Starting phenix.real_space_refine on Fri Dec 27 06:24:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wma_37647/12_2024/8wma_37647_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wma_37647/12_2024/8wma_37647.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wma_37647/12_2024/8wma_37647.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wma_37647/12_2024/8wma_37647.map" model { file = "/net/cci-nas-00/data/ceres_data/8wma_37647/12_2024/8wma_37647_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wma_37647/12_2024/8wma_37647_neut.cif" } resolution = 3.47 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= 0.014 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 21 5.16 5 C 2089 2.51 5 N 506 2.21 5 O 556 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 3172 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2490 Classifications: {'peptide': 323} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 316} Chain breaks: 1 Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 81 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 62 Chain: "C" Number of atoms: 682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 682 Classifications: {'peptide': 90} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 3, 'TRANS': 86} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 29 Time building chain proxies: 2.86, per 1000 atoms: 0.90 Number of scatterers: 3172 At special positions: 0 Unit cell: (89.1, 99, 51.7, 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 21 16.00 O 556 8.00 N 506 7.00 C 2089 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 204 " - pdb=" SG CYS A 282 " distance=2.03 Simple disulfide: pdb=" SG CYS A 302 " - pdb=" SG CYS A 377 " distance=2.05 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 Time building additional restraints: 1.04 Conformation dependent library (CDL) restraints added in 438.9 milliseconds 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 780 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 3 sheets defined 67.8% alpha, 5.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 212 through 244 removed outlier: 3.798A pdb=" N ASP A 244 " --> pdb=" O THR A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 276 removed outlier: 3.960A pdb=" N PHE A 257 " --> pdb=" O ARG A 253 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N TYR A 269 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE A 270 " --> pdb=" O SER A 266 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ARG A 272 " --> pdb=" O ALA A 268 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU A 273 " --> pdb=" O TYR A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 281 Processing helix chain 'A' and resid 295 through 298 removed outlier: 3.584A pdb=" N LYS A 298 " --> pdb=" O GLU A 295 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 295 through 298' Processing helix chain 'A' and resid 299 through 332 removed outlier: 3.796A pdb=" N ALA A 303 " --> pdb=" O ASN A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 342 No H-bonds generated for 'chain 'A' and resid 340 through 342' Processing helix chain 'A' and resid 343 through 366 Proline residue: A 355 - end of helix Processing helix chain 'A' and resid 383 through 391 removed outlier: 3.538A pdb=" N LEU A 387 " --> pdb=" O ASN A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 422 removed outlier: 3.879A pdb=" N LEU A 395 " --> pdb=" O VAL A 391 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LYS A 422 " --> pdb=" O SER A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 461 removed outlier: 3.839A pdb=" N GLU A 431 " --> pdb=" O THR A 427 " (cutoff:3.500A) Proline residue: A 447 - end of helix Processing helix chain 'A' and resid 461 through 467 removed outlier: 3.889A pdb=" N PHE A 465 " --> pdb=" O