Starting phenix.real_space_refine on Tue Feb 13 12:09:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dcp_30638/02_2024/7dcp_30638_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dcp_30638/02_2024/7dcp_30638.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dcp_30638/02_2024/7dcp_30638.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dcp_30638/02_2024/7dcp_30638.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dcp_30638/02_2024/7dcp_30638_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dcp_30638/02_2024/7dcp_30638_updated.pdb" } resolution = 3.15 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= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 168 atoms to isotropic. 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 P 2 5.49 5 Mg 1 5.21 5 S 35 5.16 5 C 3741 2.51 5 N 1001 2.21 5 O 1088 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "x ARG 220": "NH1" <-> "NH2" Residue "x ARG 401": "NH1" <-> "NH2" Residue "x ARG 402": "NH1" <-> "NH2" Residue "x ARG 555": "NH1" <-> "NH2" Residue "x PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 5868 Number of models: 1 Model: "" Number of chains: 3 Chain: "x" Number of atoms: 5355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 670, 5355 Classifications: {'peptide': 670} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 636} Chain breaks: 2 Chain: "y" Number of atoms: 485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 485 Classifications: {'peptide': 62} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 57} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "x" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.63, per 1000 atoms: 0.62 Number of scatterers: 5868 At special positions: 0 Unit cell: (92.75, 90.7625, 83.475, 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) S 35 16.00 P 2 15.00 Mg 1 11.99 O 1088 8.00 N 1001 7.00 C 3741 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 2.05 Conformation dependent library (CDL) restraints added in 1.0 seconds 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1382 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 34 helices and 5 sheets defined 43.0% alpha, 12.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.42 Creating SS restraints... Processing helix chain 'x' and resid 13 through 15 No H-bonds generated for 'chain 'x' and resid 13 through 15' Processing helix chain 'x' and resid 216 through 221 removed outlier: 3.720A pdb=" N ARG x 220 " --> pdb=" O ILE x 216 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LYS x 221 " --> pdb=" O GLN x 217 " (cutoff:3.500A) No H-bonds generated for 'chain 'x' and resid 216 through 221' Processing helix chain 'x' and resid 224 through 227 No H-bonds generated for 'chain 'x' and resid 224 through 227' Processing helix chain 'x' and resid 229 through 238 removed outlier: 3.515A pdb=" N GLN x 234 " --> pdb=" O ASP x 230 " (cutoff:3.500A) Processing helix chain 'x' and resid 252 through 263 removed outlier: 3.573A pdb=" N LEU x 256 " --> pdb=" O LYS x 252 " (cutoff:3.500A) Proline residue: x 257 - end of helix Processing helix chain 'x' and resid 280 through 294 removed outlier: 3.584A pdb=" N VAL x 286 " --> pdb=" O ALA x 282 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA x 287 " --> pdb=" O ALA x 283 " (cutoff:3.500A) Processing helix chain 'x' and resid 324 through 333 removed outlier: 3.759A pdb=" N LEU x 328 " --> pdb=" O ASP x 324 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE x 331 " --> pdb=" O LEU x 327 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LEU x 332 " --> pdb=" O LEU x 328 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N THR x 333 " --> pdb=" O ARG x 329 " (cutoff:3.500A) Processing helix chain 'x' and resid 348 through 350 No H-bonds generated for 'chain 'x' and resid 348 through 350' Processing helix chain 'x' and resid 353 through 368 removed outlier: 3.736A pdb=" N ASP x 364 " --> pdb=" O GLY x 360 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE x 365 " --> pdb=" O LEU x 361 " (cutoff:3.500A) Proline residue: x 367 - end of helix Processing helix chain 'x' and resid 384 through 389 Processing helix chain 'x' and resid 417 through 431 removed outlier: 3.628A pdb=" N THR x 431 " --> pdb=" O GLN x 427 " (cutoff:3.500A) Processing helix chain 'x' and resid 445 through 462 Processing helix chain 'x' and resid 480 through 483 No H-bonds generated for 'chain 'x' and resid 480 through 483' Processing helix chain 'x' and resid 503 through 506 No H-bonds generated for 'chain 'x' and resid 503 through 506' Processing helix chain 'x' and resid 543 through 554 removed outlier: 4.147A pdb=" N ARG x 552 " --> pdb=" O GLN x 548 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N ALA x 553 " --> pdb=" O ARG x 549 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N