Starting phenix.real_space_refine on Wed Oct 9 18:03:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b1f_44077/10_2024/9b1f_44077.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b1f_44077/10_2024/9b1f_44077.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b1f_44077/10_2024/9b1f_44077.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b1f_44077/10_2024/9b1f_44077.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b1f_44077/10_2024/9b1f_44077.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9b1f_44077/10_2024/9b1f_44077.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.031 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 Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 30 5.16 5 C 2565 2.51 5 N 662 2.21 5 O 679 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 3936 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 515, 3922 Classifications: {'peptide': 515} Link IDs: {'PTRANS': 29, 'TRANS': 485} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.17, per 1000 atoms: 1.06 Number of scatterers: 3936 At special positions: 0 Unit cell: (58.41, 85.668, 103.191, 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 30 16.00 O 679 8.00 N 662 7.00 C 2565 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 113 " distance=2.03 Simple disulfide: pdb=" SG CYS A 85 " - pdb=" SG CYS A 136 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 Links applied NAG-ASN " NAG A 601 " - " ASN A 56 " Time building additional restraints: 1.02 Conformation dependent library (CDL) restraints added in 651.1 milliseconds 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 950 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 2 sheets defined 84.5% alpha, 1.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 3 through 11 Processing helix chain 'A' and resid 14 through 37 Processing helix chain 'A' and resid 37 through 42 Processing helix chain 'A' and resid 51 through 56 Processing helix chain 'A' and resid 65 through 74 Processing helix chain 'A' and resid 92 through 97 removed outlier: 3.735A pdb=" N ASP A 97 " --> pdb=" O GLN A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 105 removed outlier: 3.547A pdb=" N TRP A 105 " --> pdb=" O ALA A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 108 No H-bonds generated for 'chain 'A' and resid 106 through 108' Processing helix chain 'A' and resid 127 through 133 Processing helix chain 'A' and resid 135 through 139 Processing helix chain 'A' and resid 140 through 168 removed outlier: 3.927A pdb=" N GLY A 161 " --> pdb=" O ALA A 157 " (cutoff:3.500A) Proline residue: A 162 - end of helix Processing helix chain 'A' and resid 168 through 189 removed outlier: 3.583A pdb=" N VAL A 172 " --> pdb=" O GLY A 168 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE A 189 " --> pdb=" O THR A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 221 removed outlier: 3.873A pdb=" N GLY A 209 " --> pdb=" O PHE A 205 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY A 215 " --> pdb=" O MET A 211 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N TRP A 221 " --> pdb=" O LEU A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 252 removed outlier: 3.894A pdb=" N PHE A 238 " --> pdb=" O ASN A 234 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER A 239 " --> pdb=" O SER A 235 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N HIS A 242 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLY A 243 " --> pdb=" O SER A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 264 Processing helix chain 'A' and resid 264 through 273 removed outlier: 4.129A pdb=" N LEU A 268 " --> pdb=" O VAL A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 276 No H-bonds generated for 'chain 'A' and resid 274 through 276' Processing helix chain 'A' and resid 279 through 287 Processing helix chain 'A' and resid 288 through 303 Processing helix chain 'A' and