Starting phenix.real_space_refine on Tue Apr 29 17:32:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7bw7_30229/04_2025/7bw7_30229.cif Found real_map, /net/cci-nas-00/data/ceres_data/7bw7_30229/04_2025/7bw7_30229.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7bw7_30229/04_2025/7bw7_30229.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7bw7_30229/04_2025/7bw7_30229.map" model { file = "/net/cci-nas-00/data/ceres_data/7bw7_30229/04_2025/7bw7_30229.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7bw7_30229/04_2025/7bw7_30229.cif" } resolution = 4.1 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 56 5.16 5 C 5621 2.51 5 N 1509 2.21 5 O 1638 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 46 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 8824 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 647, 5224 Classifications: {'peptide': 647} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 613} Chain breaks: 5 Chain: "C" Number of atoms: 3224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3224 Classifications: {'peptide': 396} Link IDs: {'PTRANS': 19, 'TRANS': 376} Chain breaks: 4 Chain: "D" Number of atoms: 376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 376 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 1, 'TRANS': 46} Chain breaks: 1 Time building chain proxies: 5.25, per 1000 atoms: 0.59 Number of scatterers: 8824 At special positions: 0 Unit cell: (91.79, 108.23, 153.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 56 16.00 O 1638 8.00 N 1509 7.00 C 5621 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, symmetry=0 Simple disulfide: pdb=" SG CYS A 8 " - pdb=" SG CYS A 26 " distance=2.03 Simple disulfide: pdb=" SG CYS A 192 " - pdb=" SG CYS A 201 " distance=2.03 Simple disulfide: pdb=" SG CYS A 196 " - pdb=" SG CYS A 207 " distance=2.03 Simple disulfide: pdb=" SG CYS A 208 " - pdb=" SG CYS A 216 " distance=2.02 Simple disulfide: pdb=" SG CYS A 212 " - pdb=" SG CYS A 225 " distance=2.04 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 237 " distance=2.03 Simple disulfide: pdb=" SG CYS A 241 " - pdb=" SG CYS A 253 " distance=2.03 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 284 " distance=2.04 Simple disulfide: pdb=" SG CYS A 266 " - pdb=" SG CYS A 274 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 312 " - pdb=" SG CYS A 333 " distance=2.04 Simple disulfide: pdb=" SG CYS A 435 " - pdb=" SG CYS A 468 " distance=2.03 Simple disulfide: pdb=" SG CYS A 786 " - pdb=" SG CYS A 795 " distance=2.03 Simple disulfide: pdb=" SG CYS C 786 " - pdb=" SG CYS C 795 " distance=2.03 Simple disulfide: pdb=" SG CYS D 7 " - pdb=" SG CYS D 62 " distance=2.03 Simple disulfide: pdb=" SG CYS D 19 " - pdb=" SG CYS D 75 " distance=2.04 Simple disulfide: pdb=" SG CYS D 61 " - pdb=" SG CYS D 66 " 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: 2.33 Conformation dependent library (CDL) restraints added in 993.9 milliseconds 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2068 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 14 sheets defined 13.2% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'A' and resid 16 through 20 removed outlier: 3.745A pdb=" N ARG A 19 " --> pdb=" O ASN A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 137 Processing helix chain 'A' and resid 139 through 143 removed outlier: 3.558A pdb=" N ASP A 142 " --> pdb=" O SER A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 200 removed outlier: 3.956A pdb=" N HIS A 199 " --> pdb=" O CYS A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 268 removed outlier: 3.854A pdb=" N CYS A 259 " --> pdb=" O ASN A 255 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS A 265 " --> pdb=" O ASP A 261 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N CYS A 266 " --> pdb=" O LEU A 262 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ASN A 268 " --> pdb=" O HIS A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 318 removed outlier: 3.751A pdb=" N GLY A 317 " --> pdb=" O LEU A 314 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU A 318 " --> pdb=" O LEU A 315 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 