ASN A 461 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ARG A 466 " --> pdb=" O TRP A 462 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N TYR A 467 " --> pdb=" O ALA A 463 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 461 through 467' Processing helix chain 'A' and resid 470 through 490 removed outlier: 4.092A pdb=" N MET A 474 " --> pdb=" O ASP A 470 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA A 475 " --> pdb=" O ASP A 471 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N VAL A 487 " --> pdb=" O MET A 483 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N GLY A 488 " --> pdb=" O SER A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 511 removed outlier: 3.595A pdb=" N LEU A 511 " --> pdb=" O PHE A 507 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 431 Processing helix chain 'C' and resid 455 through 465 Processing helix chain 'C' and resid 474 through 485 removed outlier: 3.743A pdb=" N TYR C 478 " --> pdb=" O GLU C 474 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA C 479 " --> pdb=" O ALA C 475 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N SER C 480 " --> pdb=" O ARG C 476 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 191 through 194 Processing sheet with id=AA2, first strand: chain 'A' and resid 369 through 370 Processing sheet with id=AA3, first strand: chain 'C' and resid 440 through 444 removed outlier: 5.683A pdb=" N ARG C 440 " --> pdb=" O ASN C 451 " (cutoff:3.500A) removed outlier: 8.856A pdb=" N ASN C 451 " --> pdb=" O PHE C 505 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N PHE C 505 " --> pdb=" O ASN C 451 " (cutoff:3.500A) 204 hydrogen bonds defined for protein. 603 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: 0.87 Time building geometry restraints manager: 1.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 955 1.35 - 1.47: 910 1.47 - 1.59: 1357 1.59 - 1.71: 0 1.71 - 1.84: 33 Bond restraints: 3255 Sorted by residual: bond pdb=" N ASP C 441 " pdb=" CA ASP C 441 " ideal model delta sigma weight residual 1.454 1.488 -0.033 1.15e-02 7.56e+03 8.46e+00 bond pdb=" N MET C 443 " pdb=" CA MET C 443 " ideal model delta sigma weight residual 1.457 1.488 -0.030 1.23e-02 6.61e+03 6.10e+00 bond pdb=" N ARG C 442 " pdb=" CA ARG C 442 " ideal model delta sigma weight residual 1.455 1.485 -0.030 1.21e-02 6.83e+03 6.07e+00 bond pdb=" N ARG C 440 " pdb=" CA ARG C 440 " ideal model delta sigma weight residual 1.459 1.488 -0.030 1.41e-02 5.03e+03 4.41e+00 bond pdb=" CA PRO C 470 " pdb=" C PRO C 470 " ideal model delta sigma weight residual 1.520 1.548 -0.029 1.42e-02 4.96e+03 4.12e+00 ... (remaining 3250 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 4161 1.49 - 2.98: 227 2.98 - 4.47: 41 4.47 - 5.96: 6 5.96 - 7.45: 6 Bond angle restraints: 4441 Sorted by residual: angle pdb=" C ARG C 472 " pdb=" CA ARG C 472 " pdb=" CB ARG C 472 " ideal model delta sigma weight residual 110.37 103.10 7.27 1.54e+00 4.22e-01 2.23e+01 angle pdb=" C TYR A 206 " pdb=" CA TYR A 206 " pdb=" CB TYR A 206 " ideal model delta sigma weight residual 110.79 104.73 6.06 1.66e+00 3.63e-01 1.33e+01 angle pdb=" N TYR A 206 " pdb=" CA TYR A 206 " pdb=" C TYR A 206 " ideal model delta sigma weight residual 111.28 114.85 -3.57 1.09e+00 8.42e-01 1.07e+01 angle pdb=" C VAL A 271 " pdb=" N ARG A 272 " pdb=" CA ARG A 272 " ideal model delta sigma weight residual 120.29 115.66 4.63 1.42e+00 4.96e-01 1.07e+01 angle pdb=" C THR A 274 " pdb=" N VAL A 275 " pdb=" CA VAL A 275 " ideal model delta sigma weight residual 122.66 119.78 2.88 9.70e-01 1.06e+00 8.81e+00 ... (remaining 4436 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.06: 1657 13.06 - 26.12: 138 26.12 - 39.18: 56 39.18 - 52.24: 10 52.24 - 65.30: 4 Dihedral angle restraints: 1865 sinusoidal: 656 harmonic: 