Starting phenix.real_space_refine on Thu Mar 6 00:27:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y2d_38851/03_2025/8y2d_38851.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y2d_38851/03_2025/8y2d_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/cci-nas-00/data/ceres_data/8y2d_38851/03_2025/8y2d_38851.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y2d_38851/03_2025/8y2d_38851.map" model { file = "/net/cci-nas-00/data/ceres_data/8y2d_38851/03_2025/8y2d_38851.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y2d_38851/03_2025/8y2d_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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 3.47, per 1000 atoms: 0.83 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: 1.07 Conformation dependent library (CDL) restraints added in 522.9 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: 0.40 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: 1.11 Time building geometry restraints manager: 1.30 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: 11.140 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 14.960 Find NCS groups from input model: 0.050 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:53.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.010 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.767 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 1.3196 time to fit residues: 72.0386 Evaluate side-chains 44 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.461 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.137129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.117246 restraints weight = 5016.471| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 1.68 r_work: 0.3100 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.0611 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 7.228 5886 Z= 0.271 Chirality : 0.038 0.122 665 Planarity : 0.004 0.045 721 Dihedral : 4.039 25.564 570 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 to be fit. rotamer outliers: 16 poor density : 43 time to evaluate : 0.450 Fit side-chains REVERT: A 610 ARG cc_start: 0.7266 (OUTLIER) cc_final: 0.6741 (ttm110) outliers start: 16 outliers final: 7 residues processed: 54 average time/residue: 1.0320 time to fit residues: 58.4886 Evaluate side-chains 49 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.468 ------------------------------------------------------------------------------- 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 1 optimal weight: 0.6980 chunk 42 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 2 optimal weight: 0.4980 chunk 21 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 23 optimal weight: 0.0470 chunk 33 optimal weight: 0.6980 overall best weight: 0.5878 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.139980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.119898 restraints weight = 5003.338| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 1.70 r_work: 0.3139 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.0716 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= 0.142 Angle : 0.468 6.159 5886 Z= 0.240 Chirality : 0.037 0.115 665 Planarity : 0.004 0.041 721 Dihedral : 3.884 24.637 570 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.16 % Allowed : 24.38 % 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: 1.15 (0.38), residues: 522 helix: 1.76 (0.28), residues: 369 sheet: None (None), residues: 0 loop : -1.79 (0.48), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 132 HIS 0.001 0.000 HIS A 165 PHE 0.008 0.001 PHE A 412 TYR 0.016 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 55 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 41 time to evaluate : 0.425 Fit side-chains REVERT: A 593 TYR cc_start: 0.7746 (m-80) cc_final: 0.7469 (m-80) REVERT: A 610 ARG cc_start: 0.7206 (OUTLIER) cc_final: 0.6694 (ttm110) outliers start: 14 outliers final: 5 residues processed: 51 average time/residue: 0.9669 time to fit residues: 51.7656 Evaluate side-chains 47 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 0.453 ------------------------------------------------------------------------------- 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 398 ILE 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 28 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 33 optimal weight: 6.9990 chunk 50 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.129967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.109104 restraints weight = 5078.833| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 1.69 r_work: 0.3079 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.0793 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= 0.176 Angle : 0.494 6.059 5886 Z= 0.254 Chirality : 0.037 0.118 665 Planarity : 0.004 0.042 721 Dihedral : 3.936 24.561 570 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 1.