Starting phenix.real_space_refine on Wed Feb 14 02:49:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hbf_34627/02_2024/8hbf_34627_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hbf_34627/02_2024/8hbf_34627.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hbf_34627/02_2024/8hbf_34627.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hbf_34627/02_2024/8hbf_34627.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hbf_34627/02_2024/8hbf_34627_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hbf_34627/02_2024/8hbf_34627_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.145 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Fe 1 7.16 5 P 3 5.49 5 Mg 2 5.21 5 S 58 5.16 5 C 5438 2.51 5 N 1434 2.21 5 O 1511 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 134": "OE1" <-> "OE2" Residue "A PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 295": "OD1" <-> "OD2" Residue "A GLU 325": "OE1" <-> "OE2" Residue "A TYR 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 486": "OD1" <-> "OD2" Residue "A PHE 634": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 96": "OE1" <-> "OE2" Residue "B ASP 124": "OD1" <-> "OD2" Residue "B TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 331": "OD1" <-> "OD2" Residue "B TYR 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8448 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 3894 Classifications: {'peptide': 522} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PTRANS': 23, 'TRANS': 498} Chain breaks: 9 Unresolved non-hydrogen bonds: 238 Unresolved non-hydrogen angles: 286 Unresolved non-hydrogen dihedrals: 196 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 9, 'PHE:plan': 2, 'GLU:plan': 15, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 158 Chain: "B" Number of atoms: 4444 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 573, 4442 Classifications: {'peptide': 573} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 549} Chain breaks: 2 Unresolved non-hydrogen bonds: 132 Unresolved non-hydrogen angles: 158 Unresolved non-hydrogen dihedrals: 106 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 18, 'ASN:plan1': 1, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 101 Conformer: "B" Number of residues, atoms: 573, 4442 Classifications: {'peptide': 573} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 549} Chain breaks: 2 Unresolved non-hydrogen bonds: 132 Unresolved non-hydrogen angles: 158 Unresolved non-hydrogen dihedrals: 106 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 18, 'ASN:plan1': 1, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 101 bond proxies already assigned to first conformer: 4530 Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 34 Unusual residues: {' MG': 2, 'G2P': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 76 Unusual residues: {' NO': 1, 'GZO': 1, 'HEM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 6.69, per 1000 atoms: 0.79 Number of scatterers: 8448 At special positions: 0 Unit cell: (65.835, 107.635, 150.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Fe 1 26.01 S 58 16.00 P 3 15.00 Mg 2 11.99 F 1 9.00 O 1511 8.00 N 1434 7.00 C 5438 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.37 Conformation dependent library (CDL) restraints added in 2.3 seconds 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2060 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 41 helices and 9 sheets defined 44.0% alpha, 15.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.85 Creating SS restraints... Processing helix chain 'A' and resid 71 through 82 Processing helix chain 'A' and resid 86 through 97 removed outlier: 3.628A pdb=" N GLN A 94 " --> pdb=" O ASN A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 125 Processing helix chain 'A' and resid 129 through 148 removed outlier: 3.714A pdb=" N ASP A 148 " --> pdb=" O CYS A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 154 No H-bonds generated for 'chain 'A' and resid 152 through 154' Processing helix chain 'A' and resid 159 through 170 removed outlier: 3.716A pdb=" N PHE A 166 " --> pdb=" O PHE A 162 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N SER A 167 " --> pdb=" O LEU A 163 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N THR A 168 " --> pdb=" O ASN A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 225 Proline residue: A 216 - end of helix Processing helix chain 'A' and resid 279 through 285 Processing helix chain 'A' and resid 303 through 308 removed outlier: 3.763A pdb=" N LEU A 308 " --> pdb=" O GLY A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 323 No H-bonds generated for 'chain 'A' and resid 320 through 323' Processing helix chain 'A' and resid 335 through 340 Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'A' and resid 409 through 457 removed outlier: 3.931A pdb=" N LYS A 449 " --> pdb=" O GLU A 445 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N THR A 450 " --> pdb=" O GLU A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 467 Processing helix chain 'A' and resid 490 through 496 Processing helix chain 'A' and resid 499 through 