=" O LEU B 150 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 122 through 127 removed outlier: 3.501A pdb=" N ARG B 166 " --> pdb=" O SER B 163 " (cutoff:3.500A) 269 hydrogen bonds defined for protein. 609 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: 1.12 Time building geometry restraints manager: 1.77 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: 794 1.33 - 1.45: 986 1.45 - 1.57: 2273 1.57 - 1.69: 0 1.69 - 1.81: 38 Bond restraints: 4091 Sorted by residual: bond pdb=" CA VAL B 131 " pdb=" C VAL B 131 " ideal model delta sigma weight residual 1.524 1.557 -0.033 8.30e-03 1.45e+04 1.63e+01 bond pdb=" N ARG A 326 " pdb=" CA ARG A 326 " ideal model delta sigma weight residual 1.462 1.489 -0.027 8.50e-03 1.38e+04 1.03e+01 bond pdb=" C ASP B 179 " pdb=" N PRO B 180 " ideal model delta sigma weight residual 1.332 1.366 -0.034 1.12e-02 7.97e+03 9.43e+00 bond pdb=" N GLU B 120 " pdb=" CA GLU B 120 " ideal model delta sigma weight residual 1.453 1.492 -0.039 1.31e-02 5.83e+03 8.95e+00 bond pdb=" N GLY B 103 " pdb=" CA GLY B 103 " ideal model delta sigma weight residual 1.443 1.483 -0.041 1.37e-02 5.33e+03 8.87e+00 ... (remaining 4086 not shown) Histogram of bond angle deviations from ideal: 100.09 - 106.93: 118 106.93 - 113.76: 2159 113.76 - 120.60: 1857 120.60 - 127.43: 1412 127.43 - 134.27: 38 Bond angle restraints: 5584 Sorted by residual: angle pdb=" C TYR A 113 " pdb=" CA TYR A 113 " pdb=" CB TYR A 113 " ideal model delta sigma weight residual 110.88 102.05 8.83 1.57e+00 4.06e-01 3.17e+01 angle pdb=" N ILE B 142 " pdb=" CA ILE B 142 " pdb=" C ILE B 142 " ideal model delta sigma weight residual 108.12 114.95 -6.83 1.34e+00 5.57e-01 2.59e+01 angle pdb=" C THR B 28 " pdb=" CA THR B 28 " pdb=" CB THR B 28 " ideal model delta sigma weight residual 109.51 117.98 -8.47 1.71e+00 3.42e-01 2.46e+01 angle pdb=" N VAL B 50 " pdb=" CA VAL B 50 " pdb=" C VAL B 50 " ideal model delta sigma weight residual 109.30 115.19 -5.89 1.25e+00 6.40e-01 2.22e+01 angle pdb=" N LEU B 101 " pdb=" CA LEU B 101 " pdb=" C LEU B 101 " ideal model delta sigma weight residual 110.48 103.68 6.80 1.48e+00 4.57e-01 2.11e+01 ... (remaining 5579 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.02: 2073 17.02 - 34.04: 190 34.04 - 51.07: 41 51.07 - 68.09: 13 68.09 - 85.11: 4 Dihedral angle restraints: 2321 sinusoidal: 661 harmonic: 1660 Sorted by residual: dihedral pdb=" CA PRO A 348 " pdb=" C PRO A 348 " pdb=" N LEU A 349 " pdb=" CA LEU A 349 " ideal model delta harmonic sigma weight residual 180.00 140.49 39.51 0 5.00e+00 4.00e-02 6.24e+01 dihedral pdb=" C VAL B 50 " pdb=" N VAL B 50 " pdb=" CA VAL B 50 " pdb=" CB VAL B 50 " ideal model delta harmonic sigma weight residual -122.00 -139.11 17.11 0 2.50e+00 1.60e-01 4.68e+01 dihedral pdb=" N VAL B 50 " pdb=" C VAL B 50 " pdb=" CA VAL B 50 " pdb=" CB VAL B 50 " ideal model delta harmonic sigma weight residual 123.40 139.16 -15.76 0 2.50e+00 1.60e-01 3.97e+01 ... (remaining 2318 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 580 0.112 - 0.224: 62 0.224 - 0.337: 10 0.337 - 0.449: 6 0.449 - 0.561: 3 Chirality restraints: 661 Sorted by residual: chirality pdb=" CA VAL B 50 " pdb=" N VAL B 50 " pdb=" C VAL B 50 " pdb=" CB VAL B 50 " both_signs ideal model delta sigma weight residual False 2.44 1.88 0.56 2.00e-01 2.50e+01 7.87e+00 chirality pdb=" CA GLU B 172 " pdb=" N GLU B 172 " pdb=" C GLU B 172 " pdb=" CB GLU B 172 " both_signs ideal model delta sigma weight residual False 2.51 1.95 0.56 2.00e-01 2.50e+01 7.78e+00 chirality pdb=" CA GLU B 155 " pdb=" N GLU B 155 " pdb=" C GLU B 155 " pdb=" CB GLU B 155 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.73e+00 ... (remaining 658 not shown) Planarity restraints: 715 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY B 103 " 0.013 2.00e-02 2.50e+03 2.55e-02 6.50e+00 pdb=" C GLY B 103 " -0.044 2.00e-02 2.50e+03 pdb=" O GLY B 103 " 0.016 2.00e-02 2.50e+03 pdb=" N PRO B 104 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 27 " -0.012 2.00e-02 2.50e+03 2.35e-02 5.52e+00 pdb=" C PHE A 27 " 0.041 2.00e-02 2.50e+03 pdb=" O PHE A 27 " -0.015 2.00e-02 