Starting phenix.real_space_refine (version: 1.21rc1) on Tue Oct 3 06:12:41 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dcp_30638/10_2023/7dcp_30638_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dcp_30638/10_2023/7dcp_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_30638/10_2023/7dcp_30638.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dcp_30638/10_2023/7dcp_30638.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dcp_30638/10_2023/7dcp_30638_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dcp_30638/10_2023/7dcp_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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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: 3.57, per 1000 atoms: 0.61 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: 1.96 Conformation dependent library (CDL) restraints added in 954.6 milliseconds 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: 1.06 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: 1.56 Time building geometry restraints manager: 2.18 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: 1.120 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: 0.010 Extract box with map and model: 5.880 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 18.940 Find NCS groups from input model: 0.150 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.190 ------------------------------------------------------------------------------- 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 *********************** 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 : 0.708 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 171 average time/residue: 0.2582 time to fit residues: 53.5359 Evaluate side-chains 89 residues out of total 657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 88 time to evaluate : 0.698 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0590 time to fit residues: 1.0887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 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: 1.7586 ------------------------------------------------------------------------------- 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 796 GLN x 834 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.2553 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= 0.305 Angle : 0.652 7.182 8075 Z= 0.327 Chirality : 0.046 0.181 931 Planarity : 0.006 0.044 1018 Dihedral : 7.124 108.464 799 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.74 % Allowed : 8.54 % Favored : 88.72 % 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: -0.85 (0.28), residues: 718 helix: -0.68 (0.26), residues: 294 sheet: 0.62 (0.46), residues: 105 loop : -0.71 (0.33), residues: 319 *********************** 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 101 residues out of total 657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 83 time to evaluate : 0.692 Fit side-chains outliers start: 18 outliers final: 12 residues processed: 96 average time/residue: 0.2190 time to fit residues: 26.7348 Evaluate side-chains 89 residues out of total 657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 77 time to evaluate : 0.696 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0562 time to fit residues: 2.2136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 55 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** x 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.8115 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5975 Z= 0.212 Angle : 0.572 7.075 8075 Z= 0.282 Chirality : 0.043 0.185 931 Planarity : 0.004 0.033 1018 Dihedral : 6.363 88.967 799 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.68 % Allowed : 10.67 % Favored : 87.65 % 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: 0.20 (0.30), residues: 718 helix: 0.61 (0.29), residues: 299 sheet: 0.71 (0.46), residues: 110 loop : -0.45 (0.35), residues: 309 *********************** 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 94 residues out of total 657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 83 time to evaluate : 0.639 Fit side-chains outliers start: 11 outliers final: 7 residues processed: 90 average time/residue: 0.2054 time to fit residues: 23.7454 Evaluate side-chains 81 residues out of total 657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 74 time to evaluate : 0.679 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0557 time to fit residues: 1.6159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 65 optimal weight: 0.0770 chunk 49 optimal weight: 7.9990 chunk 34 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 chunk 44 optimal weight: 0.4980 chunk 66 optimal weight: 3.9990 chunk 70 optimal weight: 9.9990 chunk 63 optimal weight: 0.8980 chunk 19 optimal weight: 0.0370 chunk 58 optimal weight: 1.9990 overall best weight: 0.7018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** x 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 445 GLN x 477 ASN ** x 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 727 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.3104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 5975 Z= 0.153 Angle : 0.540 7.725 8075 Z= 0.262 Chirality : 0.042 0.172 931 Planarity : 0.004 0.032 1018 Dihedral : 5.964 80.743 799 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.68 % Allowed : 11.59 % 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: 0.72 (0.31), residues: 718 helix: 1.24 (0.30), residues: 299 sheet: 0.82 (0.47), residues: 110 loop : -0.33 (0.35), residues: 309 *********************** 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 91 residues out of total 657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 80 time to evaluate : 0.675 Fit side-chains outliers start: 11 outliers final: 7 residues processed: 88 average time/residue: 0.2125 time to fit residues: 24.1828 Evaluate side-chains 79 residues out of total 657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 72 time to evaluate : 0.718 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1010 time to fit residues: 2.0178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 40 optimal weight: 4.9990 chunk 1 optimal weight: 9.9990 chunk 52 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 60 optimal weight: 0.1980 chunk 48 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 36 optimal weight: 5.9990 chunk 63 optimal weight: 0.6980 chunk 17 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** x 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.8156 moved from start: 0.3301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5975 Z= 0.262 Angle : 0.601 7.389 8075 Z= 0.294 Chirality : 0.045 0.197 931 Planarity : 0.004 0.031 1018 Dihedral : 6.096 74.962 799 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.22 % Allowed : 13.26 % Favored : 85.52 % 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: 0.81 (0.31), residues: 718 helix: 1.27 (0.30), residues: 299 sheet: 0.77 (0.46), residues: 124 loop : -0.23 (0.36), residues: 295 *********************** 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 80 residues out of total 657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 72 time to evaluate : 0.731 Fit side-chains outliers start: 8 outliers final: 7 residues processed: 76 average time/residue: 0.2211 time to fit residues: 21.5876 Evaluate side-chains 74 residues out of total 657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 67 time to evaluate : 0.698 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0654 time to fit residues: 1.7514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 63 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 70 optimal weight: 8.9990 chunk 58 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 5 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 68 optimal weight: 8.