314 through 318' Processing helix chain 'A' and resid 323 through 328 Processing helix chain 'A' and resid 350 through 358 removed outlier: 3.515A pdb=" N LEU A 354 " --> pdb=" O LEU A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 447 removed outlier: 3.777A pdb=" N GLY A 447 " --> pdb=" O GLU A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 500 Processing helix chain 'A' and resid 638 through 642 Processing helix chain 'C' and resid 314 through 316 No H-bonds generated for 'chain 'C' and resid 314 through 316' Processing helix chain 'C' and resid 323 through 328 Processing helix chain 'C' and resid 329 through 331 No H-bonds generated for 'chain 'C' and resid 329 through 331' Processing helix chain 'C' and resid 352 through 357 Processing helix chain 'C' and resid 435 through 440 removed outlier: 4.208A pdb=" N ILE C 439 " --> pdb=" O CYS C 435 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N HIS C 440 " --> pdb=" O LEU C 436 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 435 through 440' Processing helix chain 'C' and resid 440 through 445 Processing helix chain 'C' and resid 496 through 500 Processing helix chain 'C' and resid 692 through 710 removed outlier: 3.730A pdb=" N GLU C 698 " --> pdb=" O LYS C 694 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N SER C 700 " --> pdb=" O LEU C 696 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N LYS C 703 " --> pdb=" O SER C 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 19 removed outlier: 3.824A pdb=" N CYS D 19 " --> pdb=" O LEU D 15 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 14 removed outlier: 6.586A pdb=" N VAL A 66 " --> pdb=" O LEU A 37 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 56 through 57 removed outlier: 3.517A pdb=" N ILE A 82 " --> pdb=" O ASN A 111 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 95 through 96 removed outlier: 6.816A pdb=" N ASN A 148 " --> pdb=" O LYS A 121 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 246 through 248 removed outlier: 3.736A pdb=" N VAL A 254 " --> pdb=" O TYR A 246 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE A 248 " --> pdb=" O ARG A 252 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 278 through 280 Processing sheet with id=AA6, first strand: chain 'A' and resid 292 through 294 Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 312 removed outlier: 3.521A pdb=" N CYS A 312 " --> pdb=" O VAL A 335 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 475 through 480 removed outlier: 6.560A pdb=" N ARG A 488 " --> pdb=" O SER A 476 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ILE A 478 " --> pdb=" O LEU A 486 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LEU A 486 " --> pdb=" O ILE A 478 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 530 through 533 removed outlier: 3.948A pdb=" N THR A 530 " --> pdb=" O TYR A 507 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N TYR A 507 " --> pdb=" O THR A 530 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N VAL A 566 " --> pdb=" O ASP A 584 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N ASP A 584 " --> pdb=" O VAL A 566 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 599 through 602 removed outlier: 6.607A pdb=" N LYS A 614 " --> pdb=" O PRO A 601 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 318 through 321 removed outlier: 6.590A pdb=" N LYS C 319 " --> pdb=" O ILE C 341 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N LEU C 340 " --> pdb=" O LYS C 369 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 531 through 533 removed outlier: 3.542A pdb=" N VAL C 532 " --> pdb=" O LEU C 505 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 599 through 605 removed outlier: 4.858A pdb=" N ASP C 600 " --> pdb=" O LYS C 616 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 630 through 631 removed outlier: 3.651A pdb=" N GLU C 782 " --> pdb=" O PHE C 631 " (cutoff:3.500A) 119 hydrogen bonds defined for protein. 279 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: 2.19 Time building geometry restraints manager: 2.