GLY x 554 " --> pdb=" O ALA x 550 " (cutoff:3.500A) Processing helix chain 'x' and resid 568 through 571 No H-bonds generated for 'chain 'x' and resid 568 through 571' Processing helix chain 'x' and resid 581 through 583 No H-bonds generated for 'chain 'x' and resid 581 through 583' Processing helix chain 'x' and resid 588 through 597 Processing helix chain 'x' and resid 613 through 625 Processing helix chain 'x' and resid 637 through 642 Processing helix chain 'x' and resid 649 through 660 removed outlier: 3.602A pdb=" N ALA x 659 " --> pdb=" O LEU x 655 " (cutoff:3.500A) Processing helix chain 'x' and resid 668 through 679 removed outlier: 3.605A pdb=" N THR x 673 " --> pdb=" O GLU x 669 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N HIS x 679 " --> pdb=" O VAL x 675 " (cutoff:3.500A) Processing helix chain 'x' and resid 681 through 683 No H-bonds generated for 'chain 'x' and resid 681 through 683' Processing helix chain 'x' and resid 689 through 696 removed outlier: 3.573A pdb=" N SER x 695 " --> pdb=" O ASP x 691 " (cutoff:3.500A) Processing helix chain 'x' and resid 703 through 716 removed outlier: 3.536A pdb=" N PHE x 711 " --> pdb=" O TYR x 707 " (cutoff:3.500A) Processing helix chain 'x' and resid 721 through 727 removed outlier: 3.501A pdb=" N GLN x 725 " --> pdb=" O ARG x 721 " (cutoff:3.500A) Processing helix chain 'x' and resid 731 through 751 removed outlier: 3.646A pdb=" N ARG x 736 " --> pdb=" O LYS x 732 " (cutoff:3.500A) Processing helix chain 'x' and resid 753 through 764 removed outlier: 3.501A pdb=" N LYS x 763 " --> pdb=" O GLN x 759 " (cutoff:3.500A) Processing helix chain 'x' and resid 768 through 782 removed outlier: 4.015A pdb=" N ASN x 772 " --> pdb=" O ALA x 768 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ALA x 773 " --> pdb=" O GLY x 769 " (cutoff:3.500A) Processing helix chain 'x' and resid 814 through 821 Processing helix chain 'x' and resid 853 through 858 Processing helix chain 'x' and resid 860 through 866 removed outlier: 5.709A pdb=" N ASP x 865 " --> pdb=" O GLN x 861 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU x 866 " --> pdb=" O ILE x 862 " (cutoff:3.500A) Processing helix chain 'y' and resid 96 through 99 No H-bonds generated for 'chain 'y' and resid 96 through 99' Processing helix chain 'y' and resid 102 through 113 removed outlier: 3.779A pdb=" N GLY y 106 " --> pdb=" O VAL y 102 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ASP y 107 " --> pdb=" O GLU y 103 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY y 112 " --> pdb=" O ALA y 108 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'x' and resid 395 through 398 removed outlier: 8.031A pdb=" N PHE x 396 " --> pdb=" O VAL x 241 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ILE x 243 " --> pdb=" O PHE x 396 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N VAL x 398 " --> pdb=" O ILE x 243 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N MET x 245 " --> pdb=" O VAL x 398 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N LEU x 374 " --> pdb=" O LEU x 242 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N ILE x 244 " --> pdb=" O LEU x 374 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ILE x 376 " --> pdb=" O ILE x 244 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N GLY x 246 " --> pdb=" O ILE x 376 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N SER x 378 " --> pdb=" O GLY x 246 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N GLN x 272 " --> pdb=" O SER x 341 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ILE x 343 " --> pdb=" O GLN x 272 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ALA x 274 " --> pdb=" O ILE x 343 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N ILE x 345 " --> pdb=" O ALA x 274 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N THR x 276 " --> pdb=" O ILE x 345 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'x' and resid 405 through 409 removed outlier: 6.714A pdb=" N GLY x 559 " --> pdb=" O ASP x 406 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N HIS x 408 " --> pdb=" O GLY x 559 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N CYS x 561 " --> pdb=" O HIS x 408 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ASP x 437 " --> pdb=" O ARG x 514 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N VAL x 516 " --> pdb=" O ASP x 437 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N LEU x 439 " --> pdb=" O VAL x 516 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N ASP x 518 " --> pdb=" O LEU x 439 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N PHE x 441 " --> pdb=" O ASP x 518 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N GLN x 468 " --> pdb=" O ARG x 495 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N VAL x 497 " --> pdb=" O GLN x 468 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N ILE x 470 " --> pdb=" O VAL x 497 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N LEU x 499 " --> pdb=" O ILE x 470 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N THR x 472 " --> pdb=" O LEU x 499 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'x' and resid 521 through 528 removed outlier: 3.639A pdb=" N MET x 533 " --> pdb=" O VAL x 528 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'x' and resid 795 through 797 removed outlier: 3.980A pdb=" N TYR x 829 " --> pdb=" O ILE x 849 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'x' and resid 834 through 837 186 hydrogen bonds defined for protein. 