resid 305 through 310 removed outlier: 3.688A pdb=" N ALA A 308 " --> pdb=" O HIS A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 325 removed outlier: 5.377A pdb=" N GLU A 322 " --> pdb=" O SER A 318 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N GLU A 323 " --> pdb=" O SER A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 329 removed outlier: 4.054A pdb=" N GLU A 329 " --> pdb=" O SER A 326 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 326 through 329' Processing helix chain 'A' and resid 332 through 339 removed outlier: 3.544A pdb=" N LEU A 336 " --> pdb=" O SER A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 364 removed outlier: 4.320A pdb=" N ARG A 345 " --> pdb=" O GLY A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 371 removed outlier: 3.883A pdb=" N LEU A 370 " --> pdb=" O ASP A 366 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY A 371 " --> pdb=" O LEU A 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 366 through 371' Processing helix chain 'A' and resid 373 through 400 removed outlier: 3.673A pdb=" N GLY A 382 " --> pdb=" O GLN A 378 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE A 386 " --> pdb=" O GLY A 382 " (cutoff:3.500A) Proline residue: A 387 - end of helix removed outlier: 3.651A pdb=" N GLY A 400 " --> pdb=" O LEU A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 422 removed outlier: 3.710A pdb=" N THR A 404 " --> pdb=" O GLY A 400 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N THR A 420 " --> pdb=" O ILE A 416 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU A 421 " --> pdb=" O LEU A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 456 removed outlier: 4.171A pdb=" N SER A 453 " --> pdb=" O THR A 449 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLU A 454 " --> pdb=" O ILE A 450 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N PHE A 456 " --> pdb=" O SER A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 482 removed outlier: 4.384A pdb=" N MET A 462 " --> pdb=" O THR A 458 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N THR A 463 " --> pdb=" O VAL A 459 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE A 477 " --> pdb=" O ARG A 473 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU A 478 " --> pdb=" O GLY A 474 " (cutoff:3.500A) Proline residue: A 480 - end of helix Processing helix chain 'A' and resid 483 through 489 removed outlier: 3.650A pdb=" N VAL A 487 " --> pdb=" O LEU A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 509 removed outlier: 3.662A pdb=" N LEU A 494 " --> pdb=" O PRO A 490 " (cutoff:3.500A) Proline residue: A 501 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 49 Processing sheet with id=AA2, first strand: chain 'A' and resid 86 through 88 275 hydrogen bonds defined for protein. 795 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: 1.09 Time building geometry restraints manager: 1.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1239 1.34 - 1.46: 926 1.46 - 1.58: 1823 1.58 - 1.70: 0 1.70 - 1.82: 47 Bond restraints: 4035 Sorted by residual: bond pdb=" CA VAL A 500 " pdb=" CB VAL A 500 " ideal model delta sigma weight residual 1.539 1.548 -0.009 5.40e-03 3.43e+04 2.52e+00 bond pdb=" C1 NAG A 601 " pdb=" O5 NAG A 601 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.33e+00 bond pdb=" CA PRO A 75 " pdb=" C PRO A 75 " ideal model delta sigma weight residual 1.517 1.528 -0.011 9.30e-03 1.16e+04 1.34e+00 bond pdb=" C5 NAG A 601 " pdb=" O5 NAG A 601 " ideal model delta sigma weight residual 1.413 1.435 -0.022 2.00e-02 2.50e+03 1.22e+00 bond pdb=" C3 NAG A 601 " pdb=" O3 NAG A 601 " ideal model delta sigma weight residual 1.403 1.425 -0.022 2.00e-02 2.50e+03 1.16e+00 ... (remaining 4030 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.92: 5017 0.92 - 1.84: 390 1.84 - 2.76: 52 2.76 - 3.69: 33 3.69 - 4.61: 12 Bond angle restraints: 5504 Sorted