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2764 1.34 - 1.46: 2073 1.46 - 1.58: 4125 1.58 - 1.71: 0 1.71 - 1.83: 70 Bond restraints: 9032 Sorted by residual: bond pdb=" C VAL C 597 " pdb=" N PRO C 598 " ideal model delta sigma weight residual 1.330 1.377 -0.047 1.25e-02 6.40e+03 1.41e+01 bond pdb=" CA LEU C 696 " pdb=" C LEU C 696 " ideal model delta sigma weight residual 1.522 1.457 0.064 1.72e-02 3.38e+03 1.39e+01 bond pdb=" N VAL A 377 " pdb=" CA VAL A 377 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.08e-02 8.57e+03 1.24e+01 bond pdb=" N GLY C 580 " pdb=" CA GLY C 580 " ideal model delta sigma weight residual 1.446 1.485 -0.039 1.13e-02 7.83e+03 1.19e+01 bond pdb=" N THR C 578 " pdb=" CA THR C 578 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.20e-02 6.94e+03 1.02e+01 ... (remaining 9027 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 11418 1.95 - 3.90: 687 3.90 - 5.86: 101 5.86 - 7.81: 18 7.81 - 9.76: 9 Bond angle restraints: 12233 Sorted by residual: angle pdb=" C TYR C 579 " pdb=" CA TYR C 579 " pdb=" CB TYR C 579 " ideal model delta sigma weight residual 110.04 100.28 9.76 1.51e+00 4.39e-01 4.18e+01 angle pdb=" N PRO C 621 " pdb=" CA PRO C 621 " pdb=" C PRO C 621 " ideal model delta sigma weight residual 113.86 106.93 6.93 1.25e+00 6.40e-01 3.07e+01 angle pdb=" N PRO A 432 " pdb=" CA PRO A 432 " pdb=" C PRO A 432 " ideal model delta sigma weight residual 113.40 120.78 -7.38 1.34e+00 5.57e-01 3.04e+01 angle pdb=" C VAL C 597 " pdb=" N PRO C 598 " pdb=" CA PRO C 598 " ideal model delta sigma weight residual 120.21 125.30 -5.09 9.60e-01 1.09e+00 2.81e+01 angle pdb=" N VAL A 324 " pdb=" CA VAL A 324 " pdb=" C VAL A 324 " ideal model delta sigma weight residual 111.89 104.50 7.39 1.44e+00 4.82e-01 2.64e+01 ... (remaining 12228 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 4697 17.95 - 35.90: 610 35.90 - 53.85: 129 53.85 - 71.80: 14 71.80 - 89.75: 9 Dihedral angle restraints: 5459 sinusoidal: 2267 harmonic: 3192 Sorted by residual: dihedral pdb=" CB CYS D 19 " pdb=" SG CYS D 19 " pdb=" SG CYS D 75 " pdb=" CB CYS D 75 " ideal model delta sinusoidal sigma weight residual -86.00 -151.20 65.20 1 1.00e+01 1.00e-02 5.57e+01 dihedral pdb=" CB CYS A 228 " pdb=" SG CYS A 228 " pdb=" SG CYS A 237 " pdb=" CB CYS A 237 " ideal model delta sinusoidal sigma weight residual -86.00 -145.19 59.19 1 1.00e+01 1.00e-02 4.68e+01 dihedral pdb=" CA CYS A 207 " pdb=" C CYS A 207 " pdb=" N CYS A 208 " pdb=" CA CYS A 208 " ideal model delta harmonic sigma weight residual -180.00 -151.36 -28.64 0 5.00e+00 4.00e-02 3.28e+01 ... (remaining 5456 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1020 0.067 - 0.133: 274 0.133 - 0.200: 39 0.200 - 0.266: 3 0.266 - 0.333: 1 Chirality restraints: 1337 Sorted by residual: chirality pdb=" CA PRO A 432 " pdb=" N PRO A 432 " pdb=" C PRO A 432 " pdb=" CB PRO A 432 " both_signs ideal model delta sigma weight residual False 2.72 2.39 0.33 2.00e-01 2.50e+01 2.77e+00 chirality pdb=" CG LEU C 434 " pdb=" CB LEU C 434 " pdb=" CD1 LEU C 434 " pdb=" CD2 LEU C 434 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CA ILE C 457 " pdb=" N ILE C 457 " pdb=" C ILE C 457 " pdb=" CB ILE C 457 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 1334 not shown) Planarity restraints: 1568 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG C 577 " -0.022 2.00e-02 2.50e+03 4.53e-02 2.05e+01 pdb=" C ARG C 577 " 0.078 2.00e-02 2.50e+03 pdb=" O ARG C 577 " -0.029 2.00e-02 2.50e+03 pdb=" N THR C 578 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO C 494 " -0.044 5.00e-02 4.00e+02 6.62e-02 7.01e+00 pdb=" N PRO C 495 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO C 495 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 495 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP C 591 " 0.012 2.00e-02 2.50e+03 2.43e-02 5.92e+00 pdb=" C ASP C 591 " -0.042 2.00e-02 2.50e+03 pdb=" O ASP C 591 " 0.016 2.00e-02 2.50e+03 pdb=" N ALA C 592 " 0.015 2.00e-02 2.50e+03 ... (remaining 1565 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 245 2.62 - 3.19: 8823 3.19 - 3.76: 13629 3.76 - 4.33: 18090 4.33 - 4.90: 27791 Nonbonded interactions: 68578 Sorted by model