549 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: 1.67 Time building geometry restraints manager: 2.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1869 1.34 - 1.46: 828 1.46 - 1.57: 3217 1.57 - 1.69: 4 1.69 - 1.81: 57 Bond restraints: 5975 Sorted by residual: bond pdb=" CA ARG x 584 " pdb=" CB ARG x 584 " ideal model delta sigma weight residual 1.527 1.607 -0.080 2.48e-02 1.63e+03 1.04e+01 bond pdb=" N LEU x 375 " pdb=" CA LEU x 375 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.21e-02 6.83e+03 6.56e+00 bond pdb=" N LEU x 374 " pdb=" CA LEU x 374 " ideal model delta sigma weight residual 1.456 1.487 -0.030 1.21e-02 6.83e+03 6.26e+00 bond pdb=" N LYS x 373 " pdb=" CA LYS x 373 " ideal model delta sigma weight residual 1.456 1.486 -0.030 1.21e-02 6.83e+03 5.99e+00 bond pdb=" CA THR y 93 " pdb=" CB THR y 93 " ideal model delta sigma weight residual 1.532 1.568 -0.035 2.01e-02 2.48e+03 3.11e+00 ... (remaining 5970 not shown) Histogram of bond angle deviations from ideal: 99.12 - 106.52: 209 106.52 - 113.93: 3401 113.93 - 121.33: 3023 121.33 - 128.74: 1407 128.74 - 136.15: 35 Bond angle restraints: 8075 Sorted by residual: angle pdb=" C THR x 838 " pdb=" N SER x 839 " pdb=" CA SER x 839 " ideal model delta sigma weight residual 121.54 130.30 -8.76 1.91e+00 2.74e-01 2.10e+01 angle pdb=" CA ARG x 584 " pdb=" CB ARG x 584 " pdb=" CG ARG x 584 " ideal model delta sigma weight residual 114.10 123.00 -8.90 2.00e+00 2.50e-01 1.98e+01 angle pdb=" C VAL y 92 " pdb=" N THR y 93 " pdb=" CA THR y 93 " ideal model delta sigma weight residual 122.19 132.24 -10.05 2.30e+00 1.89e-01 1.91e+01 angle pdb=" C VAL x 174 " pdb=" N PHE x 175 " pdb=" CA PHE x 175 " ideal model delta sigma weight residual 121.70 129.33 -7.63 1.80e+00 3.09e-01 1.80e+01 angle pdb=" C ASP x 601 " pdb=" N LEU x 602 " pdb=" CA LEU x 602 " ideal model delta sigma weight residual 121.54 128.61 -7.07 1.91e+00 2.74e-01 1.37e+01 ... (remaining 8070 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.63: 3593 28.63 - 57.25: 66 57.25 - 85.88: 8 85.88 - 114.51: 1 114.51 - 143.14: 1 Dihedral angle restraints: 3669 sinusoidal: 1538 harmonic: 2131 Sorted by residual: dihedral pdb=" O1B ADP x1001 " pdb=" O3A ADP x1001 " pdb=" PB ADP x1001 " pdb=" PA ADP x1001 " ideal model delta sinusoidal sigma weight residual 300.00 156.86 143.14 1 2.00e+01 2.50e-03 4.32e+01 dihedral pdb=" O2A ADP x1001 " pdb=" O3A ADP x1001 " pdb=" PA ADP x1001 " pdb=" PB ADP x1001 " ideal model delta sinusoidal sigma weight residual -60.00 33.71 -93.71 1 2.00e+01 2.50e-03 2.56e+01 dihedral pdb=" CA ALA y 161 " pdb=" C ALA y 161 " pdb=" N SER y 162 " pdb=" CA SER y 162 " ideal model delta harmonic sigma weight residual -180.00 -158.60 -21.40 0 5.00e+00 4.00e-02 1.83e+01 ... (remaining 3666 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 582 0.038 - 0.076: 220 0.076 - 0.115: 80 0.115 - 0.153: 44 0.153 - 0.191: 5 Chirality restraints: 931 Sorted by residual: chirality pdb=" CB ILE x 635 " pdb=" CA ILE x 635 " pdb=" CG1 ILE x 635 " pdb=" CG2 ILE x 635 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.13e-01 chirality pdb=" CB THR x 538 " pdb=" CA THR x 538 " pdb=" OG1 THR x 538 " pdb=" CG2 THR x 538 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 8.77e-01 chirality pdb=" CA ILE x 767 " pdb=" N ILE x 767 " pdb=" C ILE x 767 " pdb=" CB ILE x 767 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.97e-01 ... (remaining 928 not shown) Planarity restraints: 1018 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET x 577 " 0.040 5.00e-02 4.00e+02 6.00e-02 5.75e+00 pdb=" N PRO x 578 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO x 578 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO x 578 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP x 518 " 0.036 5.00e-02 4.00e+02 5.43e-02 4.72e+00 pdb=" N PRO x 519 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO x 519 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO x 519 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS x 810 " -0.035 5.00e-02 4.00e+02 5.24e-02 4.40e+00 pdb=" N PRO x 811 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO x 811 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO x 811 " -0.029 5.00e-02 4.00e+02 ... (remaining 1015 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 76 2.65 - 3.21: 5049 3.21 - 3.78: 8812 3.78 - 4.34: 12658 4.34 - 4.90: 20354 Nonbonded interactions: 46949 Sorted by model distance: nonbonded pdb=" O3B ADP x1001 " pdb="MG MG x1002 " model vdw 2.092 2.170 nonbonded pdb=" OG1 THR x 253 " pdb="MG MG x1002 " model vdw 2.094 2.170 nonbonded pdb=" O GLN x 427 " pdb=" OG1 THR x 431 " model vdw 2.262 2.440 nonbonded pdb=" O GLU x 581 " pdb=" OG1 THR x 585 " model vdw 2.273 2.440 nonbonded pdb=" O SER x 530 " pdb=" OG SER x 801 " model vdw 2.284 2.440 ... (remaining 46944 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: 1.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 6.090 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 19.690 Find NCS groups from input model: 0.340 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:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 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 : 0.005 0.080 5975 Z= 0.302 Angle : 0.917 10.046 8075 Z= 0.478 Chirality : 0.052 0.191 931 Planarity : 0.007 0.060 1018 Dihedral : 11.275 143.137 2287 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.61 % Allowed : 3.51 % Favored : 95.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.88 (0.25), residues: 718 helix: -3.17 (0.15), residues: 294 sheet: 0.94 (0.49), residues: 106 loop : -1.50 (0.31), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP x 723 HIS 0.006 0.002 HIS x 704 PHE 0.023 0.002 PHE x 308 TYR 0.029 0.003 TYR x 321 ARG 0.004 0.001 ARG x 289 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 168 time to evaluate : 0.813 Fit side-chains REVERT: x 280 ARG cc_start: 0.7505 (ttp-110) cc_final: 0.7126 (ttm110) REVERT: x 335 SER cc_start: 0.8158 (m) cc_final: 0.7907 (p) REVERT: x 341 SER cc_start: 0.8794 (t) cc_final: 0.8257 (p) REVERT: x 534 THR cc_start: 0.8690 (t) cc_final: 0.8428 (m) REVERT: x 560 LYS cc_start: 0.8202 (mttt) cc_final: 0.7979 (mtpp) REVERT: x 575 GLU cc_start: 0.7257 (mm-30) cc_final: 0.7048 (mp0) REVERT: x 632 LYS cc_start: 0.8573 (mptm) cc_final: 0.8299 (mmtt) REVERT: x 770 TYR cc_start: 0.6622 (m-10) cc_final: 0.6395 (m-80) outliers start: 4 outliers final: 1 residues processed: 171 average time/residue: 0.2650 time to fit residues: 55.1304 Evaluate side-chains 95 residues out of total 657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 94 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 374 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 61 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 18 optimal weight: 6.9990 chunk 37 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: x 255 GLN x 258 GLN x 382 ASN x 397 ASN x 408 HIS x 427 GLN x 429 HIS x 548 GLN x 663 GLN x 834 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 5975 Z= 0.332 Angle : 0.664 7.340 8075 Z= 0.332 Chirality : 0.046 0.186 931 Planarity : 0.006 0.047 1018 Dihedral : 7.458 106.643 801 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.90 % Allowed : 8.69 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: -0.88 (0.28), residues: 718 helix: -0.72 (0.26), residues: 298 sheet: 0.40 (0.46), residues: 107 loop : -0.62 (0.34), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP x 723 HIS 0.007 0.002 HIS x 704 PHE 0.024 0.002 PHE x 426 TYR 0.014 0.002 TYR x 171 ARG 0.004 0.001 ARG x 514 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 86 time to evaluate : 0.725 Fit side-chains REVERT: x 335 SER cc_start: 0.8211 (m) cc_final: 0.7932 (p) REVERT: x 560 LYS cc_start: 0.8097 (mttt) cc_final: 0.7853 (mtmt) REVERT: x 632 LYS cc_start: 0.8656 (mptm) cc_final: 0.8387 (mmtm) REVERT: x 759 GLN cc_start: 0.7493 (mt0) cc_final: 0.7276 (pt0) outliers start: 19 outliers final: 13 residues processed: 99 average time/residue: 0.2418 time to fit residues: 31.2610 Evaluate side-chains 94 residues out of total 657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 81 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 239 ASN Chi-restraints excluded: chain x residue 250 SER Chi-restraints excluded: chain x residue 254 THR Chi-restraints excluded: chain x residue 297 VAL Chi-restraints excluded: chain x residue 323 THR Chi-restraints excluded: chain x residue 333 THR Chi-restraints excluded: chain x residue 374 LEU Chi-restraints excluded: chain x residue 502 ASN Chi-restraints excluded: chain x residue 509 THR Chi-restraints excluded: chain x residue 585 THR Chi-restraints excluded: chain x residue 722 SER Chi-restraints excluded: chain x residue 859 VAL Chi-restraints excluded: chain x residue 865 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 36 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 71 