by residual: angle pdb=" C PHE A 380 " pdb=" N ILE A 381 " pdb=" CA ILE A 381 " ideal model delta sigma weight residual 120.47 116.59 3.88 1.58e+00 4.01e-01 6.04e+00 angle pdb=" CA TYR A 272 " pdb=" CB TYR A 272 " pdb=" CG TYR A 272 " ideal model delta sigma weight residual 113.90 118.20 -4.30 1.80e+00 3.09e-01 5.71e+00 angle pdb=" C PHE A 360 " pdb=" N PHE A 361 " pdb=" CA PHE A 361 " ideal model delta sigma weight residual 121.58 117.31 4.27 1.95e+00 2.63e-01 4.79e+00 angle pdb=" C ALA A 192 " pdb=" N PHE A 193 " pdb=" CA PHE A 193 " ideal model delta sigma weight residual 120.26 123.05 -2.79 1.34e+00 5.57e-01 4.33e+00 angle pdb=" CA ARG A 227 " pdb=" C ARG A 227 " pdb=" N PRO A 228 " ideal model delta sigma weight residual 120.77 118.78 1.99 9.70e-01 1.06e+00 4.22e+00 ... (remaining 5499 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 2259 17.73 - 35.47: 113 35.47 - 53.20: 13 53.20 - 70.94: 3 70.94 - 88.67: 3 Dihedral angle restraints: 2391 sinusoidal: 919 harmonic: 1472 Sorted by residual: dihedral pdb=" CA PRO A 457 " pdb=" C PRO A 457 " pdb=" N THR A 458 " pdb=" CA THR A 458 " ideal model delta harmonic sigma weight residual -180.00 -159.74 -20.26 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CA LEU A 54 " pdb=" C LEU A 54 " pdb=" N ASP A 55 " pdb=" CA ASP A 55 " ideal model delta harmonic sigma weight residual -180.00 -162.21 -17.79 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CA HIS A 398 " pdb=" C HIS A 398 " pdb=" N LEU A 399 " pdb=" CA LEU A 399 " ideal model delta harmonic sigma weight residual 180.00 -164.37 -15.63 0 5.00e+00 4.00e-02 9.78e+00 ... (remaining 2388 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 420 0.028 - 0.056: 149 0.056 - 0.084: 53 0.084 - 0.112: 23 0.112 - 0.140: 6 Chirality restraints: 651 Sorted by residual: chirality pdb=" CA PHE A 361 " pdb=" N PHE A 361 " pdb=" C PHE A 361 " pdb=" CB PHE A 361 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.88e-01 chirality pdb=" CA PRO A 501 " pdb=" N PRO A 501 " pdb=" C PRO A 501 " pdb=" CB PRO A 501 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.71e-01 chirality pdb=" CA ILE A 74 " pdb=" N ILE A 74 " pdb=" C ILE A 74 " pdb=" CB ILE A 74 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.60e-01 ... (remaining 648 not shown) Planarity restraints: 685 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 479 " -0.022 5.00e-02 4.00e+02 3.27e-02 1.71e+00 pdb=" N PRO A 480 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO A 480 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 480 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 381 " -0.006 2.00e-02 2.50e+03 1.22e-02 1.49e+00 pdb=" C ILE A 381 " 0.021 2.00e-02 2.50e+03 pdb=" O ILE A 381 " -0.008 2.00e-02 2.50e+03 pdb=" N GLY A 382 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 492 " 0.020 5.00e-02 4.00e+02 2.95e-02 1.40e+00 pdb=" N PRO A 493 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO A 493 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 493 " 0.017 5.00e-02 4.00e+02 ... (remaining 682 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 1195 2.83 - 3.35: 3949 3.35 - 3.86: 6339 3.86 - 4.38: 7558 4.38 - 4.90: 12633 Nonbonded interactions: 31674 Sorted by model distance: nonbonded pdb=" O TRP A 30 " pdb=" OG1 THR A 33 " model vdw 2.311 3.040 nonbonded pdb=" OH TYR A 451 " pdb=" O PRO A 512 " model vdw 2.326 3.040 nonbonded pdb=" OD1 ASN A 56 " pdb=" OG1 THR A 58 " model vdw 2.408 3.040 nonbonded pdb=" OE1 GLU A 220 " pdb=" OG SER A 279 " model vdw 2.444 3.040 nonbonded pdb=" OG SER A 239 " pdb=" OD2 ASP A 385 " model vdw 2.451 3.040 ... (remaining 31669 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.380 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: 0.020 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 15.350 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 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 0.031 4035 Z= 0.258 Angle : 0.608 4.607 5504 Z= 0.335 Chirality : 0.037 0.140 651 Planarity : 0.004 0.033 684 Dihedral : 11.292 88.675 1435 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 1.