distance: nonbonded pdb=" OG SER C 437 " pdb=" O GLU C 517 " model vdw 2.050 3.040 nonbonded pdb=" OG SER A 116 " pdb=" OD1 ASN A 143 " model vdw 2.118 3.040 nonbonded pdb=" OG SER A 198 " pdb=" NE ARG A 229 " model vdw 2.122 3.120 nonbonded pdb=" OH TYR A 628 " pdb=" OE2 GLU A 766 " model vdw 2.136 3.040 nonbonded pdb=" OG SER D 67 " pdb=" OE1 GLN D 70 " model vdw 2.141 3.040 ... (remaining 68573 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.310 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: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 22.650 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 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: 0.010 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6795 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.078 9049 Z= 0.396 Angle : 1.062 9.759 12267 Z= 0.608 Chirality : 0.060 0.333 1337 Planarity : 0.006 0.066 1568 Dihedral : 16.200 89.747 3340 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 40.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 23.38 % Favored : 76.62 % Rotamer: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -5.62 (0.21), residues: 1065 helix: -3.74 (0.35), residues: 101 sheet: -3.83 (0.34), residues: 190 loop : -4.03 (0.19), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP A 183 HIS 0.007 0.002 HIS D 5 PHE 0.029 0.003 PHE A 400 TYR 0.027 0.003 TYR D 26 ARG 0.009 0.001 ARG A 118 Details of bonding type rmsd hydrogen bonds : bond 0.20597 ( 119) hydrogen bonds : angle 11.12800 ( 279) SS BOND : bond 0.00511 ( 17) SS BOND : angle 2.36126 ( 34) covalent geometry : bond 0.00771 ( 9032) covalent geometry : angle 1.05605 (12233) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 LEU cc_start: 0.7987 (tt) cc_final: 0.7682 (tp) REVERT: A 246 TYR cc_start: 0.7658 (m-80) cc_final: 0.7110 (m-80) REVERT: A 382 PHE cc_start: 0.8574 (m-10) cc_final: 0.8320 (m-10) REVERT: A 513 GLN cc_start: 0.7419 (tp-100) cc_final: 0.6743 (mp10) REVERT: A 616 LYS cc_start: 0.9016 (tppt) cc_final: 0.8632 (tppt) REVERT: A 780 ARG cc_start: 0.7569 (ptt180) cc_final: 0.7125 (ptm-80) REVERT: C 355 GLU cc_start: 0.7858 (tt0) cc_final: 0.7392 (pt0) REVERT: C 382 PHE cc_start: 0.8463 (t80) cc_final: 0.7999 (t80) REVERT: C 552 LEU cc_start: 0.9076 (tp) cc_final: 0.8812 (tp) REVERT: C 780 ARG cc_start: 0.7148 (ttt-90) cc_final: 0.6133 (mtp85) outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.2971 time to fit residues: 60.5554 Evaluate side-chains 117 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 3.9990 chunk 81 optimal weight: 6.9990 chunk 45 optimal weight: 8.9990 chunk 27 optimal weight: 30.0000 chunk 54 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 chunk 62 optimal weight: 8.9990 chunk 97 optimal weight: 0.7980 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 GLN ** A 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4775 r_free = 0.4775 target = 0.180339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.140953 restraints weight = 19247.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.142745 restraints weight = 14796.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.143369 restraints weight = 12732.135| |-----------------------------------------------------------------------------| r_work (final): 0.4275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6724 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 9049 Z= 0.230 Angle : 0.886 12.144 12267 Z= 0.453 Chirality : 0.052 0.177 1337 Planarity : 0.006 0.055 1568 Dihedral : 7.855 27.085 1184 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 23.