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 chunk 65 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** x 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 622 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5975 Z= 0.209 Angle : 0.568 7.085 8075 Z= 0.281 Chirality : 0.043 0.198 931 Planarity : 0.004 0.031 1018 Dihedral : 6.497 88.433 801 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.51 % Allowed : 9.76 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.26 (0.30), residues: 718 helix: 0.63 (0.29), residues: 299 sheet: 0.81 (0.44), residues: 124 loop : -0.48 (0.35), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP x 568 HIS 0.004 0.001 HIS x 704 PHE 0.015 0.001 PHE x 426 TYR 0.012 0.001 TYR x 171 ARG 0.003 0.000 ARG x 514 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 83 time to evaluate : 0.625 Fit side-chains REVERT: x 335 SER cc_start: 0.8121 (m) cc_final: 0.7886 (p) REVERT: x 374 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8810 (tp) REVERT: x 575 GLU cc_start: 0.7334 (mm-30) cc_final: 0.7043 (mp0) outliers start: 23 outliers final: 16 residues processed: 100 average time/residue: 0.1970 time to fit residues: 25.5846 Evaluate side-chains 95 residues out of total 657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 78 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 250 SER Chi-restraints excluded: chain x residue 254 THR Chi-restraints excluded: chain x residue 297 VAL Chi-restraints excluded: chain x residue 323 THR Chi-restraints excluded: chain x residue 333 THR Chi-restraints excluded: chain x residue 374 LEU Chi-restraints excluded: chain x residue 502 ASN Chi-restraints excluded: chain x residue 506 THR Chi-restraints excluded: chain x residue 509 THR Chi-restraints excluded: chain x residue 534 THR Chi-restraints excluded: chain x residue 537 LEU Chi-restraints excluded: chain x residue 538 THR Chi-restraints excluded: chain x residue 585 THR Chi-restraints excluded: chain x residue 603 ILE Chi-restraints excluded: chain x residue 686 ILE Chi-restraints excluded: chain x residue 722 SER Chi-restraints excluded: chain x residue 865 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 65 optimal weight: 0.9990 chunk 49 optimal weight: 7.9990 chunk 34 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 44 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 63 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: x 445 GLN x 477 ASN ** x 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5975 Z= 0.180 Angle : 0.546 7.110 8075 Z= 0.268 Chirality : 0.042 0.193 931 Planarity : 0.004 0.031 1018 Dihedral : 6.062 79.307 801 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.90 % Allowed : 11.89 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.65 (0.31), residues: 718 helix: 1.19 (0.30), residues: 299 sheet: 0.67 (0.47), residues: 110 loop : -0.33 (0.35), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP x 568 HIS 0.003 0.001 HIS x 704 PHE 0.013 0.001 PHE x 426 TYR 0.011 0.001 TYR x 171 ARG 0.003 0.000 ARG x 514 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 81 time to evaluate : 0.700 Fit side-chains REVERT: x 335 SER cc_start: 0.8098 (m) cc_final: 0.7864 (p) REVERT: x 575 GLU cc_start: 0.7304 (mm-30) cc_final: 0.6994 (mp0) outliers start: 19 outliers final: 17 residues processed: 92 average time/residue: 0.1958 time to fit residues: 23.4319 Evaluate side-chains 96 residues out of total 657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 79 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 250 SER Chi-restraints excluded: chain x residue 254 THR Chi-restraints excluded: chain x residue 297 VAL Chi-restraints excluded: chain x residue 323 THR Chi-restraints excluded: chain x residue 333 THR Chi-restraints excluded: chain x residue 364 ASP Chi-restraints excluded: chain x residue 502 ASN Chi-restraints excluded: chain x residue 506 THR Chi-restraints excluded: chain x residue 509 THR Chi-restraints excluded: chain x residue 534 THR Chi-restraints excluded: chain x residue 537 LEU Chi-restraints excluded: chain x residue 538 THR Chi-restraints excluded: chain x residue 585 THR Chi-restraints excluded: chain x residue 603 ILE Chi-restraints excluded: chain x residue 722 SER Chi-restraints excluded: chain x residue 751 VAL Chi-restraints excluded: chain x residue 865 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 40 optimal weight: 5.9990 chunk 1 optimal weight: 9.9990 chunk 52 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 chunk 60 optimal weight: 0.5980 chunk 48 optimal weight: 0.9990 chunk 0 optimal weight: 9.9990 chunk 36 optimal weight: 0.3980 chunk 63 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: x 445 GLN x 477 ASN ** x 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.3182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 