1209 Sorted by residual: dihedral pdb=" CB CYS A 302 " pdb=" SG CYS A 302 " pdb=" SG CYS A 377 " pdb=" CB CYS A 377 " ideal model delta sinusoidal sigma weight residual 93.00 27.70 65.30 1 1.00e+01 1.00e-02 5.59e+01 dihedral pdb=" CA ASP A 423 " pdb=" C ASP A 423 " pdb=" N GLY A 424 " pdb=" CA GLY A 424 " ideal model delta harmonic sigma weight residual -180.00 -160.42 -19.58 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CA PRO C 470 " pdb=" C PRO C 470 " pdb=" N GLU C 471 " pdb=" CA GLU C 471 " ideal model delta harmonic sigma weight residual 180.00 -160.90 -19.10 0 5.00e+00 4.00e-02 1.46e+01 ... (remaining 1862 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 406 0.054 - 0.108: 93 0.108 - 0.162: 19 0.162 - 0.216: 2 0.216 - 0.271: 1 Chirality restraints: 521 Sorted by residual: chirality pdb=" CA ASP A 207 " pdb=" N ASP A 207 " pdb=" C ASP A 207 " pdb=" CB ASP A 207 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" CA TRP A 319 " pdb=" N TRP A 319 " pdb=" C TRP A 319 " pdb=" CB TRP A 319 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.18 2.00e-01 2.50e+01 7.66e-01 chirality pdb=" CA TYR A 378 " pdb=" N TYR A 378 " pdb=" C TYR A 378 " pdb=" CB TYR A 378 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.76e-01 ... (remaining 518 not shown) Planarity restraints: 535 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 259 " -0.012 2.00e-02 2.50e+03 2.33e-02 5.43e+00 pdb=" C SER A 259 " 0.040 2.00e-02 2.50e+03 pdb=" O SER A 259 " -0.015 2.00e-02 2.50e+03 pdb=" N MET A 260 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 260 " -0.010 2.00e-02 2.50e+03 2.10e-02 4.39e+00 pdb=" C MET A 260 " 0.036 2.00e-02 2.50e+03 pdb=" O MET A 260 " -0.014 2.00e-02 2.50e+03 pdb=" N CYS A 261 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 222 " -0.017 2.00e-02 2.50e+03 1.11e-02 3.07e+00 pdb=" CG TRP A 222 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 TRP A 222 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 TRP A 222 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP A 222 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP A 222 " -0.009 2.00e-02 2.50e+03 pdb=" CE3 TRP A 222 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 222 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 222 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 222 " -0.000 2.00e-02 2.50e+03 ... (remaining 532 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.37: 7 2.37 - 3.00: 1852 3.00 - 3.64: 4590 3.64 - 4.27: 6467 4.27 - 4.90: 10774 Nonbonded interactions: 23690 Sorted by model distance: nonbonded pdb=" CG1 VAL C 426 " pdb=" OH TYR C 478 " model vdw 1.739 3.460 nonbonded pdb=" O THR A 237 " pdb=" OG1 THR A 240 " model vdw 2.230 3.040 nonbonded pdb=" OD2 ASP A 371 " pdb=" OG1 THR A 374 " model vdw 2.234 3.040 nonbonded pdb=" OG SER C 498 " pdb=" OE1 GLN C 500 " model vdw 2.253 3.040 nonbonded pdb=" OE1 GLU C 471 " pdb=" NH2 ARG C 473 " model vdw 2.294 3.120 ... (remaining 23685 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.340 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7034 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 : 0.007 0.061 3255 Z= 0.483 Angle : 0.804 7.452 4441 Z= 0.485 Chirality : 0.050 0.271 521 Planarity : 0.004 0.034 535 Dihedral : 11.972 63.055 1079 Min Nonbonded Distance : 1.739 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 0.31 % Allowed : 1.86 % Favored : 97.83 % 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: -0.62 (0.39), residues: 407 helix: 0.47 (0.30), residues: 251 sheet: -2.12 (1.74), residues: 10 loop : -1.81 (0.47), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP A 222 HIS 0.004 0.001 HIS A 348 PHE 0.022 0.002 PHE A 312 TYR 0.022 0.003 TYR A 378 ARG 0.001 0.000 ARG A 417 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 