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.81 % Favored : 80.19 % Rotamer: Outliers : 0.20 % Allowed : 13.52 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -5.31 (0.22), residues: 1065 helix: -3.27 (0.37), residues: 101 sheet: -3.85 (0.32), residues: 202 loop : -3.75 (0.20), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 632 HIS 0.005 0.001 HIS C 429 PHE 0.024 0.003 PHE A 381 TYR 0.032 0.002 TYR A 430 ARG 0.007 0.001 ARG A 371 Details of bonding type rmsd hydrogen bonds : bond 0.05659 ( 119) hydrogen bonds : angle 9.54327 ( 279) SS BOND : bond 0.00484 ( 17) SS BOND : angle 1.72477 ( 34) covalent geometry : bond 0.00522 ( 9032) covalent geometry : angle 0.88226 (12233) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 155 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 ARG cc_start: 0.6888 (mmm160) cc_final: 0.6261 (mmt180) REVERT: A 98 MET cc_start: 0.7328 (mmm) cc_final: 0.7076 (mmm) REVERT: A 246 TYR cc_start: 0.7043 (m-80) cc_final: 0.6548 (m-80) REVERT: A 294 MET cc_start: 0.6146 (ppp) cc_final: 0.5887 (ppp) REVERT: A 355 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.8287 (pp20) REVERT: A 426 LEU cc_start: 0.7711 (tt) cc_final: 0.7352 (tt) REVERT: A 427 PHE cc_start: 0.6957 (t80) cc_final: 0.6698 (t80) REVERT: A 472 LEU cc_start: 0.6914 (tp) cc_final: 0.6645 (pt) REVERT: A 504 MET cc_start: 0.3066 (mmm) cc_final: 0.2865 (mmm) REVERT: A 513 GLN cc_start: 0.7393 (tp-100) cc_final: 0.6738 (mp10) REVERT: A 616 LYS cc_start: 0.8835 (tppt) cc_final: 0.8420 (tppt) REVERT: C 355 GLU cc_start: 0.7782 (tt0) cc_final: 0.7305 (pt0) REVERT: C 381 PHE cc_start: 0.8639 (p90) cc_final: 0.8110 (p90) REVERT: C 409 ARG cc_start: 0.6208 (mtt90) cc_final: 0.5974 (mmt90) REVERT: C 552 LEU cc_start: 0.9178 (tp) cc_final: 0.8098 (tp) REVERT: C 577 ARG cc_start: 0.6734 (tpt-90) cc_final: 0.6529 (tpt-90) REVERT: C 614 LYS cc_start: 0.8548 (ptpp) cc_final: 0.8342 (ptmt) REVERT: C 780 ARG cc_start: 0.6979 (ttt-90) cc_final: 0.5912 (mtp85) outliers start: 2 outliers final: 1 residues processed: 156 average time/residue: 0.2564 time to fit residues: 53.2304 Evaluate side-chains 115 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 113 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 59 optimal weight: 10.0000 chunk 4 optimal weight: 6.9990 chunk 44 optimal weight: 7.9990 chunk 25 optimal weight: 0.3980 chunk 10 optimal weight: 2.9990 chunk 49 optimal weight: 0.0060 chunk 15 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 overall best weight: 1.8802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 90 ASN A 100 HIS ** A 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 462 ASN A 594 ASN ** C 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 711 ASN ** D 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5017 r_free = 0.5017 target = 0.224175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4842 r_free = 0.4842 target = 0.193875 restraints weight = 22325.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.4890 r_free = 0.4890 target = 0.192070 restraints weight = 27006.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4881 r_free = 0.4881 target = 0.192700 restraints weight = 20750.126| |-----------------------------------------------------------------------------| r_work (final): 0.4491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6390 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 9049 Z= 0.182 Angle : 0.835 10.606 12267 Z= 0.428 Chirality : 0.051 0.173 1337 Planarity : 0.005 0.049 1568 Dihedral : 7.449 28.371 1184 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 20.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.46 % Favored : 82.54 % Rotamer: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -5.02 (0.22), residues: 1065 helix: -3.04 (0.40), residues: 109 sheet: -3.75 (0.34), residues: 186 loop : -3.54 (0.19), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 251 HIS 0.006 0.001 HIS C 429 PHE 0.016 0.002 PHE A 382 TYR 0.022 0.002 TYR A 60 ARG 0.004 0.001 ARG A 118 Details of bonding type rmsd hydrogen bonds : bond 0.05055 ( 119) hydrogen bonds : angle 8.95369 ( 279) SS BOND : bond 0.00381 ( 17) SS BOND : angle 2.07782 ( 34) covalent geometry : bond 0.00419 ( 9032) covalent geometry : angle 0.82854 (12233) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 1.