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % 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: 0.97 (0.37), residues: 513 helix: 0.62 (0.26), residues: 378 sheet: None (None), residues: 0 loop : 1.20 (0.58), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 353 HIS 0.002 0.001 HIS A 139 PHE 0.015 0.002 PHE A 356 TYR 0.018 0.002 TYR A 272 ARG 0.004 0.001 ARG A 483 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 0.397 Fit side-chains REVERT: A 73 SER cc_start: 0.8258 (t) cc_final: 0.7460 (m) REVERT: A 92 GLN cc_start: 0.7032 (mm-40) cc_final: 0.6717 (mm110) REVERT: A 256 THR cc_start: 0.8603 (m) cc_final: 0.8365 (p) REVERT: A 281 ARG cc_start: 0.7673 (mtp-110) cc_final: 0.7352 (mtm-85) REVERT: A 470 MET cc_start: 0.7778 (mmt) cc_final: 0.7562 (tpp) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 1.2319 time to fit residues: 82.9560 Evaluate side-chains 46 residues out of total 416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 43 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 39 optimal weight: 0.8980 chunk 15 optimal weight: 0.0970 chunk 24 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 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 90 GLN A 213 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4035 Z= 0.222 Angle : 0.575 6.374 5504 Z= 0.296 Chirality : 0.040 0.134 651 Planarity : 0.005 0.035 684 Dihedral : 4.587 28.565 569 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 2.64 % Allowed : 7.21 % Favored : 90.14 % 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: 1.83 (0.38), residues: 513 helix: 1.27 (0.27), residues: 375 sheet: -1.11 (1.44), residues: 10 loop : 1.68 (0.63), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 353 HIS 0.002 0.001 HIS A 139 PHE 0.019 0.002 PHE A 266 TYR 0.025 0.002 TYR A 272 ARG 0.002 0.000 ARG A 301 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 47 time to evaluate : 0.384 Fit side-chains REVERT: A 92 GLN cc_start: 0.7058 (mm-40) cc_final: 0.6707 (mm110) REVERT: A 263 SER cc_start: 0.8107 (m) cc_final: 0.7848 (m) REVERT: A 272 TYR cc_start: 0.7281 (OUTLIER) cc_final: 0.6115 (t80) REVERT: A 281 ARG cc_start: 0.7801 (mtp-110) cc_final: 0.7480 (mtm-85) REVERT: A 390 MET cc_start: 0.6626 (OUTLIER) cc_final: 0.5383 (mtp) REVERT: A 470 MET cc_start: 0.7771 (mmt) cc_final: 0.7534 (tpp) outliers start: 11 outliers final: 3 residues processed: 53 average time/residue: 1.1490 time to fit residues: 63.6406 Evaluate side-chains 49 residues out of total 416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 44 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 272 TYR Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 390 MET Chi-restraints excluded: chain A residue 449 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 25 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 46 optimal weight: 5.9990 chunk 50 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 45 optimal weight: 0.0070 overall best weight: 0.5998 ------------------------------------------------------------------------------- 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: 0.7813 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4035 Z= 0.205 Angle : 0.529 6.782 5504 Z= 0.268 Chirality : 0.039 0.148 651 Planarity : 0.005 0.035 684 Dihedral : 4.232 25.189 569 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.92 % Allowed : 10.34 % Favored : 87.74 % 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: 2.16 (0.38), residues: 513 helix: 1.54 (0.27), residues: 377 sheet: -1.71 (1.35), residues: 10 loop : 1.75 (0.63), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 353 HIS 0.003 0.001 HIS A 139 PHE 0.015 0.001 PHE A 266 TYR 