74 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 263 ASN cc_start: 0.7282 (t0) cc_final: 0.6945 (t0) REVERT: A 366 ARG cc_start: 0.6590 (mmt-90) cc_final: 0.6318 (mmt-90) REVERT: A 479 LEU cc_start: 0.7769 (tp) cc_final: 0.7545 (tp) REVERT: C 500 GLN cc_start: 0.7293 (mp10) cc_final: 0.6909 (mp10) outliers start: 1 outliers final: 0 residues processed: 75 average time/residue: 0.1528 time to fit residues: 13.8046 Evaluate side-chains 71 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 0.0870 chunk 31 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 12 optimal weight: 0.1980 chunk 19 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 37 optimal weight: 7.9990 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 381 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6995 moved from start: 0.1315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 3255 Z= 0.244 Angle : 0.603 8.928 4441 Z= 0.314 Chirality : 0.042 0.194 521 Planarity : 0.004 0.033 535 Dihedral : 4.297 18.636 440 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.24 % Allowed : 9.32 % Favored : 89.44 % 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: -0.05 (0.40), residues: 407 helix: 1.04 (0.31), residues: 253 sheet: -2.74 (1.59), residues: 12 loop : -1.75 (0.47), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 222 HIS 0.004 0.001 HIS A 502 PHE 0.017 0.001 PHE A 312 TYR 0.017 0.002 TYR C 478 ARG 0.001 0.000 ARG C 442 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 64 time to evaluate : 0.347 Fit side-chains REVERT: A 260 MET cc_start: 0.7355 (ttm) cc_final: 0.7045 (ttm) REVERT: A 263 ASN cc_start: 0.7293 (t0) cc_final: 0.7015 (t0) REVERT: A 479 LEU cc_start: 0.7674 (tp) cc_final: 0.7456 (tp) REVERT: A 480 LYS cc_start: 0.7584 (ttmm) cc_final: 0.7372 (ttmm) REVERT: C 500 GLN cc_start: 0.7467 (mp10) cc_final: 0.7018 (mp10) outliers start: 4 outliers final: 3 residues processed: 65 average time/residue: 0.1221 time to fit residues: 10.1417 Evaluate side-chains 67 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 64 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain C residue 426 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 0.5980 chunk 11 optimal weight: 0.4980 chunk 30 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 10 optimal weight: 0.0670 chunk 37 optimal weight: 5.9990 chunk 40 optimal weight: 0.0870 chunk 33 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 overall best weight: 0.3696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 381 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6982 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 3255 Z= 0.215 Angle : 0.552 7.233 4441 Z= 0.289 Chirality : 0.040 0.142 521 Planarity : 0.003 0.033 535 Dihedral : 4.030 16.455 440 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.17 % Allowed : 11.80 % Favored : 86.02 % 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: 0.29 (0.40), residues: 407 helix: 1.35 (0.31), residues: 255 sheet: -2.96 (1.54), residues: 12 loop : -1.71 (0.48), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 222 HIS 0.002 0.001 HIS A 502 PHE 0.017 0.001 PHE A 312 TYR 0.014 0.002 TYR A 444 ARG 0.001 0.000 ARG A 432 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 67 time to evaluate : 0.357 Fit side-chains revert: symmetry clash REVERT: A 260 MET cc_start: 0.7229 (ttm) cc_final: 0.6939 (ttm) REVERT: A 263 ASN cc_start: 0.7319 (t0) cc_final: 0.7058 (t0) REVERT: A 479 LEU cc_start: 0.7672 (tp) cc_final: 0.7410 (tp) REVERT: C 500 GLN cc_start: 0.7494 (mp10) cc_final: 0.7009 (mp10) outliers start: 7 outliers final: 5 residues processed: 69 average time/residue: 0.1479 time to fit residues: 12.6192 Evaluate side-chains 70 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 65 