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 ARG cc_start: 0.6766 (mmm160) cc_final: 0.6082 (mmt180) REVERT: A 294 MET cc_start: 0.5918 (ppp) cc_final: 0.5632 (ppp) REVERT: A 374 TYR cc_start: 0.8568 (t80) cc_final: 0.8365 (t80) REVERT: A 404 ASP cc_start: 0.8541 (t70) cc_final: 0.8092 (t0) REVERT: A 427 PHE cc_start: 0.6607 (t80) cc_final: 0.6389 (t80) REVERT: A 513 GLN cc_start: 0.7336 (tp-100) cc_final: 0.6793 (mp10) REVERT: A 616 LYS cc_start: 0.8531 (tppt) cc_final: 0.8138 (tppt) REVERT: A 765 LYS cc_start: 0.7768 (mttp) cc_final: 0.7319 (mttm) REVERT: A 783 LEU cc_start: 0.9032 (tp) cc_final: 0.8519 (tp) REVERT: C 370 ILE cc_start: 0.8210 (mm) cc_final: 0.7925 (mm) REVERT: C 382 PHE cc_start: 0.8091 (t80) cc_final: 0.7709 (t80) REVERT: C 552 LEU cc_start: 0.8948 (tp) cc_final: 0.8646 (tp) REVERT: C 780 ARG cc_start: 0.6847 (ttt-90) cc_final: 0.6351 (mtp-110) outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 0.2773 time to fit residues: 58.3787 Evaluate side-chains 116 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 15 optimal weight: 9.9990 chunk 88 optimal weight: 4.9990 chunk 94 optimal weight: 5.9990 chunk 102 optimal weight: 20.0000 chunk 2 optimal weight: 6.9990 chunk 74 optimal weight: 0.4980 chunk 79 optimal weight: 0.1980 chunk 93 optimal weight: 1.9990 chunk 69 optimal weight: 8.9990 chunk 67 optimal weight: 20.0000 chunk 39 optimal weight: 0.9980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 429 HIS ** C 452 GLN ** 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 = 0.5028 r_free = 0.5028 target = 0.224711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4850 r_free = 0.4850 target = 0.195461 restraints weight = 21890.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4867 r_free = 0.4867 target = 0.194578 restraints weight = 25401.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4876 r_free = 0.4876 target = 0.194405 restraints weight = 19848.272| |-----------------------------------------------------------------------------| r_work (final): 0.4572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6350 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9049 Z= 0.162 Angle : 0.779 9.567 12267 Z= 0.400 Chirality : 0.050 0.164 1337 Planarity : 0.005 0.048 1568 Dihedral : 7.101 28.874 1184 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 17.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.15 % Favored : 83.85 % Rotamer: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -4.83 (0.22), residues: 1065 helix: -2.81 (0.41), residues: 113 sheet: -3.58 (0.34), residues: 185 loop : -3.44 (0.20), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 529 HIS 0.005 0.001 HIS C 627 PHE 0.014 0.002 PHE A 382 TYR 0.024 0.002 TYR A 430 ARG 0.006 0.001 ARG C 539 Details of bonding type rmsd hydrogen bonds : bond 0.04479 ( 119) hydrogen bonds : angle 8.38380 ( 279) SS BOND : bond 0.00388 ( 17) SS BOND : angle 1.69152 ( 34) covalent geometry : bond 0.00368 ( 9032) covalent geometry : angle 0.77522 (12233) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 ARG cc_start: 0.6806 (mmm160) cc_final: 0.6113 (mmt180) REVERT: A 98 MET cc_start: 0.7070 (mmm) cc_final: 0.6778 (tpt) REVERT: A 294 MET cc_start: 0.5751 (ppp) cc_final: 0.5481 (ppp) REVERT: A 425 LYS cc_start: 0.7282 (ttmt) cc_final: 0.7034 (tmtt) REVERT: A 513 GLN cc_start: 0.7262 (tp-100) cc_final: 0.6639 (mp10) REVERT: A 616 LYS cc_start: 0.8507 (tppt) cc_final: 0.8149 (tppt) REVERT: A 765 LYS cc_start: 0.7689 (mttp) cc_final: 0.7253 (mttm) REVERT: C 552 LEU cc_start: 0.9023 (tp) cc_final: 0.8711 (tp) REVERT: C 577 ARG cc_start: 0.6443 (tpt-90) cc_final: 0.6147 (tpt-90) outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 0.2211 time to fit residues: 46.1451 Evaluate side-chains 114 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 10 optimal weight: 0.0000 chunk 38 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 63 optimal weight: 9.9990 chunk 36 optimal weight: 3.9990 chunk 20 optimal weight: 7.9990 chunk 24 optimal weight: 9.9990 chunk 61 optimal weight: 5.9990 chunk 99 optimal weight: 9.9990 overall best weight: 2.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 406 GLN ** A 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 470 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 = 0.5013 r_free = 0.5013 target = 0.222355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4818 r_free = 0.4818 target = 0.191532 restraints weight = 21859.