2.50e+03 pdb=" N ILE A 28 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 347 " 0.036 5.00e-02 4.00e+02 5.44e-02 4.73e+00 pdb=" N PRO A 348 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO A 348 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 348 " 0.030 5.00e-02 4.00e+02 ... (remaining 712 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 111 2.68 - 3.24: 4168 3.24 - 3.79: 5829 3.79 - 4.35: 7340 4.35 - 4.90: 11780 Nonbonded interactions: 29228 Sorted by model distance: nonbonded pdb=" O GLN A 291 " pdb=" ND1 HIS A 292 " model vdw 2.126 2.520 nonbonded pdb=" O THR A 352 " pdb=" N GLY A 355 " model vdw 2.212 2.520 nonbonded pdb=" OG1 THR A 108 " pdb=" OE1 GLN A 111 " model vdw 2.227 2.440 nonbonded pdb=" O LYS A 297 " pdb=" OH TYR A 353 " model vdw 2.248 2.440 nonbonded pdb=" O VAL B 221 " pdb=" OG1 THR B 224 " model vdw 2.293 2.440 ... (remaining 29223 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 Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 25 5.16 5 C 2604 2.51 5 N 679 2.21 5 O 698 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.030 Check model and map are aligned: 0.060 Convert atoms to be neutral: 0.040 Process input model: 15.840 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6142 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 : 0.008 0.042 4091 Z= 0.583 Angle : 1.172 8.839 5584 Z= 0.795 Chirality : 0.088 0.561 661 Planarity : 0.005 0.054 715 Dihedral : 15.050 85.110 1267 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 17.56 Ramachandran Plot: Outliers : 0.17 % Allowed : 11.11 % Favored : 88.72 % Rotamer Outliers : 5.25 % Cbeta Deviations : 1.90 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -4.02 (0.29), residues: 585 helix: -2.79 (0.21), residues: 333 sheet: 0.27 (0.53), residues: 94 loop : -3.79 (0.39), residues: 158 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 96 time to evaluate : 0.436 Fit side-chains outliers start: 17 outliers final: 4 residues processed: 106 average time/residue: 0.1372 time to fit residues: 18.5543 Evaluate side-chains 74 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 70 time to evaluate : 0.454 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0491 time to fit residues: 0.9528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 48 optimal weight: 30.0000 chunk 43 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 15 optimal weight: 0.3980 chunk 29 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 33 optimal weight: 7.9990 chunk 52 optimal weight: 20.0000 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 165 ASN A 260 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6332 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 4091 Z= 0.265 Angle : 0.740 8.046 5584 Z= 0.388 Chirality : 0.046 0.157 661 Planarity : 0.006 0.062 715 Dihedral : 4.928 30.152 620 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer Outliers : 3.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -1.95 (0.34), residues: 585 helix: -1.02 (0.27), residues: 326 sheet: 1.05 (0.50), residues: 105 loop : -3.40 (0.45), residues: 154 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 88 time to evaluate : 0.447 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 11 residues processed: 96 average time/residue: 0.1320 time to fit residues: 16.4640 Evaluate side-chains 89 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 78 time to evaluate : 0.412 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0462 time to fit residues: 1.4853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 29 optimal weight: 0.5980 chunk 16 optimal weight: 0.6980 chunk 43 optimal weight: 50.0000 chunk 35 optimal weight: 0.0470 chunk 14 optimal weight: 2.9990 chunk 52 optimal weight: 50.0000 chunk 57 optimal weight: 0.9980 chunk 46 optimal weight: 8.9990 chunk 17 optimal weight: 0.0020 chunk 42 optimal weight: 20.0000 chunk 39 optimal weight: 50.0000 overall best weight: 0.4686 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 292 HIS ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6266 moved from start: 0.3626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 4091 Z= 0.183 Angle : 0.670 7.142 5584 Z= 0.345 Chirality : 0.042 0.130 661 Planarity : 0.005 0.062 715 Dihedral : 4.508 22.789 620 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer Outliers : 2.