0.020 0.002 TYR A 272 ARG 0.006 0.000 ARG A 86 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 47 time to evaluate : 0.413 Fit side-chains REVERT: A 89 ARG cc_start: 0.6889 (ttm-80) cc_final: 0.6263 (mtt180) REVERT: A 92 GLN cc_start: 0.7045 (mm-40) cc_final: 0.6778 (mm-40) REVERT: A 263 SER cc_start: 0.8107 (m) cc_final: 0.7880 (m) REVERT: A 281 ARG cc_start: 0.7814 (mtp-110) cc_final: 0.7435 (mtm-85) REVERT: A 470 MET cc_start: 0.7776 (mmt) cc_final: 0.7532 (tpp) outliers start: 8 outliers final: 3 residues processed: 51 average time/residue: 1.2665 time to fit residues: 67.1362 Evaluate side-chains 46 residues out of total 416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 43 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 379 MET Chi-restraints excluded: chain A residue 384 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 34 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 49 optimal weight: 0.0970 chunk 44 optimal weight: 0.9990 chunk 13 optimal weight: 0.4980 chunk 41 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 GLN ** A 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4035 Z= 0.218 Angle : 0.549 8.255 5504 Z= 0.272 Chirality : 0.039 0.148 651 Planarity : 0.005 0.035 684 Dihedral : 4.110 22.127 569 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.92 % Allowed : 11.30 % Favored : 86.78 % 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: 2.19 (0.38), residues: 513 helix: 1.58 (0.27), residues: 377 sheet: -1.87 (1.37), residues: 10 loop : 1.70 (0.63), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 353 HIS 0.002 0.001 HIS A 139 PHE 0.016 0.002 PHE A 266 TYR 0.022 0.002 TYR A 272 ARG 0.006 0.000 ARG A 86 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 43 time to evaluate : 0.427 Fit side-chains REVERT: A 17 GLN cc_start: 0.7345 (OUTLIER) cc_final: 0.6283 (mm110) REVERT: A 73 SER cc_start: 0.7975 (t) cc_final: 0.7127 (m) REVERT: A 89 ARG cc_start: 0.6973 (ttm-80) cc_final: 0.6392 (mtt180) REVERT: A 92 GLN cc_start: 0.7059 (mm-40) cc_final: 0.6784 (mm-40) REVERT: A 263 SER cc_start: 0.8077 (m) cc_final: 0.7860 (m) REVERT: A 281 ARG cc_start: 0.7830 (mtp-110) cc_final: 0.7463 (ttm-80) REVERT: A 470 MET cc_start: 0.7779 (mmt) cc_final: 0.6648 (ttt) outliers start: 8 outliers final: 5 residues processed: 46 average time/residue: 1.2037 time to fit residues: 57.6376 Evaluate side-chains 50 residues out of total 416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 44 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 17 GLN Chi-restraints excluded: chain A residue 379 MET Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 421 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 0 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 25 optimal weight: 0.4980 chunk 44 optimal weight: 0.7980 chunk 12 optimal weight: 0.3980 chunk 16 optimal weight: 0.9990 chunk 9 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4035 Z= 0.224 Angle : 0.537 7.069 5504 Z= 0.268 Chirality : 0.039 0.155 651 Planarity : 0.005 0.037 684 Dihedral : 4.045 20.177 569 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 3.37 % Allowed : 11.06 % Favored : 85.58 % 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: 2.19 (0.38), residues: 513 helix: 1.63 (0.27), residues: 375 sheet: -1.91 (1.41), residues: 10 loop : 1.53 (0.61), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 353 HIS 0.002 0.001 HIS A 139 PHE 0.015 0.002 PHE A 266 TYR 0.022 0.002 TYR A 272 ARG 0.006 0.000 ARG A 86 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 47 time to evaluate : 0.442 Fit side-chains REVERT: A 73 SER cc_start: 0.7978 (t) cc_final: 0.7130 (m) REVERT: A 89 ARG cc_start: 0.6978 (ttm-80) cc_final: 0.6675 (mtt-85) REVERT: A 92 GLN cc_start: 0.7057 (mm-40) cc_final: 0.6780 (mm-40) REVERT: A 272 TYR cc_start: 0.7362 (OUTLIER) cc_final: 0.6133 (t80) REVERT: A 281 ARG cc_start: 0.7831 (mtp-110) cc_final: 0.7482 (ttm-80) REVERT: A 449 THR cc_start: 0.7930 (OUTLIER) cc_final: 0.7333 (p) REVERT: A 470 MET cc_start: 0.7778 (mmt) cc_final: 0.6651 (ttt) outliers start: 14 outliers final: 7 residues processed: 54 average time/residue: 1.1492 time to fit residues: 64.7340 Evaluate side-chains 53 residues out of total 416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 44 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 272 TYR Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 379 MET Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 449 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 12 optimal weight: 0.0770 chunk 49 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 chunk 5 optimal weight: 0.1980 chunk 28 optimal weight: 0.5980 chunk 36 optimal weight: 0.9980 overall best weight: 0.5138 ------------------------------------------------------------------------------- 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: 0.7808 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4035 Z= 0.190 Angle : 0.550 12.643 5504 Z= 0.265 Chirality : 0.038 0.153 651 Planarity : 0.004 0.036 684 Dihedral : 3.906 17.972 569 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.64 % Allowed : 13.70 % Favored : 83.65 % 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: 2.23 (0.38), residues: 513 helix: 1.71 (0.27), residues: 377 sheet: -1.92 (1.43), residues: 10 loop : 1.36 (0.59), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 353 HIS 0.002 0.001 HIS A 139 PHE 0.013 0.001 PHE A 266 TYR 0.020 0.002 TYR A 272 ARG 0.007 0.000 ARG A 86 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 44 time to evaluate : 0.480 Fit side-chains REVERT: A 73 SER cc_start: 0.7967 (t) cc_final: 0.7126 (m) REVERT: A 89 ARG cc_start: 0.6941 (ttm-80) cc_final: 0.6397 (mtt180) REVERT: A 92 GLN cc_start: 0.7042 (mm-40) cc_final: 0.6739 (mm110) REVERT: A 281 ARG cc_start: 0.7834 (mtp-110) cc_final: 0.7492 (ttm-80) REVERT: A 390 MET cc_start: 0.6552 (OUTLIER) cc_final: 0.6124 (mmt) REVERT: A 470 MET cc_start: 0.7755 (mmt) cc_final: 0.6629 (ttt) outliers start: 11 outliers final: 6 residues processed: 50 average time/residue: 1.0827 time to fit residues: 56.4481 Evaluate side-chains 49 residues out of total 416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 42 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 379 MET Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 390 MET Chi-restraints excluded: chain A residue 421 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 27 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 14 optimal weight: 0.5980 chunk 9 optimal weight: 10.0000 chunk 31 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4035 Z= 0.228 Angle : 0.577 12.354 5504 Z= 0.279 Chirality : 0.040 0.158 651 Planarity : 0.005 0.035 684 Dihedral : 4.002 16.547 569 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 3.12 % Allowed : 13.46 % Favored : 83.41 % 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: 2.05 (0.37), residues: 513 helix: 1.58 (0.27), residues: 377 sheet: -1.94 (1.49), residues: 10 loop : 1.28 (0.59), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 221 HIS 0.002 0.001 HIS A 139 PHE 0.014 0.002 PHE A 358 TYR 0.022 0.002 TYR A 272 ARG 0.006 0.000 ARG A 86 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 43 time to evaluate : 0.546 Fit side-chains REVERT: A 17 GLN cc_start: 0.7343 (OUTLIER) cc_final: 0.6059 (mm110) REVERT: A 73 SER cc_start: 0.7973 (t) cc_final: 0.7125 (m) REVERT: A 87 ARG cc_start: 0.8272 (OUTLIER) cc_final: 0.8013 (ptt180) REVERT: A 89 ARG cc_start: 0.6955 (ttm-80) cc_final: 0.6432 (mtt180) REVERT: A 92 GLN cc_start: 0.7058 (mm-40) cc_final: 0.6756 (mm110) REVERT: A 281 ARG cc_start: 0.7840 (mtp-110) cc_final: 0.7494 (ttm-80) REVERT: A 379 MET cc_start: 0.8741 (OUTLIER) cc_final: 0.8536 (ttt) REVERT: A 390 MET cc_start: 0.6607 (OUTLIER) cc_final: 