5975 Z= 0.156 Angle : 0.526 7.070 8075 Z= 0.256 Chirality : 0.042 0.179 931 Planarity : 0.004 0.032 1018 Dihedral : 5.620 66.557 799 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.35 % Allowed : 11.89 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.94 (0.31), residues: 718 helix: 1.55 (0.30), residues: 299 sheet: 0.60 (0.48), residues: 112 loop : -0.22 (0.35), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP x 568 HIS 0.002 0.001 HIS x 704 PHE 0.012 0.001 PHE x 426 TYR 0.010 0.001 TYR x 171 ARG 0.003 0.000 ARG x 514 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 81 time to evaluate : 0.625 Fit side-chains REVERT: x 335 SER cc_start: 0.8094 (m) cc_final: 0.7893 (p) REVERT: x 575 GLU cc_start: 0.7343 (mm-30) cc_final: 0.7029 (mp0) outliers start: 22 outliers final: 18 residues processed: 95 average time/residue: 0.1876 time to fit residues: 23.5343 Evaluate side-chains 92 residues out of total 657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 74 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 247 GLU Chi-restraints excluded: chain x residue 250 SER Chi-restraints excluded: chain x residue 254 THR Chi-restraints excluded: chain x residue 297 VAL Chi-restraints excluded: chain x residue 323 THR Chi-restraints excluded: chain x residue 333 THR Chi-restraints excluded: chain x residue 364 ASP Chi-restraints excluded: chain x residue 502 ASN Chi-restraints excluded: chain x residue 506 THR Chi-restraints excluded: chain x residue 509 THR Chi-restraints excluded: chain x residue 534 THR Chi-restraints excluded: chain x residue 537 LEU Chi-restraints excluded: chain x residue 538 THR Chi-restraints excluded: chain x residue 585 THR Chi-restraints excluded: chain x residue 603 ILE Chi-restraints excluded: chain x residue 722 SER Chi-restraints excluded: chain x residue 751 VAL Chi-restraints excluded: chain x residue 865 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 63 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 chunk 23 optimal weight: 8.9990 chunk 37 optimal weight: 0.6980 chunk 68 optimal weight: 9.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: x 445 GLN x 477 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.3368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5975 Z= 0.280 Angle : 0.599 7.567 8075 Z= 0.293 Chirality : 0.045 0.191 931 Planarity : 0.004 0.031 1018 Dihedral : 5.953 66.655 799 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 3.51 % Allowed : 12.04 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 0.93 (0.31), residues: 718 helix: 1.47 (0.30), residues: 299 sheet: 0.60 (0.46), residues: 124 loop : -0.17 (0.36), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP x 568 HIS 0.005 0.001 HIS x 704 PHE 0.022 0.002 PHE x 426 TYR 0.013 0.002 TYR x 171 ARG 0.003 0.000 ARG x 543 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 72 time to evaluate : 0.605 Fit side-chains REVERT: x 335 SER cc_start: 0.8111 (m) cc_final: 0.7887 (p) outliers start: 23 outliers final: 20 residues processed: 89 average time/residue: 0.1991 time to fit residues: 23.1512 Evaluate side-chains 88 residues out of total 657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 68 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 247 GLU Chi-restraints excluded: chain x residue 250 SER Chi-restraints excluded: chain x residue 254 THR Chi-restraints excluded: chain x residue 276 THR Chi-restraints excluded: chain x residue 297 VAL Chi-restraints excluded: chain x residue 323 THR Chi-restraints excluded: chain x residue 333 THR Chi-restraints excluded: chain x residue 364 ASP Chi-restraints excluded: chain x residue 502 ASN Chi-restraints excluded: chain x residue 506 THR Chi-restraints excluded: chain x residue 509 THR Chi-restraints excluded: chain x residue 534 THR Chi-restraints excluded: chain x residue 537 LEU Chi-restraints excluded: chain x residue 538 THR Chi-restraints excluded: chain x residue 585 THR Chi-restraints excluded: chain x residue 603 ILE Chi-restraints excluded: chain x residue 686 ILE Chi-restraints excluded: chain x residue 722 SER Chi-restraints excluded: chain x residue 751 VAL Chi-restraints excluded: chain x residue 865 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 7 optimal weight: 1.9990 chunk 40 optimal weight: 0.0670 chunk 51 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 43 optimal weight: 0.4980 chunk 28 optimal weight: 3.9990 overall best weight: 0.7124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: x 477 ASN ** x 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.3414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 5975 Z= 0.157 Angle : 0.535 7.340 8075 Z= 0.259 Chirality : 0.042 0.183 931 Planarity : 0.003 0.029 1018 Dihedral : 5.521 56.268 799 