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 445 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 0.5980 chunk 28 optimal weight: 0.0270 chunk 19 optimal weight: 0.9990 chunk 4 optimal weight: 0.4980 chunk 17 optimal weight: 0.2980 chunk 25 optimal weight: 0.6980 chunk 37 optimal weight: 0.1980 chunk 39 optimal weight: 0.0070 chunk 35 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 overall best weight: 0.2056 ------------------------------------------------------------------------------- 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: 0.6942 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3255 Z= 0.161 Angle : 0.516 6.454 4441 Z= 0.270 Chirality : 0.039 0.130 521 Planarity : 0.003 0.031 535 Dihedral : 3.813 14.299 440 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.17 % Allowed : 13.04 % Favored : 84.78 % 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: 0.68 (0.41), residues: 407 helix: 1.69 (0.32), residues: 255 sheet: -3.00 (1.51), residues: 12 loop : -1.61 (0.48), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 222 HIS 0.002 0.001 HIS A 502 PHE 0.016 0.001 PHE A 312 TYR 0.013 0.001 TYR A 444 ARG 0.004 0.001 ARG A 272 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.282 Fit side-chains revert: symmetry clash REVERT: A 223 MET cc_start: 0.6650 (ttm) cc_final: 0.6440 (ttm) REVERT: A 260 MET cc_start: 0.7153 (ttm) cc_final: 0.6817 (ttm) REVERT: A 263 ASN cc_start: 0.7328 (t0) cc_final: 0.7100 (t0) REVERT: A 272 ARG cc_start: 0.7662 (tmm-80) cc_final: 0.6902 (tmm-80) REVERT: A 415 LYS cc_start: 0.6919 (ttmm) cc_final: 0.6693 (mtpt) REVERT: A 477 GLU cc_start: 0.7299 (mm-30) cc_final: 0.7090 (mm-30) REVERT: A 479 LEU cc_start: 0.7691 (tp) cc_final: 0.7488 (tp) REVERT: A 480 LYS cc_start: 0.7722 (ttmm) cc_final: 0.7422 (ttmm) REVERT: C 500 GLN cc_start: 0.7532 (mp10) cc_final: 0.6987 (mp10) outliers start: 7 outliers final: 5 residues processed: 71 average time/residue: 0.1563 time to fit residues: 13.5123 Evaluate side-chains 74 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 69 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain C residue 445 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 29 optimal weight: 0.7980 chunk 16 optimal weight: 0.1980 chunk 33 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 35 optimal weight: 0.0770 chunk 10 optimal weight: 0.3980 chunk 13 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 overall best weight: 0.4938 ------------------------------------------------------------------------------- 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: 0.6999 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3255 Z= 0.253 Angle : 0.551 6.586 4441 Z= 0.286 Chirality : 0.041 0.163 521 Planarity : 0.003 0.036 535 Dihedral : 3.868 16.742 440 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.17 % Allowed : 16.15 % Favored : 81.68 % 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: 0.60 (0.41), residues: 407 helix: 1.62 (0.31), residues: 255 sheet: -2.91 (1.55), residues: 12 loop : -1.66 (0.47), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 222 HIS 0.004 0.001 HIS A 337 PHE 0.018 0.001 PHE A 312 TYR 0.012 0.002 TYR C 463 ARG 0.003 0.000 ARG A 272 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 73 time to evaluate : 0.342 Fit side-chains revert: symmetry clash REVERT: A 260 MET cc_start: 0.7264 (ttm) cc_final: 0.6953 (ttm) REVERT: A 263 ASN cc_start: 0.7361 (t0) cc_final: 0.7132 (t0) REVERT: A 272 ARG cc_start: 0.7748 (tmm-80) cc_final: 0.7024 (tmm-80) REVERT: A 434 MET cc_start: 0.6461 (ptp) cc_final: 0.6166 (mtm) REVERT: A 441 SER cc_start: 0.8094 (p) cc_final: 0.7800 (p) REVERT: A 477 GLU cc_start: 0.7361 (mm-30) cc_final: 0.7148 (mm-30) REVERT: C 463 TYR cc_start: 0.6137 (t80) cc_final: 0.5689 (t80) REVERT: C 500 GLN cc_start: 