Starting phenix.real_space_refine on Wed Oct 9 19:00:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y2d_38851/10_2024/8y2d_38851.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y2d_38851/10_2024/8y2d_38851.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y2d_38851/10_2024/8y2d_38851.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y2d_38851/10_2024/8y2d_38851.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y2d_38851/10_2024/8y2d_38851.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y2d_38851/10_2024/8y2d_38851.cif" } resolution = 2.8 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= 0.068 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: 6 Type Number sf(0) Gaussians S 23 5.16 5 Cl 1 4.86 5 Na 2 4.78 5 C 2791 2.51 5 N 658 2.21 5 O 714 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 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: 4189 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4171 Classifications: {'peptide': 528} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 504} Chain breaks: 2 Chain: "A" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 18 Unusual residues: {' CL': 1, ' NA': 2, 'LDP': 1} Classifications: {'undetermined': 4, 'water': 4} Link IDs: {None: 7} Time building chain proxies: 3.28, per 1000 atoms: 0.78 Number of scatterers: 4189 At special positions: 0 Unit cell: (71.4, 68, 92.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 23 16.00 Na 2 11.00 O 714 8.00 N 658 7.00 C 2791 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 180 " - pdb=" SG CYS A 189 " 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 Time building additional restraints: 1.13 Conformation dependent library (CDL) restraints added in 552.6 milliseconds 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 972 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 1 sheets defined 78.0% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 68 through 78 removed outlier: 3.986A pdb=" N SER A 72 " --> pdb=" O ASP A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 84 removed outlier: 4.008A pdb=" N VAL A 83 " --> pdb=" O ASP A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 93 Processing helix chain 'A' and resid 98 through 125 removed outlier: 5.078A pdb=" N MET A 111 " --> pdb=" O VAL A 107 " (cutoff:3.500A) Proline residue: A 112 - end of helix Processing helix chain 'A' and resid 129 through 134 removed outlier: 3.761A pdb=" N TRP A 132 " --> pdb=" O ALA A 129 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LYS A 133 " --> pdb=" O GLY A 130 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ILE A 134 " --> pdb=" O VAL A 131 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 129 through 134' Processing helix chain 'A' and resid 140 through 170 removed outlier: 3.573A pdb=" N VAL A 145 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE A 146 " --> pdb=" O GLY A 142 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE A 154 " --> pdb=" O LEU A 150 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N PHE A 155 " --> pdb=" O TYR A 151 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ASN A 157 " --> pdb=" O GLY A 153 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N VAL A 158 " --> pdb=" O PHE A 154 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ILE A 159 " --> pdb=" O PHE A 155 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE A 160 " --> pdb=" O TYR A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 220 Processing helix chain 'A' and resid 223 through 227 Processing helix chain 'A' and resid 237 through 255 removed outlier: 3.507A pdb=" N ALA A 242 " --> pdb=" O TRP A 238 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N CYS A 243 " --> pdb=" O GLN A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 287 removed outlier: 4.119A pdb=" N THR A 271 " --> pdb=" O TRP A 267 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N MET A 272 " --> pdb=" O ILE A 268 " (cutoff:3.500A) Proline residue: A 273 - end of helix removed outlier: 3.638A pdb=" N THR A 286 " --> pdb=" O LEU A 282 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU A 287 " --> pdb=" O ARG A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 298 removed outlier: 3.900A pdb=" N GLY A 293 " --> pdb=" O GLY A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 323 Processing helix chain 'A' and resid 327 through 334 removed outlier: 3.566A pdb=" N ALA A 331 " --> pdb=" O GLY A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 375 removed outlier: 3.679A pdb=" N ASP A 345 " --> pdb=" O ASN A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 382 Processing helix chain 'A' and resid 388 through 397 removed outlier: 3.872A pdb=" N