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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 (0.35), residues: 585 helix: -0.48 (0.29), residues: 326 sheet: 0.90 (0.49), residues: 113 loop : -2.94 (0.50), residues: 146 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 84 time to evaluate : 0.467 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 88 average time/residue: 0.1285 time to fit residues: 14.9794 Evaluate side-chains 76 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 73 time to evaluate : 0.438 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0389 time to fit residues: 0.7923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 27 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 25 optimal weight: 0.2980 chunk 35 optimal weight: 0.8980 chunk 52 optimal weight: 40.0000 chunk 56 optimal weight: 0.2980 chunk 50 optimal weight: 50.0000 chunk 15 optimal weight: 0.9990 chunk 46 optimal weight: 20.0000 chunk 31 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6299 moved from start: 0.4194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 4091 Z= 0.181 Angle : 0.647 6.782 5584 Z= 0.332 Chirality : 0.042 0.129 661 Planarity : 0.005 0.061 715 Dihedral : 4.343 22.189 620 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer Outliers : 4.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.98 (0.35), residues: 585 helix: -0.31 (0.29), residues: 331 sheet: 1.04 (0.48), residues: 113 loop : -2.69 (0.50), residues: 141 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 83 time to evaluate : 0.427 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 9 residues processed: 94 average time/residue: 0.1144 time to fit residues: 14.3508 Evaluate side-chains 84 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 75 time to evaluate : 0.427 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0412 time to fit residues: 1.2396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 41 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 chunk 47 optimal weight: 8.9990 chunk 38 optimal weight: 5.9990 chunk 0 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 50 optimal weight: 30.0000 chunk 14 optimal weight: 0.0870 chunk 18 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 32 optimal weight: 0.7980 overall best weight: 0.6358 ------------------------------------------------------------------------------- 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: 0.6296 moved from start: 0.4472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 4091 Z= 0.180 Angle : 0.673 12.189 5584 Z= 0.335 Chirality : 0.042 0.125 661 Planarity : 0.005 0.061 715 Dihedral : 4.334 22.156 620 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer Outliers : 1.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.87 (0.35), residues: 585 helix: -0.24 (0.30), residues: 323 sheet: 1.25 (0.48), residues: 113 loop : -2.63 (0.49), residues: 149 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 84 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 86 average time/residue: 0.1148 time to fit residues: 13.1582 Evaluate side-chains 81 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 79 time to evaluate : 0.416 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0376 time to fit residues: 0.7147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 13 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 46 optimal weight: 30.0000 chunk 25 optimal weight: 0.0970 chunk 4 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 54 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 40 optimal weight: 4.9990 overall best weight: 0.7378 ------------------------------------------------------------------------------- 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: 0.6322 moved from start: 0.4754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 4091 Z= 0.191 Angle : 0.663 10.984 5584 Z= 0.332 Chirality : 0.042 0.128 661 Planarity : 0.005 0.061 715 Dihedral : 4.309 22.326 620 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer Outliers : 2.