0.6342 (mmt) REVERT: A 470 MET cc_start: 0.7759 (mmt) cc_final: 0.6638 (ttt) outliers start: 13 outliers final: 5 residues processed: 50 average time/residue: 1.3206 time to fit residues: 68.7066 Evaluate side-chains 51 residues out of total 416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 42 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 17 GLN Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 379 MET Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 390 MET Chi-restraints excluded: chain A residue 449 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 24 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 45 optimal weight: 0.4980 chunk 27 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 35 optimal weight: 0.3980 chunk 14 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4035 Z= 0.210 Angle : 0.550 11.655 5504 Z= 0.268 Chirality : 0.039 0.158 651 Planarity : 0.004 0.035 684 Dihedral : 3.915 15.264 569 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 2.16 % Allowed : 14.18 % Favored : 83.65 % 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: 2.10 (0.37), residues: 513 helix: 1.64 (0.27), residues: 377 sheet: -2.00 (1.49), residues: 10 loop : 1.25 (0.59), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 353 HIS 0.002 0.001 HIS A 139 PHE 0.014 0.001 PHE A 358 TYR 0.020 0.002 TYR A 272 ARG 0.007 0.000 ARG A 86 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 44 time to evaluate : 0.423 Fit side-chains REVERT: A 73 SER cc_start: 0.7960 (t) cc_final: 0.7108 (m) REVERT: A 87 ARG cc_start: 0.8277 (OUTLIER) cc_final: 0.8015 (ptt180) REVERT: A 89 ARG cc_start: 0.6915 (ttm-80) cc_final: 0.6469 (mtt180) REVERT: A 92 GLN cc_start: 0.7067 (mm-40) cc_final: 0.6764 (mm110) REVERT: A 272 TYR cc_start: 0.7403 (OUTLIER) cc_final: 0.6162 (t80) REVERT: A 281 ARG cc_start: 0.7875 (mtp-110) cc_final: 0.7540 (ttm-80) REVERT: A 390 MET cc_start: 0.6588 (OUTLIER) cc_final: 0.6183 (mmt) REVERT: A 470 MET cc_start: 0.7744 (mmt) cc_final: 0.6628 (ttt) outliers start: 9 outliers final: 4 residues processed: 50 average time/residue: 1.2767 time to fit residues: 66.2913 Evaluate side-chains 48 residues out of total 416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 41 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain A residue 272 TYR Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 390 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 41 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 45 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 GLN A 213 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 4035 Z= 0.248 Angle : 0.580 11.463 5504 Z= 0.283 Chirality : 0.040 0.161 651 Planarity : 0.005 0.036 684 Dihedral : 3.944 15.455 569 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.40 % Allowed : 14.42 % Favored : 83.17 % 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: 2.01 (0.37), residues: 513 helix: 1.57 (0.27), residues: 375 sheet: -1.95 (1.50), residues: 10 loop : 1.21 (0.58), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 353 HIS 0.002 0.001 HIS A 139 PHE 0.014 0.002 PHE A 358 TYR 0.022 0.002 TYR A 272 ARG 0.008 0.000 ARG A 86 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 42 time to evaluate : 0.423 Fit side-chains REVERT: A 17 GLN cc_start: 0.7395 (OUTLIER) cc_final: 0.6032 (mm110) REVERT: A 73 SER cc_start: 0.7959 (t) cc_final: 0.7103 (m) REVERT: A 87 ARG cc_start: 0.8292 (OUTLIER) cc_final: 0.8036 (ptt180) REVERT: A 89 ARG cc_start: 0.6950 (ttm-80) cc_final: 0.6476 (mtt180) REVERT: A 92 GLN cc_start: 0.7079 (mm-40) cc_final: 0.6807 (mm-40) REVERT: A 272 TYR cc_start: 0.7483 (OUTLIER) cc_final: 0.6178 (t80) REVERT: A 281 ARG cc_start: 0.7880 (mtp-110) cc_final: 0.7524 (ttm-80) REVERT: A 376 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.8066 (mp) REVERT: A 390 MET cc_start: 0.6617 (OUTLIER) cc_final: 0.6224 (mmt) REVERT: A 426 