TYR A 394 " --> pdb=" O ILE A 390 " (cutoff:3.500A) Proline residue: A 395 - end of helix Processing helix chain 'A' and resid 403 through 438 removed outlier: 3.628A pdb=" N TRP A 407 " --> pdb=" O LEU A 403 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY A 419 " --> pdb=" O LEU A 415 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ASP A 421 " --> pdb=" O THR A 417 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N SER A 422 " --> pdb=" O LEU A 418 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N MET A 427 " --> pdb=" O ALA A 423 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N PHE A 438 " --> pdb=" O LEU A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 461 Processing helix chain 'A' and resid 462 through 465 removed outlier: 3.947A pdb=" N THR A 465 " --> pdb=" O PHE A 462 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 462 through 465' Processing helix chain 'A' and resid 467 through 479 removed outlier: 4.024A pdb=" N VAL A 471 " --> pdb=" O GLY A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 498 removed outlier: 4.135A pdb=" N LEU A 485 " --> pdb=" O GLY A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 512 Processing helix chain 'A' and resid 517 through 542 removed outlier: 5.247A pdb=" N SER A 528 " --> pdb=" O TRP A 524 " (cutoff:3.500A) Proline residue: A 529 - end of helix Processing helix chain 'A' and resid 554 through 570 removed outlier: 3.659A pdb=" N ASN A 558 " --> pdb=" O PRO A 554 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER A 568 " --> pdb=" O ILE A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 583 removed outlier: 4.091A pdb=" N ILE A 574 " --> pdb=" O ALA A 570 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR A 575 " --> pdb=" O MET A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 596 Processing helix chain 'A' and resid 600 through 606 Processing helix chain 'A' and resid 609 through 613 Processing sheet with id=AA1, first strand: chain 'A' and resid 547 through 548 removed outlier: 3.632A pdb=" N TYR A 548 " --> pdb=" O TYR A 551 " (cutoff:3.500A) 256 hydrogen bonds defined for protein. 747 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: 1.21 Time building geometry restraints manager: 1.29 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: 1247 1.34 - 1.46: 1054 1.46 - 1.58: 1977 1.58 - 1.69: 0 1.69 - 1.81: 34 Bond restraints: 4312 Sorted by residual: bond pdb=" CG PRO A 584 " pdb=" CD PRO A 584 " ideal model delta sigma weight residual 1.503 1.557 -0.054 3.40e-02 8.65e+02 2.51e+00 bond pdb=" C8 LDP A 701 " pdb=" N1 LDP A 701 " ideal model delta sigma weight residual 1.456 1.484 -0.028 2.00e-02 2.50e+03 1.96e+00 bond pdb=" CB PRO A 584 " pdb=" CG PRO A 584 " ideal model delta sigma weight residual 1.492 1.540 -0.048 5.00e-02 4.00e+02 9.40e-01 bond pdb=" C7 LDP A 701 " pdb=" C8 LDP A 701 " ideal model delta sigma weight residual 1.528 1.511 0.017 2.00e-02 2.50e+03 6.90e-01 bond pdb=" C LEU A 583 " pdb=" N PRO A 584 " ideal model delta sigma weight residual 1.328 1.337 -0.009 1.25e-02 6.40e+03 5.74e-01 ... (remaining 4307 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.08: 5670 1.08 - 2.16: 152 2.16 - 3.24: 44 3.24 - 4.32: 10 4.32 - 5.40: 10 Bond angle restraints: 5886 Sorted by residual: angle pdb=" CA TYR A 88 " pdb=" CB TYR A 88 " pdb=" CG TYR A 88 " ideal model delta sigma weight residual 113.90 118.53 -4.63 1.80e+00 3.09e-01 6.61e+00 angle pdb=" CA PRO A 584 " pdb=" N PRO A 584 " pdb=" CD PRO A 584 " ideal model delta sigma weight residual 112.00 109.32 2.68 1.40e+00 5.10e-01 3.67e+00 angle pdb=" N PRO A 584 " pdb=" CA PRO A 584 " pdb=" C PRO A 584 " ideal model delta sigma weight residual 111.03 114.44 -3.41 1.78e+00 3.16e-01 3.66e+00 angle pdb=" CA TYR A 343 " pdb=" CB TYR A 343 " pdb=" CG TYR A 343 " ideal model delta sigma weight residual 113.90 117.16 -3.26 1.80e+00 3.09e-01 3.29e+00 angle pdb=" C CYS A 342 " pdb=" N TYR A 343 " pdb=" CA TYR A 343 " ideal model delta sigma weight residual 120.44 122.71 -2.27 1.30e+00 5.92e-01 3.06e+00 ... (remaining 5881 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.65: 2057 15.65 - 31.29: 260 31.29 - 46.94: 87 46.94 - 62.59: 23 62.59 - 78.23: 2 Dihedral angle restraints: 2429 sinusoidal: 908 harmonic: 1521 Sorted by residual: dihedral pdb=" CA ALA A 397 " pdb=" C ALA A 397 " pdb=" N ILE A 398 " pdb=" CA ILE A 398 " ideal model delta harmonic sigma weight residual 180.00 161.73 18.27 0 5.00e+00 4.00e-02 1.34e+01 dihedral pdb=" CA LEU A 526 " pdb=" C LEU A 526 " pdb=" N VAL A 527 " pdb=" CA VAL A 527 " ideal model delta harmonic sigma weight residual 180.00 -163.21 -16.79 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" CG ARG