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.61 (0.36), residues: 585 helix: -0.07 (0.30), residues: 329 sheet: 1.41 (0.48), residues: 113 loop : -2.58 (0.50), residues: 143 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 83 time to evaluate : 0.420 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 6 residues processed: 85 average time/residue: 0.1183 time to fit residues: 13.4714 Evaluate side-chains 84 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 78 time to evaluate : 0.395 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0449 time to fit residues: 0.9913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 31 optimal weight: 1.9990 chunk 47 optimal weight: 8.9990 chunk 55 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 35 optimal weight: 0.6980 chunk 38 optimal weight: 5.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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: 0.6405 moved from start: 0.5110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 4091 Z= 0.249 Angle : 0.696 10.834 5584 Z= 0.353 Chirality : 0.044 0.173 661 Planarity : 0.005 0.061 715 Dihedral : 4.403 22.438 620 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer Outliers : 2.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.65 (0.35), residues: 585 helix: -0.16 (0.29), residues: 329 sheet: 1.60 (0.49), residues: 113 loop : -2.63 (0.49), residues: 143 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 83 time to evaluate : 0.442 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 6 residues processed: 88 average time/residue: 0.1144 time to fit residues: 13.5707 Evaluate side-chains 88 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 82 time to evaluate : 0.429 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0883 time to fit residues: 1.3121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 27 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 43 optimal weight: 50.0000 chunk 50 optimal weight: 1.9990 chunk 53 optimal weight: 50.0000 chunk 48 optimal weight: 20.0000 chunk 52 optimal weight: 40.0000 chunk 31 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 40 optimal weight: 8.9990 chunk 15 optimal weight: 0.0970 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6447 moved from start: 0.5392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 4091 Z= 0.273 Angle : 0.760 11.426 5584 Z= 0.377 Chirality : 0.045 0.158 661 Planarity : 0.005 0.061 715 Dihedral : 4.501 22.227 620 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer Outliers : 2.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.64 (0.35), residues: 585 helix: -0.20 (0.29), residues: 331 sheet: 1.77 (0.50), residues: 111 loop : -2.60 (0.48), residues: 143 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 85 time to evaluate : 0.434 Fit side-chains outliers start: 9 outliers final: 7 residues processed: 86 average time/residue: 0.1156 time to fit residues: 13.4496 Evaluate side-chains 89 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 82 time to evaluate : 0.442 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0447 time to fit residues: 1.1835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 47 optimal weight: 6.9990 chunk 49 optimal weight: 8.9990 chunk 51 optimal weight: 20.0000 chunk 34 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 38 optimal weight: 8.9990 chunk 57 optimal weight: 0.8980 chunk 53 optimal weight: 50.0000 chunk 46 optimal weight: 10.0000 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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: 0.6473 moved from start: 0.5600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 4091 Z= 0.281 Angle : 0.757 11.210 5584 Z= 0.374 Chirality : 0.045 0.154 661 Planarity : 0.005 0.061 715 Dihedral : 4.561 22.649 620 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer Outliers : 1.