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4828 r_free = 0.4828 target = 0.190076 restraints weight = 24850.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4825 r_free = 0.4825 target = 0.189125 restraints weight = 19870.783| |-----------------------------------------------------------------------------| r_work (final): 0.4538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6452 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9049 Z= 0.192 Angle : 0.800 10.578 12267 Z= 0.410 Chirality : 0.050 0.186 1337 Planarity : 0.005 0.048 1568 Dihedral : 7.121 28.731 1184 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 19.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.00 % Favored : 83.00 % Rotamer: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -4.71 (0.23), residues: 1065 helix: -2.77 (0.42), residues: 112 sheet: -3.42 (0.34), residues: 191 loop : -3.35 (0.20), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 551 HIS 0.008 0.001 HIS D 5 PHE 0.018 0.002 PHE A 381 TYR 0.040 0.002 TYR C 430 ARG 0.008 0.001 ARG C 539 Details of bonding type rmsd hydrogen bonds : bond 0.04372 ( 119) hydrogen bonds : angle 8.45318 ( 279) SS BOND : bond 0.00405 ( 17) SS BOND : angle 1.66679 ( 34) covalent geometry : bond 0.00440 ( 9032) covalent geometry : angle 0.79581 (12233) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 MET cc_start: 0.6336 (mpp) cc_final: 0.5007 (tpt) REVERT: A 83 ARG cc_start: 0.6818 (mmm160) cc_final: 0.6095 (mmt180) REVERT: A 98 MET cc_start: 0.7174 (mmm) cc_final: 0.6969 (mmm) REVERT: A 110 MET cc_start: 0.7932 (mmm) cc_final: 0.7623 (mmm) REVERT: A 360 LEU cc_start: 0.7862 (mm) cc_final: 0.7066 (tt) REVERT: A 425 LYS cc_start: 0.7292 (ttmt) cc_final: 0.6869 (tmtt) REVERT: A 513 GLN cc_start: 0.7139 (tp-100) cc_final: 0.6632 (mp10) REVERT: A 764 ASN cc_start: 0.5727 (m-40) cc_final: 0.5500 (m-40) REVERT: A 765 LYS cc_start: 0.7221 (mttp) cc_final: 0.6801 (mttm) REVERT: A 783 LEU cc_start: 0.8928 (tp) cc_final: 0.8582 (tp) REVERT: C 430 TYR cc_start: 0.6694 (t80) cc_final: 0.6435 (t80) REVERT: C 552 LEU cc_start: 0.9163 (tp) cc_final: 0.8791 (tp) REVERT: C 780 ARG cc_start: 0.6840 (ttt-90) cc_final: 0.5985 (mtp85) outliers start: 0 outliers final: 0 residues processed: 145 average time/residue: 0.2327 time to fit residues: 45.8539 Evaluate side-chains 115 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 96 optimal weight: 9.9990 chunk 101 optimal weight: 5.9990 chunk 7 optimal weight: 0.7980 chunk 28 optimal weight: 4.9990 chunk 63 optimal weight: 10.0000 chunk 60 optimal weight: 8.9990 chunk 31 optimal weight: 0.6980 chunk 27 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 chunk 102 optimal weight: 8.9990 chunk 100 optimal weight: 1.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 189 GLN ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 513 GLN C 561 GLN C 622 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4839 r_free = 0.4839 target = 0.184906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.153664 restraints weight = 19258.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.160818 restraints weight = 27098.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4549 r_free = 0.4549 target = 0.161565 restraints weight = 14093.064| |-----------------------------------------------------------------------------| r_work (final): 0.4458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6339 moved from start: 0.3339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 9049 Z= 0.208 Angle : 0.809 9.916 12267 Z= 0.413 Chirality : 0.050 0.166 1337 Planarity : 0.005 0.066 1568 Dihedral : 7.097 29.038 1184 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 20.