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 3.16 % Allowed : 23.02 % Favored : 73.81 % 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: 1.09 (0.38), residues: 522 helix: 1.71 (0.28), residues: 370 sheet: None (None), residues: 0 loop : -1.84 (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 0.012 0.001 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 58 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 44 time to evaluate : 0.426 Fit side-chains REVERT: A 250 LEU cc_start: 0.8040 (tp) cc_final: 0.7679 (tp) REVERT: A 593 TYR cc_start: 0.7772 (m-80) cc_final: 0.7495 (m-80) REVERT: A 610 ARG cc_start: 0.7221 (OUTLIER) cc_final: 0.6710 (ttm110) outliers start: 14 outliers final: 7 residues processed: 54 average time/residue: 0.8408 time to fit residues: 47.9174 Evaluate side-chains 50 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.459 ------------------------------------------------------------------------------- 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 454 LEU 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 41 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 3 optimal weight: 0.9980 chunk 29 optimal weight: 0.5980 chunk 24 optimal weight: 7.9990 chunk 27 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.3423 r_free = 0.3423 target = 0.130795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.109837 restraints weight = 5199.811| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 1.72 r_work: 0.3091 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.0799 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= 0.153 Angle : 0.476 5.616 5886 Z= 0.245 Chirality : 0.037 0.115 665 Planarity : 0.004 0.041 721 Dihedral : 3.892 24.348 570 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 1.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.93 % Allowed : 23.48 % Favored : 73.59 % 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: 1.18 (0.38), residues: 522 helix: 1.80 (0.28), residues: 369 sheet: None (None), residues: 0 loop : -1.84 (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 0.009 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 60 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 47 time to evaluate : 0.444 Fit side-chains REVERT: A 250 LEU cc_start: 0.8010 (tp) cc_final: 0.7658 (tp) REVERT: A 510 GLN cc_start: 0.7083 (tp40) cc_final: 0.6558 (OUTLIER) REVERT: A 593 TYR cc_start: 0.7761 (m-80) cc_final: 0.7528 (m-80) REVERT: A 610 ARG cc_start: 0.7182 (OUTLIER) cc_final: 0.6683 (ttm110) outliers start: 13 outliers final: 9 residues processed: 56 average time/residue: 1.1095 time to fit residues: 64.8226 Evaluate side-chains 55 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.422 ------------------------------------------------------------------------------- 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 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 2 optimal weight: 0.9980 chunk 36 optimal weight: 0.1980 chunk 19 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 50 optimal weight: 0.0040 chunk 24 optimal weight: 7.9990 chunk 21 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 overall best weight: 0.8394 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.133034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.112723 restraints weight = 5014.250| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 1.67 r_work: 0.3103 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.0876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4312 Z= 0.164 Angle : 0.489 5.643 5886 Z= 0.250 Chirality : 0.037 0.116 665 Planarity : 0.004 0.040 721 Dihedral : 3.893 24.279 570 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 1.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.16 % Allowed : 24.15 % 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: 1.14 (0.38), residues: 522 helix: 1.77 (0.28), residues: 369 sheet: None (None), residues: 0 loop : -1.86 (0.47), residues: 153 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 0.017 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 62 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 48 time to evaluate : 0.424 Fit side-chains REVERT: A 226 GLN cc_start: 0.8202 (OUTLIER) cc_final: 0.7709 (mt0) REVERT: A 250 LEU cc_start: 0.8000 (tp) cc_final: 0.7633 (tp) REVERT: A 510 GLN cc_start: 0.7076 (tp40) cc_final: 0.6544 (OUTLIER) REVERT: A 593 TYR cc_start: 0.7698 (m-80) cc_final: 0.7452 (m-80) REVERT: A 610 ARG cc_start: 0.7139 (ttp80) cc_final: 0.6666 (ttm110) outliers start: 14 outliers final: 9 residues processed: 57 average time/residue: 0.9569 time to fit residues: 57.1042 Evaluate side-chains 51 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.421 ------------------------------------------------------------------------------- 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 355 LEU 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 34 optimal weight: 0.0570 chunk 10 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 37 optimal weight: 0.0980 chunk 36 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 50 optimal weight: 0.5980 overall best weight: 0.4298 ------------------------------------------------------------------------------- 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 = 0.3497 r_free = 0.3497 target = 0.136382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.115713 restraints weight = 5088.287| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 1.71 r_work: 0.3139 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.0988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 4312 Z= 0.127 Angle : 0.450 5.503 5886 Z= 0.231 Chirality : 0.036 0.120 665 Planarity : 0.004 0.038 721 Dihedral : 3.725 23.838 570 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.48 % Allowed : 25.06 % 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: 1.29 (0.38), residues: 522 helix: 1.79 (0.28), residues: 377 sheet: None (None), residues: 0 loop : -1.72 (0.49), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 132 HIS 0.001 0.000 HIS A 165 PHE 0.006 0.001 PHE A 114 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 55 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 44 time to evaluate : 0.475 Fit side-chains REVERT: A 226 GLN cc_start: 0.8154 (OUTLIER) cc_final: 0.7642 (mt0) REVERT: A 250 LEU cc_start: 0.7956 (tp) cc_final: 0.7694 (tt) REVERT: A 441 LEU cc_start: 0.6752 (OUTLIER) cc_final: 0.5729 (pp) REVERT: A 593 TYR cc_start: 0.7651 (m-80) cc_final: 0.7413 (m-80) REVERT: A 610 ARG cc_start: 0.7113 (OUTLIER) cc_final: 0.6651 (ttm110) outliers start: 11 outliers final: 4 residues processed: 52 average time/residue: 1.0065 time to fit residues: 55.1042 Evaluate side-chains 50 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 441 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/iotbx/cli_parser.py", line 980, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.6069 > 50: distance: 30 - 36: 25.372 distance: 36 - 37: 12.973 distance: 37 - 38: 16.977 distance: 37 - 40: 39.860 distance: 38 - 39: 10.046 distance: 38 - 47: 40.054 distance: 40 - 41: 26.090 distance: 41 - 42: 28.398 distance: 41 - 43: 19.541 distance: 42 - 44: 43.722 distance: 43 - 45: 52.447 distance: 45 - 46: 45.470 distance: 47 - 48: 10.992 distance: 48 - 49: 11.885 distance: 48 - 51: 21.242 distance: 49 - 50: 34.749 distance: 49 - 59: 10.808 distance: 51 - 52: 9.843 distance: 52 - 53: 29.301 distance: 52 - 54: 4.006 distance: 53 - 55: 30.528 distance: 54 - 56: 14.789 distance: 55 - 57: 12.322 distance: 56 - 57: 36.071 distance: 57 - 58: 38.290 distance: 59 - 60: 15.949 distance: 60 - 61: 12.319 distance: 60 - 63: 28.473 distance: 61 - 62: 34.754 distance: 61 - 70: 23.593 distance: 63 - 64: 14.666 distance: 64 - 65: 5.617 distance: 65 - 66: 19.487 distance: 66 - 67: 19.965 distance: 67 - 68: 23.994 distance: 67 - 69: 16.782 distance: 70 - 71: 10.754 distance: 71 - 72: 8.797 distance: 71 - 74: 10.254 distance: 72 - 73: 32.206 distance: 72 - 78: 21.677 distance: 74 - 75: 27.068 distance: 75 - 76: 9.918 distance: 75 - 77: 36.394 distance: 78 - 79: 23.910 distance: 79 - 80: 4.818 distance: 79 - 82: 19.456 distance: 80 - 81: 14.443 distance: 80 - 84: 12.220 distance: 82 - 83: 20.117 distance: 84 - 85: 9.989 distance: 85 - 86: 35.717 distance: 85 - 88: 19.308 distance: 86 - 87: 50.091 distance: 86 - 93: 40.028 distance: 88 - 89: 45.619 distance: 89 - 90: 26.935 distance: 90 - 91: 20.975 distance: 90 - 92: 51.067 distance: 93 - 94: 40.402 distance: 94 - 95: 22.985 distance: 94 - 97: 40.679 distance: 95 - 96: 49.468 distance: 95 - 98: 29.657 distance: 98 - 99: 31.525 distance: 99 - 100: 34.149 distance: 99 - 102: 17.606 distance: 100 - 101: 29.144 distance: 100 - 104: 39.916 distance: 101 - 133: 32.115 distance: 102 - 103: 47.710 distance: 104 - 105: 40.214 distance: 105 - 106: 47.679 distance: 105 - 108: 21.775 distance: 106 - 107: 27.669 distance: 106 - 111: 21.310 distance: 107 - 141: 31.084 distance: 108 - 109: 25.036 distance: 108 - 110: 42.569 distance: 111 - 112: 40.012 distance: 112 - 113: 11.828 distance: 112 - 115: 26.848 distance: 113 - 114: 13.107 distance: 113 - 125: 29.210 distance: 114 - 145: 35.557 distance: 115 - 116: 32.702 distance: 116 - 117: 22.935 distance: 116 - 118: 29.255 distance: 117 - 119: 42.640 distance: 118 - 120: 41.185 distance: 118 - 121: 5.164 distance: 119 - 120: 21.454 distance: 120 - 122: 27.469 distance: 121 - 123: 31.106 distance: 122 - 124: 26.350 distance: 123 - 124: 15.324