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.63 (0.35), residues: 585 helix: -0.28 (0.28), residues: 331 sheet: 1.95 (0.50), residues: 109 loop : -2.48 (0.48), residues: 145 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 79 time to evaluate : 0.453 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 82 average time/residue: 0.1185 time to fit residues: 13.0437 Evaluate side-chains 81 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 78 time to evaluate : 0.371 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0529 time to fit residues: 0.8576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 4 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 chunk 49 optimal weight: 8.9990 chunk 14 optimal weight: 0.8980 chunk 42 optimal weight: 9.9990 chunk 6 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 46 optimal weight: 20.0000 chunk 19 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6403 moved from start: 0.5736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 4091 Z= 0.203 Angle : 0.721 11.117 5584 Z= 0.353 Chirality : 0.044 0.180 661 Planarity : 0.005 0.060 715 Dihedral : 4.466 22.724 620 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer Outliers : 0.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.36 (0.35), residues: 585 helix: -0.09 (0.29), residues: 327 sheet: 2.09 (0.49), residues: 109 loop : -2.24 (0.48), residues: 149 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1170 Ramachandran restraints generated. 585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 83 time to evaluate : 0.511 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 84 average time/residue: 0.1117 time to fit residues: 12.6804 Evaluate side-chains 83 residues out of total 486 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 82 time to evaluate : 0.432 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0411 time to fit residues: 0.6432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 47 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 40 optimal weight: 4.9990 chunk 2 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 52 optimal weight: 40.0000 chunk 30 optimal weight: 0.9980 chunk 39 optimal weight: 50.0000 chunk 1 optimal weight: 0.1980 chunk 36 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4608 r_free = 0.4608 target = 0.216948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.171401 restraints weight = 5599.988| |-----------------------------------------------------------------------------| r_work (start): 0.4130 rms_B_bonded: 3.38 r_work: 0.4124 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.4117 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work: 0.4109 rms_B_bonded: 3.20 restraints_weight: 0.1250 r_work: 0.4101 rms_B_bonded: 3.24 restraints_weight: 0.0625 r_work: 0.4093 rms_B_bonded: 3.30 restraints_weight: 0.0312 r_work: 0.4085 rms_B_bonded: 3.37 restraints_weight: 0.0156 r_work: 0.4076 rms_B_bonded: 3.46 restraints_weight: 0.0078 r_work: 0.4067 rms_B_bonded: 3.56 restraints_weight: 0.0039 r_work: 0.4058 rms_B_bonded: 3.68 restraints_weight: 0.0020 r_work: 0.4049 rms_B_bonded: 3.80 restraints_weight: 0.0010 r_work: 0.4039 rms_B_bonded: 3.94 restraints_weight: 0.0005 r_work: 0.4029 rms_B_bonded: 4.10 restraints_weight: 0.0002 r_work: 0.4019 rms_B_bonded: 4.27 restraints_weight: 0.0001 r_work: 0.4008 rms_B_bonded: 4.45 restraints_weight: 0.0001 r_work: 0.3997 rms_B_bonded: 4.64 restraints_weight: 0.0000 r_work: 0.3986 rms_B_bonded: 4.86 restraints_weight: 0.0000 r_work (final): 0.3986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6699 moved from start: 0.5821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 4091 Z= 0.200 Angle : 0.717 12.494 5584 Z= 0.349 Chirality : 0.043 0.144 661 Planarity : 0.005 0.060 715 Dihedral : 4.347 22.583 620 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer Outliers : 0.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.24 (0.35), residues: 585 helix: 0.01 (0.29), residues: 327 sheet: 2.16 (0.50), residues: 109 loop : -2.20 (0.48), residues: 149 =============================================================================== Job complete usr+sys time: 1073.59 seconds wall clock time: 20 minutes 9.31 seconds (1209.31 seconds total)