0.7519 (mp10) cc_final: 0.7016 (mp10) outliers start: 7 outliers final: 5 residues processed: 74 average time/residue: 0.1481 time to fit residues: 13.4186 Evaluate side-chains 77 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 72 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain C residue 445 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 0.0470 chunk 9 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 20 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- 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: 0.7024 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 3255 Z= 0.295 Angle : 0.563 6.307 4441 Z= 0.295 Chirality : 0.041 0.151 521 Planarity : 0.004 0.039 535 Dihedral : 3.898 15.794 440 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.48 % Allowed : 15.84 % Favored : 81.68 % 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: 0.53 (0.41), residues: 407 helix: 1.56 (0.31), residues: 254 sheet: -2.99 (1.55), residues: 12 loop : -1.65 (0.48), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 222 HIS 0.004 0.001 HIS A 337 PHE 0.017 0.002 PHE A 312 TYR 0.019 0.002 TYR A 444 ARG 0.004 0.000 ARG A 417 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 0.353 Fit side-chains REVERT: A 260 MET cc_start: 0.7367 (ttm) cc_final: 0.7043 (ttm) REVERT: A 263 ASN cc_start: 0.7421 (t0) cc_final: 0.7184 (t0) REVERT: A 272 ARG cc_start: 0.7792 (tmm-80) cc_final: 0.6999 (tmm-80) REVERT: A 434 MET cc_start: 0.6458 (ptp) cc_final: 0.6175 (mtm) REVERT: A 477 GLU cc_start: 0.7373 (mm-30) cc_final: 0.7121 (mm-30) REVERT: C 463 TYR cc_start: 0.6471 (t80) cc_final: 0.5987 (t80) REVERT: C 500 GLN cc_start: 0.7526 (mp10) cc_final: 0.7125 (mp10) outliers start: 8 outliers final: 7 residues processed: 72 average time/residue: 0.1426 time to fit residues: 12.7469 Evaluate side-chains 77 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain C residue 445 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 39 optimal weight: 0.0970 chunk 24 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 15 optimal weight: 0.4980 chunk 23 optimal weight: 0.9980 chunk 11 optimal weight: 0.4980 chunk 7 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 overall best weight: 0.4778 ------------------------------------------------------------------------------- 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: 0.7009 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 3255 Z= 0.247 Angle : 0.565 8.683 4441 Z= 0.289 Chirality : 0.040 0.143 521 Planarity : 0.003 0.038 535 Dihedral : 3.819 15.357 440 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.48 % Allowed : 15.84 % Favored : 81.68 % 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: 0.56 (0.41), residues: 407 helix: 1.60 (0.31), residues: 254 sheet: -3.09 (1.52), residues: 12 loop : -1.64 (0.48), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 222 HIS 0.003 0.001 HIS A 337 PHE 0.017 0.001 PHE A 312 TYR 0.015 0.001 TYR A 444 ARG 0.003 0.000 ARG A 417 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 68 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 260 MET cc_start: 0.7268 (ttm) cc_final: 0.6956 (ttm) REVERT: A 263 ASN cc_start: 0.7423 (t0) cc_final: 0.7175 (t0) REVERT: A 434 MET cc_start: 0.6424 (ptp) cc_final: 0.6192 (mtm) REVERT: A 441 SER cc_start: 0.8082 (p) cc_final: 0.7770 (p) REVERT: A 477 GLU cc_start: 0.7361 (mm-30) cc_final: 0.7076 (mm-30) REVERT: C 463 TYR cc_start: 0.6411 (t80) cc_final: 0.5927 (t80) REVERT: C 500 GLN cc_start: 0.7537 (mp10) cc_final: 0.7104 (mp10) outliers start: 8 outliers final: 7 residues processed: 70 average time/residue: 0.1425 time to fit residues: 12.3349 Evaluate side-chains 75 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 68 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 