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.74 % Allowed : 13.11 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.32), residues: 718 helix: 1.68 (0.31), residues: 299 sheet: 0.60 (0.46), residues: 123 loop : -0.17 (0.36), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP x 568 HIS 0.002 0.001 HIS x 704 PHE 0.013 0.001 PHE x 426 TYR 0.009 0.001 TYR x 417 ARG 0.002 0.000 ARG x 514 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 74 time to evaluate : 0.634 Fit side-chains REVERT: x 335 SER cc_start: 0.8078 (m) cc_final: 0.7860 (p) REVERT: x 575 GLU cc_start: 0.7329 (mm-30) cc_final: 0.6975 (mp0) outliers start: 18 outliers final: 17 residues processed: 85 average time/residue: 0.1918 time to fit residues: 21.2882 Evaluate side-chains 88 residues out of total 657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 71 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 247 GLU Chi-restraints excluded: chain x residue 250 SER Chi-restraints excluded: chain x residue 254 THR Chi-restraints excluded: chain x residue 297 VAL Chi-restraints excluded: chain x residue 333 THR Chi-restraints excluded: chain x residue 364 ASP Chi-restraints excluded: chain x residue 502 ASN Chi-restraints excluded: chain x residue 506 THR Chi-restraints excluded: chain x residue 508 LEU Chi-restraints excluded: chain x residue 509 THR Chi-restraints excluded: chain x residue 537 LEU Chi-restraints excluded: chain x residue 538 THR Chi-restraints excluded: chain x residue 585 THR Chi-restraints excluded: chain x residue 686 ILE Chi-restraints excluded: chain x residue 722 SER Chi-restraints excluded: chain x residue 751 VAL Chi-restraints excluded: chain x residue 865 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 42 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 55 optimal weight: 0.9980 chunk 64 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 chunk 61 optimal weight: 0.3980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** x 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.3495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5975 Z= 0.172 Angle : 0.537 7.327 8075 Z= 0.261 Chirality : 0.042 0.187 931 Planarity : 0.004 0.032 1018 Dihedral : 5.357 56.093 799 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 3.05 % Allowed : 13.41 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 1.13 (0.32), residues: 718 helix: 1.74 (0.31), residues: 299 sheet: 0.47 (0.46), residues: 123 loop : -0.07 (0.37), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP x 568 HIS 0.003 0.001 HIS x 704 PHE 0.013 0.001 PHE x 426 TYR 0.009 0.001 TYR x 171 ARG 0.002 0.000 ARG x 800 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 73 time to evaluate : 0.685 Fit side-chains REVERT: x 335 SER cc_start: 0.8077 (m) cc_final: 0.7864 (p) REVERT: x 575 GLU cc_start: 0.7319 (mm-30) cc_final: 0.6957 (mp0) outliers start: 20 outliers final: 19 residues processed: 85 average time/residue: 0.1977 time to fit residues: 22.0537 Evaluate side-chains 91 residues out of total 657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 72 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 247 GLU Chi-restraints excluded: chain x residue 250 SER Chi-restraints excluded: chain x residue 254 THR Chi-restraints excluded: chain x residue 297 VAL Chi-restraints excluded: chain x residue 323 THR Chi-restraints excluded: chain x residue 333 THR Chi-restraints excluded: chain x residue 364 ASP Chi-restraints excluded: chain x residue 502 ASN Chi-restraints excluded: chain x residue 506 THR Chi-restraints excluded: chain x residue 508 LEU Chi-restraints excluded: chain x residue 509 THR Chi-restraints excluded: chain x residue 537 LEU Chi-restraints excluded: chain x residue 538 THR Chi-restraints excluded: chain x residue 585 THR Chi-restraints excluded: chain x residue 603 ILE Chi-restraints excluded: chain x residue 686 ILE Chi-restraints excluded: chain x residue 722 SER Chi-restraints excluded: chain x residue 751 VAL Chi-restraints excluded: chain x residue 865 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 65 optimal weight: 0.9980 chunk 67 optimal weight: 0.0000 chunk 39 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 20 optimal weight: 0.0870 chunk 59 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 69 optimal weight: 5.9990 chunk 42 optimal weight: 0.6980 overall best weight: 0.4762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** x 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.3572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 5975 Z= 0.132 Angle : 0.509 6.189 8075 Z= 0.247 Chirality : 0.041 0.180 931 Planarity : 0.004 0.040 1018 Dihedral : 4.978 54.941 799 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.29 % Allowed : 13.87 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 1.25 (0.32), residues: 