A 443 " pdb=" CD ARG A 443 " pdb=" NE ARG A 443 " pdb=" CZ ARG A 443 " ideal model delta sinusoidal sigma weight residual -90.00 -134.37 44.37 2 1.50e+01 4.44e-03 1.04e+01 ... (remaining 2426 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 361 0.024 - 0.047: 177 0.047 - 0.071: 85 0.071 - 0.095: 24 0.095 - 0.118: 18 Chirality restraints: 665 Sorted by residual: chirality pdb=" CA VAL A 377 " pdb=" N VAL A 377 " pdb=" C VAL A 377 " pdb=" CB VAL A 377 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.49e-01 chirality pdb=" CA PRO A 136 " pdb=" N PRO A 136 " pdb=" C PRO A 136 " pdb=" CB PRO A 136 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.38e-01 chirality pdb=" CA ASP A 232 " pdb=" N ASP A 232 " pdb=" C ASP A 232 " pdb=" CB ASP A 232 " both_signs ideal model delta sigma weight residual False 2.51 2.63 -0.12 2.00e-01 2.50e+01 3.38e-01 ... (remaining 662 not shown) Planarity restraints: 721 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS A 523 " 0.009 2.00e-02 2.50e+03 1.86e-02 3.46e+00 pdb=" C CYS A 523 " -0.032 2.00e-02 2.50e+03 pdb=" O CYS A 523 " 0.012 2.00e-02 2.50e+03 pdb=" N TRP A 524 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 494 " 0.008 2.00e-02 2.50e+03 1.67e-02 2.77e+00 pdb=" C GLY A 494 " -0.029 2.00e-02 2.50e+03 pdb=" O GLY A 494 " 0.011 2.00e-02 2.50e+03 pdb=" N VAL A 495 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 186 " -0.027 5.00e-02 4.00e+02 4.12e-02 2.72e+00 pdb=" N PRO A 187 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 187 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 187 " -0.023 5.00e-02 4.00e+02 ... (remaining 718 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 836 2.77 - 3.30: 3722 3.30 - 3.84: 6918 3.84 - 4.37: 7768 4.37 - 4.90: 14147 Nonbonded interactions: 33391 Sorted by model distance: nonbonded pdb=" O VAL A 78 " pdb="NA NA A 703 " model vdw 2.240 2.470 nonbonded pdb=" O HOH A 802 " pdb=" O HOH A 804 " model vdw 2.266 3.040 nonbonded pdb=" OD1 ASN A 82 " pdb="NA NA A 702 " model vdw 2.277 2.470 nonbonded pdb=" O ALA A 77 " pdb="NA NA A 702 " model vdw 2.292 2.470 nonbonded pdb=" NH2 ARG A 125 " pdb=" O ASN A 336 " model vdw 2.305 3.120 ... (remaining 33386 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: 0.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 15.120 Find NCS groups from input model: 0.040 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:11.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 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 : 0.003 0.054 4312 Z= 0.178 Angle : 0.505 5.405 5886 Z= 0.264 Chirality : 0.037 0.118 665 Planarity : 0.004 0.041 721 Dihedral : 16.286 78.233 1454 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 0.00 % Allowed : 25.28 % Favored : 74.72 % 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: 1.06 (0.38), residues: 522 helix: 1.59 (0.28), residues: 364 sheet: None (None), residues: 0 loop : -1.43 (0.49), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 132 HIS 0.002 0.001 HIS A 165 PHE 0.011 0.001 PHE A 412 TYR 0.021 0.001 TYR A 303 ARG 0.004 0.000 ARG A 125 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.480 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 1.1659 time to fit residues: 63.2395 Evaluate side-chains 44 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 43 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 21 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 15 optimal weight: 0.0020 chunk 24 optimal weight: 7.9990 chunk 30 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 overall best weight: 1.1192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN ** A 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.0620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4312 Z= 0.200 Angle : 0.531 7.205 5886 Z= 0.271 Chirality : 0.038 0.122 665 Planarity : 0.004 0.045 721 Dihedral : 4.042 25.586 570 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.61 % Allowed : 23.02 % Favored : 73.36 % 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: 0.90 (0.38), residues: 522 helix: 1.51 (0.28), residues: 370 sheet: None (None), residues: 0 loop : -1.74 (0.49), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 132 HIS 0.002 0.001 HIS A 165 PHE 0.014 0.001 PHE A 412 TYR 0.011 0.001 TYR A 575 ARG 0.003 0.000 ARG A 125 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 43 time to evaluate : 0.488 Fit side-chains REVERT: A 610 ARG cc_start: 0.7328 (OUTLIER) cc_final: 0.6951 (ttm110) outliers start: 16 outliers final: 7 residues processed: 54 average time/residue: 0.9839 time to fit residues: 55.8362 Evaluate side-chains 49 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 41 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 511 MET Chi-restraints excluded: chain A residue 610 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 39 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 chunk 47 optimal weight: 0.5980 chunk 51 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.0693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4312 Z= 0.168 Angle : 0.492 6.316 5886 Z= 0.253 Chirality : 0.037 0.118 665 Planarity : 0.004 0.043 721 Dihedral : 3.992 24.931 570 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 1.