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.56 % Favored : 82.44 % Rotamer: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -4.64 (0.23), residues: 1065 helix: -2.81 (0.41), residues: 112 sheet: -3.34 (0.35), residues: 181 loop : -3.31 (0.20), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 412 HIS 0.017 0.001 HIS A 429 PHE 0.025 0.003 PHE A 89 TYR 0.031 0.002 TYR C 430 ARG 0.008 0.001 ARG C 539 Details of bonding type rmsd hydrogen bonds : bond 0.04340 ( 119) hydrogen bonds : angle 8.42040 ( 279) SS BOND : bond 0.00340 ( 17) SS BOND : angle 1.69265 ( 34) covalent geometry : bond 0.00478 ( 9032) covalent geometry : angle 0.80543 (12233) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 ARG cc_start: 0.6742 (mmm160) cc_final: 0.6033 (mmt180) REVERT: A 110 MET cc_start: 0.7774 (mmm) cc_final: 0.7567 (mmm) REVERT: A 120 GLU cc_start: 0.5454 (tt0) cc_final: 0.5226 (tt0) REVERT: A 360 LEU cc_start: 0.7637 (mm) cc_final: 0.6904 (tt) REVERT: A 404 ASP cc_start: 0.8497 (t0) cc_final: 0.8258 (t0) REVERT: A 425 LYS cc_start: 0.7463 (ttmt) cc_final: 0.6843 (tmtt) REVERT: A 513 GLN cc_start: 0.7209 (tp-100) cc_final: 0.6621 (mp10) REVERT: A 616 LYS cc_start: 0.8721 (tptp) cc_final: 0.8510 (tppt) REVERT: A 765 LYS cc_start: 0.7418 (mttp) cc_final: 0.6995 (mttm) REVERT: A 783 LEU cc_start: 0.8972 (tp) cc_final: 0.8681 (tp) REVERT: C 518 PHE cc_start: 0.7467 (t80) cc_final: 0.6889 (t80) REVERT: C 552 LEU cc_start: 0.9291 (tp) cc_final: 0.8967 (tp) REVERT: C 780 ARG cc_start: 0.6664 (ttt-90) cc_final: 0.5714 (mtp85) outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.2354 time to fit residues: 43.5719 Evaluate side-chains 106 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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-5669/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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-5669/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-5669/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-5669/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-5669/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-5669/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-5669/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-5669/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-5669/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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-5669/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-5669/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-5669/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-5669/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: 68.2733 > 50: distance: 19 - 69: 34.128 distance: 37 - 73: 36.851 distance: 40 - 70: 31.952 distance: 57 - 64: 28.174 distance: 64 - 65: 35.136 distance: 65 - 66: 29.683 distance: 65 - 68: 21.874 distance: 66 - 67: 38.530 distance: 66 - 70: 38.309 distance: 68 - 69: 47.696 distance: 70 - 71: 39.451 distance: 71 - 72: 68.188 distance: 72 - 73: 40.278 distance: 72 - 78: 37.899 distance: 74 - 76: 7.513 distance: 75 - 77: 57.674 distance: 78 - 79: 5.562 distance: 78 - 84: 46.608 distance: 79 - 80: 40.639 distance: 79 - 82: 3.523 distance: 80 - 81: 38.864 distance: 80 - 85: 17.267 distance: 82 - 83: 40.348 distance: 83 - 84: 21.457 distance: 85 - 86: 27.354 distance: 86 - 87: 21.758 distance: 86 - 89: 21.347 distance: 87 - 94: 41.261 distance: 89 - 90: 40.503 distance: 90 - 91: 11.123 distance: 91 - 92: 38.474 distance: 91 - 93: 20.129 distance: 94 - 95: 27.424 distance: 95 - 98: 41.816 distance: 96 - 97: 39.387 distance: 96 - 100: 41.368 distance: 98 - 99: 12.635 distance: 99 - 154: 33.556 distance: 100 - 101: 37.652 distance: 100 - 106: 68.037 distance: 101 - 102: 68.273 distance: 101 - 104: 55.064 distance: 102 - 103: 33.488 distance: 107 - 108: 24.775 distance: 108 - 109: 23.631 distance: 108 - 111: 36.535 distance: 109 - 110: 20.849 distance: 109 - 113: 8.263 distance: 111 - 112: 62.356 distance: 113 - 114: 38.990 distance: 115 - 116: 39.308 distance: 115 - 117: 22.587 distance: 117 - 118: 37.066 distance: 118 - 119: 38.564 distance: 118 - 121: 52.269 distance: 119 - 120: 38.890 distance: 119 - 129: 36.391 distance: 121 - 122: 12.721 distance: 122 - 123: 24.482 distance: 122 - 124: 34.906 distance: 123 - 125: 11.273 distance: 124 - 126: 39.855 distance: 125 - 127: 35.985 distance: 126 - 127: 15.715 distance: 127 - 128: 32.499 distance: 129 - 130: 16.795 distance: 129 - 158: 29.782 distance: 130 - 131: 23.766 distance: 130 - 133: 59.103 distance: 131 - 132: 5.776 distance: 131 - 136: 29.001 distance: 132 - 155: 35.626 distance: 133 - 134: 16.835