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** x 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.8148 moved from start: 0.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5975 Z= 0.233 Angle : 0.580 8.534 8075 Z= 0.281 Chirality : 0.044 0.196 931 Planarity : 0.004 0.030 1018 Dihedral : 5.961 70.783 799 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.07 % Allowed : 13.72 % 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: 0.87 (0.31), residues: 718 helix: 1.36 (0.30), residues: 299 sheet: 0.68 (0.46), residues: 124 loop : -0.19 (0.36), residues: 295 *********************** 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 80 residues out of total 657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 73 time to evaluate : 0.715 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 77 average time/residue: 0.2194 time to fit residues: 21.8314 Evaluate side-chains 75 residues out of total 657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 70 time to evaluate : 0.731 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0585 time to fit residues: 1.5546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 7 optimal weight: 2.9990 chunk 40 optimal weight: 0.0270 chunk 51 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 59 optimal weight: 0.4980 chunk 70 optimal weight: 0.6980 chunk 44 optimal weight: 4.9990 chunk 42 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 43 optimal weight: 0.1980 chunk 28 optimal weight: 0.0020 overall best weight: 0.2846 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.3489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 5975 Z= 0.120 Angle : 0.522 7.544 8075 Z= 0.250 Chirality : 0.041 0.162 931 Planarity : 0.004 0.036 1018 Dihedral : 5.291 52.891 799 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.91 % Allowed : 14.02 % Favored : 85.06 % 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: 1.14 (0.32), residues: 718 helix: 1.71 (0.31), residues: 299 sheet: 0.70 (0.47), residues: 123 loop : -0.13 (0.36), residues: 296 *********************** 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 87 residues out of total 657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 81 time to evaluate : 0.691 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 84 average time/residue: 0.2369 time to fit residues: 25.1915 Evaluate side-chains 75 residues out of total 657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 72 time to evaluate : 0.710 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2243 time to fit residues: 1.8095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0010 chunk 44 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 55 optimal weight: 0.0470 chunk 64 optimal weight: 0.0770 chunk 67 optimal weight: 10.0000 chunk 61 optimal weight: 0.7980 overall best weight: 0.3642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: x 368 GLN ** 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: 0.8074 moved from start: 0.3577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 5975 Z= 0.128 Angle : 0.520 7.967 8075 Z= 0.250 Chirality : 0.041 0.172 931 Planarity : 0.003 0.038 1018 Dihedral : 4.943 53.457 799 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.15 % Allowed : 15.70 % 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: 1.32 (0.32), residues: 718 helix: 1.85 (0.31), residues: 299 sheet: 0.77 (0.47), residues: 123 loop : -0.02 (0.37), residues: 296 *********************** 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 79 residues out of total 657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 78 time to evaluate : 0.721 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 78 average time/residue: 0.2354 time to fit residues: 23.2730 Evaluate side-chains 71 residues out of total 657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 70 time to evaluate : 0.676 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0593 time to fit residues: 1.0509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 65 optimal weight: 2.9990 chunk 67 optimal weight: 0.2980 chunk 39 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 59 optimal weight: 0.7980 chunk 62 optimal weight: 0.4980 chunk 43 optimal weight: 1.9990 chunk 69 optimal weight: 7.9990 chunk 42 optimal weight: 0.7980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.3588 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= 0.156 Angle : 0.518 7.461 8075 Z= 0.251 Chirality : 0.042 0.182 931 Planarity : 0.004 0.038 1018 Dihedral : 4.876 52.440 799 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.22 % Allowed : 15.09 % 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: 1.32 (0.32), residues: 718 helix: 1.84 (0.31), residues: 299 sheet: 0.71 (0.47), residues: 123 loop : 0.04 (0.37), residues: 296 *********************** 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 84 residues out of total 657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 76 time to evaluate : 0.701 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 79 average time/residue: 0.2275 time to fit residues: 23.1548 Evaluate side-chains 81 residues out of total 657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 75 time to evaluate : 0.717 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0621 time to fit residues: 1.6690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 32 optimal weight: 0.6980 chunk 48 optimal weight: 0.5980 chunk 72 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 44 optimal weight: 0.0570 chunk 35 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 overall best weight: 0.6298 ------------------------------------------------------------------------------- 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: 0.8089 moved from start: 0.3666 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= 0.146 Angle : 0.520 8.371 8075 Z= 0.251 Chirality : 0.042 0.178 931 Planarity : 0.004 0.038 1018 Dihedral : 4.766 48.275 799 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 0.76 % Allowed : 14.63 % Favored : 84.60 % 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: 1.37 (0.32), residues: 718 helix: 1.89 (0.31), residues: 299 sheet: 0.69 (0.47), residues: 123 loop : 0.07 (0.37), residues: 296 ********************** 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 81 residues out of total 657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 76 time to evaluate : 0.699 Fit side-chains outliers start: 5 outliers final: 5 residues processed: 77 average time/residue: 0.2251 time to fit residues: 22.2228 Evaluate side-chains 78 residues out of total 657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 73 time to evaluate : 0.713 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0640 time to fit residues: 1.5455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.2980 chunk 16 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 50 optimal weight: 7.9990 chunk 3 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** x 239 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 = 0.3387 r_free = 0.3387 target = 0.128343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.101464 restraints weight = 6634.869| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 1.66 r_work: 0.2885 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.3677 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= 0.275 Angle : 0.593 8.204 8075 Z= 0.292 Chirality : 0.045 0.196 931 Planarity : 0.004 0.036 1018 Dihedral : 5.214 53.949 799 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 0.46 % Allowed : 14.63 % Favored : 84.91 % 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: 1.12 (0.32), residues: 718 helix: 1.65 (0.30), residues: 299 sheet: 0.46 (0.47), residues: 123 loop : 0.02 (0.36), residues: 296 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1691.81 seconds wall clock time: 31 minutes 5.81 seconds (1865.81 seconds total)