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.93 % Allowed : 23.93 % Favored : 73.14 % 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: 1.00 (0.38), residues: 522 helix: 1.63 (0.28), residues: 370 sheet: None (None), residues: 0 loop : -1.83 (0.48), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 132 HIS 0.002 0.001 HIS A 165 PHE 0.011 0.001 PHE A 412 TYR 0.015 0.001 TYR A 303 ARG 0.003 0.000 ARG A 125 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 41 time to evaluate : 0.467 Fit side-chains REVERT: A 610 ARG cc_start: 0.7287 (OUTLIER) cc_final: 0.6924 (ttm110) outliers start: 13 outliers final: 7 residues processed: 50 average time/residue: 1.0162 time to fit residues: 53.5150 Evaluate side-chains 47 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 39 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 511 MET Chi-restraints excluded: chain A residue 610 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 5 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.0893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4312 Z= 0.231 Angle : 0.545 6.335 5886 Z= 0.281 Chirality : 0.039 0.123 665 Planarity : 0.004 0.044 721 Dihedral : 4.163 24.917 570 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 1.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 3.39 % Allowed : 23.70 % Favored : 72.91 % 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: 0.81 (0.38), residues: 522 helix: 1.48 (0.28), residues: 371 sheet: None (None), residues: 0 loop : -1.91 (0.47), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 132 HIS 0.003 0.001 HIS A 165 PHE 0.016 0.002 PHE A 412 TYR 0.015 0.001 TYR A 303 ARG 0.002 0.000 ARG A 125 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 42 time to evaluate : 0.467 Fit side-chains REVERT: A 250 LEU cc_start: 0.8345 (tp) cc_final: 0.8000 (tp) REVERT: A 272 MET cc_start: 0.7156 (ttm) cc_final: 0.6273 (tmt) REVERT: A 593 TYR cc_start: 0.7889 (m-80) cc_final: 0.7658 (m-80) REVERT: A 610 ARG cc_start: 0.7320 (OUTLIER) cc_final: 0.6948 (ttm110) outliers start: 15 outliers final: 10 residues processed: 52 average time/residue: 0.9386 time to fit residues: 51.7615 Evaluate side-chains 51 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 40 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 511 MET Chi-restraints excluded: chain A residue 610 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 37 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 45 optimal weight: 0.0070 chunk 12 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.0827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 4312 Z= 0.150 Angle : 0.478 5.976 5886 Z= 0.247 Chirality : 0.037 0.115 665 Planarity : 0.004 0.042 721 Dihedral : 3.978 24.369 570 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 1.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.71 % Allowed : 24.15 % Favored : 73.14 % 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: 1.06 (0.38), residues: 522 helix: 1.72 (0.28), residues: 369 sheet: None (None), residues: 0 loop : -1.93 (0.47), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 132 HIS 0.001 0.000 HIS A 165 PHE 0.008 0.001 PHE A 412 TYR 0.009 0.001 TYR A 343 ARG 0.002 0.000 ARG A 125 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 46 time to evaluate : 0.478 Fit side-chains REVERT: A 250 LEU cc_start: 0.8288 (tp) cc_final: 0.7951 (tp) REVERT: A 510 GLN cc_start: 0.7210 (tp40) cc_final: 0.6761 (OUTLIER) REVERT: A 610 ARG cc_start: 0.7251 (OUTLIER) cc_final: 0.6918 (ttm110) outliers start: 12 outliers final: 9 residues processed: 55 average time/residue: 1.0358 time to fit residues: 59.6168 Evaluate side-chains 53 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 44 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 511 MET Chi-restraints excluded: chain A residue 610 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 12 optimal weight: 0.0470 chunk 50 optimal weight: 5.9990 chunk 41 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 overall best weight: 0.7080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.0892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 4312 Z= 0.150 Angle : 0.477 5.969 5886 Z= 0.246 Chirality : 0.037 0.115 665 Planarity : 0.004 0.041 721 Dihedral : 3.903 24.133 570 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.71 % Allowed : 24.60 % Favored : 72.