MET cc_start: 0.5865 (mpp) cc_final: 0.4441 (mmt) REVERT: A 470 MET cc_start: 0.7758 (mmt) cc_final: 0.6653 (ttt) outliers start: 10 outliers final: 4 residues processed: 50 average time/residue: 1.1653 time to fit residues: 60.5709 Evaluate side-chains 51 residues out of total 416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 42 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 17 GLN Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain A residue 272 TYR Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 390 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 4 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 32 optimal weight: 0.4980 chunk 43 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 4035 Z= 0.291 Angle : 0.602 11.545 5504 Z= 0.296 Chirality : 0.041 0.164 651 Planarity : 0.005 0.037 684 Dihedral : 4.009 15.670 569 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 2.40 % Allowed : 14.42 % Favored : 83.17 % 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: 1.81 (0.37), residues: 513 helix: 1.43 (0.26), residues: 375 sheet: -1.99 (1.54), residues: 10 loop : 1.10 (0.58), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 353 HIS 0.002 0.001 HIS A 139 PHE 0.014 0.002 PHE A 361 TYR 0.024 0.002 TYR A 272 ARG 0.008 0.000 ARG A 86 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 43 time to evaluate : 0.508 Fit side-chains REVERT: A 17 GLN cc_start: 0.7425 (OUTLIER) cc_final: 0.6518 (mm110) REVERT: A 73 SER cc_start: 0.7984 (t) cc_final: 0.7121 (m) REVERT: A 89 ARG cc_start: 0.6983 (ttm-80) cc_final: 0.6493 (mtt180) REVERT: A 92 GLN cc_start: 0.7077 (mm-40) cc_final: 0.6804 (mm-40) REVERT: A 272 TYR cc_start: 0.7571 (OUTLIER) cc_final: 0.6198 (t80) REVERT: A 281 ARG cc_start: 0.7881 (mtp-110) cc_final: 0.7517 (ttm-80) REVERT: A 376 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.8111 (mp) REVERT: A 390 MET cc_start: 0.6650 (OUTLIER) cc_final: 0.6379 (mmt) REVERT: A 426 MET cc_start: 0.5867 (mpp) cc_final: 0.4478 (mmt) REVERT: A 470 MET cc_start: 0.7747 (mmt) cc_final: 0.6670 (ttt) outliers start: 10 outliers final: 5 residues processed: 51 average time/residue: 1.3587 time to fit residues: 72.2963 Evaluate side-chains 52 residues out of total 416 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 43 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 17 GLN Chi-restraints excluded: chain A residue 272 TYR Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 390 MET Chi-restraints excluded: chain A residue 449 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 41 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 chunk 2 optimal weight: 0.8980 chunk 29 optimal weight: 0.6980 chunk 46 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 1 optimal weight: 0.4980 chunk 32 optimal weight: 0.0670 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.177159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.138777 restraints weight = 4233.693| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 1.83 r_work: 0.3556 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3437 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.2848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 4035 Z= 0.198 Angle : 0.555 10.983 5504 Z= 0.273 Chirality : 0.039 0.157 651 Planarity : 0.005 0.039 684 Dihedral : 3.845 14.968 569 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 2.16 % Allowed : 14.66 % Favored : 83.17 % 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: 1.98 (0.37), residues: 513 helix: 1.58 (0.27), residues: 377 sheet: -2.12 (1.51), residues: 10 loop : 1.07 (0.59), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 353 HIS 0.002 0.001 HIS A 139 PHE 0.014 0.001 PHE A 358 TYR 0.020 0.002 TYR A 272 ARG 0.008 0.000 ARG A 86 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1887.67 seconds wall clock time: 40 minutes 23.41 seconds (2423.41 seconds total)