505 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 0.3980 chunk 19 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 34 optimal weight: 0.5980 chunk 36 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 16 optimal weight: 0.0370 chunk 28 optimal weight: 1.9990 overall best weight: 0.4858 ------------------------------------------------------------------------------- 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: 0.7012 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3255 Z= 0.247 Angle : 0.559 7.606 4441 Z= 0.285 Chirality : 0.041 0.189 521 Planarity : 0.003 0.038 535 Dihedral : 3.792 15.308 440 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.80 % Allowed : 16.46 % Favored : 80.75 % 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 (0.41), residues: 407 helix: 1.65 (0.31), residues: 254 sheet: -3.15 (1.51), residues: 12 loop : -1.64 (0.48), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 222 HIS 0.004 0.001 HIS A 337 PHE 0.017 0.001 PHE A 312 TYR 0.014 0.001 TYR A 444 ARG 0.003 0.000 ARG A 417 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 67 time to evaluate : 0.366 Fit side-chains revert: symmetry clash REVERT: A 260 MET cc_start: 0.7279 (ttm) cc_final: 0.6962 (ttm) REVERT: A 263 ASN cc_start: 0.7439 (t0) cc_final: 0.7190 (t0) REVERT: A 358 LYS cc_start: 0.8241 (OUTLIER) cc_final: 0.7813 (mtmm) REVERT: A 434 MET cc_start: 0.6407 (ptp) cc_final: 0.6180 (mtm) REVERT: A 441 SER cc_start: 0.8101 (p) cc_final: 0.7791 (p) REVERT: A 477 GLU cc_start: 0.7356 (mm-30) cc_final: 0.7078 (mm-30) REVERT: C 463 TYR cc_start: 0.6420 (t80) cc_final: 0.5917 (t80) REVERT: C 500 GLN cc_start: 0.7533 (mp10) cc_final: 0.7105 (mp10) outliers start: 9 outliers final: 8 residues processed: 71 average time/residue: 0.1377 time to fit residues: 12.1626 Evaluate side-chains 76 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 67 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 358 LYS Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 505 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 34 optimal weight: 0.3980 chunk 36 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 23 optimal weight: 0.4980 chunk 18 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 40 optimal weight: 0.5980 chunk 37 optimal weight: 0.0970 overall best weight: 0.4378 ------------------------------------------------------------------------------- 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: 0.7002 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3255 Z= 0.227 Angle : 0.550 7.645 4441 Z= 0.280 Chirality : 0.039 0.142 521 Planarity : 0.003 0.037 535 Dihedral : 3.735 15.162 440 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.48 % Allowed : 17.39 % Favored : 80.12 % 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: 0.71 (0.41), residues: 407 helix: 1.71 (0.31), residues: 254 sheet: -3.18 (1.50), residues: 12 loop : -1.55 (0.49), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 222 HIS 0.004 0.001 HIS A 337 PHE 0.017 0.001 PHE A 312 TYR 0.013 0.001 TYR A 444 ARG 0.002 0.000 ARG A 417 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 0.355 Fit side-chains revert: symmetry clash REVERT: A 250 TYR cc_start: 0.7171 (m-80) cc_final: 0.6745 (m-80) REVERT: A 260 MET cc_start: 0.7255 (ttm) cc_final: 0.6942 (ttm) REVERT: A 263 ASN cc_start: 0.7454 (t0) cc_final: 0.7199 (t0) REVERT: A 434 MET cc_start: 0.6392 (ptp) cc_final: 0.6185 (mtm) REVERT: A 441 SER cc_start: 0.8101 (p) cc_final: 0.7791 (p) REVERT: A 477 GLU cc_start: 0.7346 (mm-30) cc_final: 0.7066 (mm-30) REVERT: A 480 LYS cc_start: 0.7750 (ttmm) cc_final: 0.7403 (ttmm) REVERT: C 463 TYR cc_start: 0.6463 (t80) cc_final: 0.5965 (t80) REVERT: C 500 GLN cc_start: 0.7513 (mp10) cc_final: 0.6971 (mp10) outliers start: 8 outliers final: 