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.38), residues: 522 helix: 1.76 (0.28), residues: 369 sheet: None (None), residues: 0 loop : -1.87 (0.47), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 132 HIS 0.002 0.000 HIS A 165 PHE 0.010 0.001 PHE A 412 TYR 0.018 0.001 TYR A 303 ARG 0.002 0.000 ARG A 125 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 47 time to evaluate : 0.474 Fit side-chains REVERT: A 226 GLN cc_start: 0.8299 (OUTLIER) cc_final: 0.7822 (mt0) REVERT: A 250 LEU cc_start: 0.8283 (tp) cc_final: 0.7926 (tp) REVERT: A 510 GLN cc_start: 0.7221 (tp40) cc_final: 0.6774 (OUTLIER) REVERT: A 593 TYR cc_start: 0.7815 (m-80) cc_final: 0.7580 (m-80) REVERT: A 610 ARG cc_start: 0.7205 (ttp80) cc_final: 0.6896 (ttm110) outliers start: 12 outliers final: 8 residues processed: 56 average time/residue: 1.0679 time to fit residues: 62.5465 Evaluate side-chains 48 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 40 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 226 GLN Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 511 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 28 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 30 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 34 optimal weight: 4.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.0912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4312 Z= 0.182 Angle : 0.505 5.794 5886 Z= 0.260 Chirality : 0.038 0.118 665 Planarity : 0.004 0.042 721 Dihedral : 3.981 24.219 570 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 3.61 % Allowed : 23.48 % Favored : 72.91 % 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: 1.03 (0.38), residues: 522 helix: 1.67 (0.28), residues: 370 sheet: None (None), residues: 0 loop : -1.89 (0.47), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 132 HIS 0.002 0.001 HIS A 165 PHE 0.013 0.001 PHE A 412 TYR 0.018 0.001 TYR A 303 ARG 0.002 0.000 ARG A 125 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 43 time to evaluate : 0.511 Fit side-chains REVERT: A 226 GLN cc_start: 0.8305 (OUTLIER) cc_final: 0.7849 (mt0) REVERT: A 250 LEU cc_start: 0.8306 (tp) cc_final: 0.7937 (tp) REVERT: A 272 MET cc_start: 0.7105 (ttm) cc_final: 0.6203 (tmt) REVERT: A 283 ARG cc_start: 0.8360 (OUTLIER) cc_final: 0.8056 (tpt170) REVERT: A 593 TYR cc_start: 0.7830 (m-80) cc_final: 0.7624 (m-80) REVERT: A 610 ARG cc_start: 0.7209 (OUTLIER) cc_final: 0.6903 (ttm110) outliers start: 16 outliers final: 10 residues processed: 56 average time/residue: 1.0113 time to fit residues: 60.0364 Evaluate side-chains 54 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 41 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 226 GLN Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 283 ARG Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 342 CYS Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 511 MET Chi-restraints excluded: chain A residue 610 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 6.9990 chunk 4 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 45 optimal weight: 0.4980 chunk 48 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 36 optimal weight: 0.4980 chunk 14 optimal weight: 2.9990 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 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.0919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 4312 Z= 0.152 Angle : 0.478 5.577 5886 Z= 0.247 Chirality : 0.037 0.123 665 Planarity : 0.004 0.043 721 Dihedral : 3.897 24.116 570 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.39 % Allowed : 24.15 % Favored : 72.46 % 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: 1.06 (0.38), residues: 522 helix: 1.65 (0.28), residues: 376 sheet: None (None), residues: 0 loop : -1.88 (0.49), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 132 HIS 0.002 0.000 HIS A 165 PHE 0.009 0.001 PHE A 412 TYR 0.019 0.001 TYR A 303 ARG 0.002 0.000 ARG A 125 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 43 time to evaluate : 0.491 Fit side-chains REVERT: A 250 LEU cc_start: 0.8282 (tp) cc_final: 0.7943 (tp) REVERT: A 283 ARG cc_start: 0.8362 (OUTLIER) cc_final: 0.8073 (tpt170) REVERT: A 610 ARG cc_start: 0.7170 (OUTLIER) cc_final: 0.6877 (ttm110) outliers start: 15 outliers final: 8 residues processed: 55 average time/residue: 0.9806 time to fit residues: 56.7006 Evaluate side-chains 51 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 41 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 283 ARG Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 342 CYS Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 511 MET Chi-restraints excluded: chain A residue 610 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 42 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.0935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4312 Z= 0.174 Angle : 0.500 5.817 5886 Z= 0.258 Chirality : 0.038 0.127 665 Planarity : 0.004 0.043 721 Dihedral : 3.943 24.173 570 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 1.