718 helix: 1.88 (0.31), residues: 299 sheet: 0.52 (0.46), residues: 123 loop : -0.05 (0.37), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP x 568 HIS 0.002 0.001 HIS x 704 PHE 0.009 0.001 PHE x 426 TYR 0.008 0.001 TYR x 304 ARG 0.002 0.000 ARG x 514 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 72 time to evaluate : 0.706 Fit side-chains outliers start: 15 outliers final: 13 residues processed: 80 average time/residue: 0.2062 time to fit residues: 21.5114 Evaluate side-chains 82 residues out of total 657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 69 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 276 THR Chi-restraints excluded: chain x residue 297 VAL Chi-restraints excluded: chain x residue 323 THR Chi-restraints excluded: chain x residue 333 THR Chi-restraints excluded: chain x residue 364 ASP Chi-restraints excluded: chain x residue 502 ASN Chi-restraints excluded: chain x residue 506 THR Chi-restraints excluded: chain x residue 509 THR Chi-restraints excluded: chain x residue 537 LEU Chi-restraints excluded: chain x residue 538 THR Chi-restraints excluded: chain x residue 585 THR Chi-restraints excluded: chain x residue 746 ARG Chi-restraints excluded: chain x residue 865 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 32 optimal weight: 0.7980 chunk 48 optimal weight: 4.9990 chunk 72 optimal weight: 10.0000 chunk 66 optimal weight: 0.5980 chunk 57 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** x 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.3593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5975 Z= 0.166 Angle : 0.518 6.495 8075 Z= 0.253 Chirality : 0.042 0.183 931 Planarity : 0.004 0.039 1018 Dihedral : 4.950 52.140 799 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.59 % Allowed : 13.72 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 1.27 (0.32), residues: 718 helix: 1.88 (0.31), residues: 300 sheet: 0.51 (0.46), residues: 123 loop : -0.01 (0.37), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP x 568 HIS 0.003 0.001 HIS x 704 PHE 0.013 0.001 PHE x 426 TYR 0.009 0.001 TYR x 171 ARG 0.001 0.000 ARG x 514 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1436 Ramachandran restraints generated. 718 Oldfield, 0 Emsley, 718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 73 time to evaluate : 0.678 Fit side-chains REVERT: x 575 GLU cc_start: 0.7500 (mm-30) cc_final: 0.7074 (mp0) outliers start: 17 outliers final: 16 residues processed: 82 average time/residue: 0.1683 time to fit residues: 18.4159 Evaluate side-chains 87 residues out of total 657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 71 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 247 GLU Chi-restraints excluded: chain x residue 250 SER Chi-restraints excluded: chain x residue 276 THR Chi-restraints excluded: chain x residue 297 VAL Chi-restraints excluded: chain x residue 323 THR Chi-restraints excluded: chain x residue 333 THR Chi-restraints excluded: chain x residue 364 ASP Chi-restraints excluded: chain x residue 502 ASN Chi-restraints excluded: chain x residue 506 THR Chi-restraints excluded: chain x residue 509 THR Chi-restraints excluded: chain x residue 537 LEU Chi-restraints excluded: chain x residue 538 THR Chi-restraints excluded: chain x residue 585 THR Chi-restraints excluded: chain x residue 686 ILE Chi-restraints excluded: chain x residue 746 ARG Chi-restraints excluded: chain x residue 865 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 53 optimal weight: 2.9990 chunk 8 optimal weight: 0.3980 chunk 16 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 50 optimal weight: 7.9990 chunk 3 optimal weight: 0.7980 chunk 41 optimal weight: 0.4980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** x 502 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 = 0.3447 r_free = 0.3447 target = 0.133112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.106175 restraints weight = 6532.419| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 1.67 r_work: 0.2912 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.3654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 5975 Z= 0.156 Angle : 0.511 6.427 8075 Z= 0.250 Chirality : 0.042 0.179 931 Planarity : 0.004 0.041 1018 Dihedral : 4.808 47.753 799 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.44 % Allowed : 14.02 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 1.32 (0.32), residues: 718 helix: 1.94 (0.31), residues: 299 sheet: 0.49 (0.46), residues: 123 loop : 0.02 (0.37), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP x 568 HIS 0.002 0.001 HIS x 704 PHE 0.011 0.001 PHE x 426 TYR 0.009 0.001 TYR x 171 ARG 0.001 0.000 ARG x 514 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1743.19 seconds wall clock time: 32 minutes 21.25 seconds (1941.25 seconds total)