8 residues processed: 72 average time/residue: 0.1307 time to fit residues: 11.8898 Evaluate side-chains 76 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 68 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 505 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 25 optimal weight: 0.0370 chunk 19 optimal weight: 0.8980 chunk 34 optimal weight: 0.0060 chunk 9 optimal weight: 0.7980 chunk 29 optimal weight: 0.4980 chunk 4 optimal weight: 0.2980 chunk 13 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 6 optimal weight: 0.3980 overall best weight: 0.2474 ------------------------------------------------------------------------------- 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: 0.6961 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3255 Z= 0.168 Angle : 0.559 11.544 4441 Z= 0.275 Chirality : 0.039 0.141 521 Planarity : 0.003 0.035 535 Dihedral : 3.623 13.961 440 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.11 % Allowed : 17.70 % Favored : 79.19 % 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: 0.85 (0.41), residues: 407 helix: 1.87 (0.32), residues: 255 sheet: -3.22 (1.47), residues: 12 loop : -1.62 (0.48), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 222 HIS 0.003 0.001 HIS A 337 PHE 0.017 0.001 PHE A 312 TYR 0.010 0.001 TYR A 444 ARG 0.002 0.000 ARG A 366 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 814 Ramachandran restraints generated. 407 Oldfield, 0 Emsley, 407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 0.351 Fit side-chains revert: symmetry clash REVERT: A 250 TYR cc_start: 0.7032 (m-80) cc_final: 0.6638 (m-80) REVERT: A 260 MET cc_start: 0.7211 (ttm) cc_final: 0.6894 (ttm) REVERT: A 263 ASN cc_start: 0.7438 (t0) cc_final: 0.7197 (t0) REVERT: A 358 LYS cc_start: 0.8154 (OUTLIER) cc_final: 0.7770 (mtmm) REVERT: A 418 SER cc_start: 0.8308 (t) cc_final: 0.8081 (p) REVERT: A 441 SER cc_start: 0.8100 (p) cc_final: 0.7788 (p) REVERT: A 477 GLU cc_start: 0.7263 (mm-30) cc_final: 0.6962 (mm-30) REVERT: A 480 LYS cc_start: 0.7734 (ttmm) cc_final: 0.7398 (ttmm) REVERT: C 463 TYR cc_start: 0.6565 (t80) cc_final: 0.5999 (t80) REVERT: C 500 GLN cc_start: 0.7525 (mp10) cc_final: 0.7257 (mp10) outliers start: 10 outliers final: 7 residues processed: 77 average time/residue: 0.1414 time to fit residues: 13.5407 Evaluate side-chains 81 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 73 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 358 LYS Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain C residue 445 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 23 optimal weight: 0.2980 chunk 37 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 27 optimal weight: 0.2980 chunk 26 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 40 optimal weight: 0.2980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 = 0.4034 r_free = 0.4034 target = 0.156564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.126926 restraints weight = 4854.890| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 2.46 r_work: 0.3526 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3255 Z= 0.237 Angle : 0.590 11.017 4441 Z= 0.293 Chirality : 0.040 0.149 521 Planarity : 0.003 0.036 535 Dihedral : 3.679 14.375 440 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.48 % Allowed : 18.63 % Favored : 78.88 % 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: 0.70 (0.41), residues: 407 helix: 1.67 (0.31), residues: 254 sheet: -3.25 (1.47), residues: 12 loop : -1.49 (0.49), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 222 HIS 0.004 0.001 HIS A 337 PHE 0.017 0.001 PHE A 312 TYR 0.013 0.001 TYR A 444 ARG 0.002 0.000 ARG A 417 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1139.24 seconds wall clock time: 21 minutes 18.35 seconds (1278.35 seconds total)