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.93 % Allowed : 24.38 % Favored : 72.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.38), residues: 522 helix: 1.70 (0.28), residues: 370 sheet: None (None), residues: 0 loop : -1.88 (0.48), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 132 HIS 0.002 0.000 HIS A 165 PHE 0.011 0.001 PHE A 412 TYR 0.019 0.001 TYR A 303 ARG 0.002 0.000 ARG A 125 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 42 time to evaluate : 0.522 Fit side-chains REVERT: A 250 LEU cc_start: 0.8307 (tp) cc_final: 0.7961 (tp) REVERT: A 272 MET cc_start: 0.7111 (ttm) cc_final: 0.6216 (tmt) REVERT: A 283 ARG cc_start: 0.8356 (OUTLIER) cc_final: 0.8061 (tpt170) REVERT: A 510 GLN cc_start: 0.7226 (OUTLIER) cc_final: 0.6844 (mp10) REVERT: A 610 ARG cc_start: 0.7165 (OUTLIER) cc_final: 0.6872 (ttm110) outliers start: 13 outliers final: 8 residues processed: 53 average time/residue: 1.1360 time to fit residues: 62.9328 Evaluate side-chains 53 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 42 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 283 ARG Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 342 CYS Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 510 GLN Chi-restraints excluded: chain A residue 511 MET Chi-restraints excluded: chain A residue 610 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 chunk 12 optimal weight: 0.0980 chunk 38 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.0961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4312 Z= 0.179 Angle : 0.507 5.991 5886 Z= 0.261 Chirality : 0.038 0.129 665 Planarity : 0.004 0.043 721 Dihedral : 3.972 24.299 570 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 1.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.93 % Allowed : 24.15 % Favored : 72.91 % 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: 1.04 (0.38), residues: 522 helix: 1.69 (0.28), residues: 370 sheet: None (None), residues: 0 loop : -1.89 (0.47), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 132 HIS 0.002 0.001 HIS A 165 PHE 0.012 0.001 PHE A 412 TYR 0.019 0.001 TYR A 303 ARG 0.002 0.000 ARG A 125 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 43 time to evaluate : 0.487 Fit side-chains REVERT: A 250 LEU cc_start: 0.8312 (tp) cc_final: 0.7931 (tp) REVERT: A 272 MET cc_start: 0.7123 (ttm) cc_final: 0.6219 (tmt) REVERT: A 283 ARG cc_start: 0.8358 (OUTLIER) cc_final: 0.8055 (tpt170) REVERT: A 510 GLN cc_start: 0.7214 (OUTLIER) cc_final: 0.6778 (mp10) REVERT: A 610 ARG cc_start: 0.7163 (OUTLIER) cc_final: 0.6872 (ttm110) outliers start: 13 outliers final: 9 residues processed: 54 average time/residue: 1.1223 time to fit residues: 63.7048 Evaluate side-chains 53 residues out of total 443 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 41 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 283 ARG Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 342 CYS Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 510 GLN Chi-restraints excluded: chain A residue 511 MET Chi-restraints excluded: chain A residue 610 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 5 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.131594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.110927 restraints weight = 5064.616| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 1.69 r_work: 0.3074 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.0937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4312 Z= 0.178 Angle : 0.509 6.174 5886 Z= 0.263 Chirality : 0.038 0.131 665 Planarity : 0.004 0.043 721 Dihedral : 3.980 24.335 570 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.71 % Allowed : 24.38 % Favored : 72.91 % 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: 1.04 (0.38), residues: 522 helix: 1.68 (0.28), residues: 370 sheet: None (None), residues: 0 loop : -1.88 (0.48), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 132 HIS 0.002 0.000 HIS A 165 PHE 0.012 0.001 PHE A 412 TYR 0.010 0.001 TYR A 593 ARG 0.002 0.000 ARG A 125 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1691.45 seconds wall clock time: 37 minutes 10.48 seconds (2230.48 seconds total)