520 removed outlier: 3.783A pdb=" N ARG A 512 " --> pdb=" O ALA A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 562 removed outlier: 4.122A pdb=" N ASP A 561 " --> pdb=" O MET A 557 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLU A 562 " --> pdb=" O GLU A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 609 Processing helix chain 'A' and resid 620 through 626 Processing helix chain 'A' and resid 639 through 641 No H-bonds generated for 'chain 'A' and resid 639 through 641' Processing helix chain 'B' and resid 3 through 17 Processing helix chain 'B' and resid 19 through 28 Processing helix chain 'B' and resid 45 through 58 Processing helix chain 'B' and resid 63 through 80 removed outlier: 3.944A pdb=" N LYS B 72 " --> pdb=" O GLN B 68 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N MET B 73 " --> pdb=" O MET B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 88 Processing helix chain 'B' and resid 94 through 99 Processing helix chain 'B' and resid 101 through 111 Processing helix chain 'B' and resid 145 through 158 Processing helix chain 'B' and resid 210 through 216 Processing helix chain 'B' and resid 234 through 239 removed outlier: 3.545A pdb=" N ARG B 238 " --> pdb=" O ASN B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 243 No H-bonds generated for 'chain 'B' and resid 241 through 243' Processing helix chain 'B' and resid 250 through 253 No H-bonds generated for 'chain 'B' and resid 250 through 253' Processing helix chain 'B' and resid 265 through 270 Processing helix chain 'B' and resid 330 through 335 Processing helix chain 'B' and resid 349 through 397 removed outlier: 3.566A pdb=" N GLU B 370 " --> pdb=" O THR B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 407 removed outlier: 4.004A pdb=" N GLU B 405 " --> pdb=" O SER B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 436 Processing helix chain 'B' and resid 440 through 460 removed outlier: 4.221A pdb=" N ALA B 443 " --> pdb=" O GLY B 440 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N TYR B 454 " --> pdb=" O ASN B 451 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N THR B 455 " --> pdb=" O ASP B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 509 removed outlier: 4.564A pdb=" N GLY B 508 " --> pdb=" O MET B 504 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N GLN B 509 " --> pdb=" O GLU B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 556 Processing helix chain 'B' and resid 566 through 572 Processing sheet with id= A, first strand: chain 'A' and resid 190 through 193 removed outlier: 3.841A pdb=" N HIS A 201 " --> pdb=" O LEU A 193 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU A 254 " --> pdb=" O MET A 236 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 289 through 292 Processing sheet with id= C, first strand: chain 'A' and resid 475 through 477 Processing sheet with id= D, first strand: chain 'A' and resid 523 through 526 removed outlier: 7.155A pdb=" N CYS A 533 " --> pdb=" O VAL A 525 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N LYS A 615 " --> pdb=" O ILE A 575 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N LEU A 577 " --> pdb=" O LYS A 615 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ASN A 617 " --> pdb=" O LEU A 577 " (cutoff:3.500A) removed outlier: 8.530A pdb=" N SER A 579 " --> pdb=" O ASN A 617 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 632 through 636 removed outlier: 3.730A pdb=" N ALA A 659 " --> pdb=" O VAL A 633 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N THR A 635 " --> pdb=" O LEU A 657 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N LEU A 657 " --> pdb=" O THR A 635 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 119 through 124 removed outlier: 3.677A pdb=" N GLU B 182 " --> pdb=" O ASP B 163 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 254 through 258 removed outlier: 6.592A pdb=" N VAL B 277 " --> pdb=" O VAL B 257 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 415 through 417 Processing sheet with id= I, first strand: chain 'B' and resid 470 through 473 removed outlier: 7.025A pdb=" N MET B 480 " --> pdb=" O VAL B 472 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N THR B 421 " --> pdb=" O SER B 483 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ILE B 562 " --> pdb=" O LEU B 604 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY B 588 " --> pdb=" O VAL B 601 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N PHE B 603 " --> pdb=" O HIS B 586 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N HIS B 586 " --> pdb=" O PHE B 603 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N SER B 605 " --> pdb=" O LEU B 584 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N LEU B 584 " --> pdb=" O SER B 605 " (cutoff:3.500A) 421 hydrogen bonds defined for protein. 1155 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.78 Time building geometry restraints manager: 3.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.36: 2763 1.36 - 1.55: 5755 1.55 - 1.73: 8 1.73 - 1.91: 91 1.91 - 2.09: 3 Bond restraints: 8620 Sorted by residual: bond pdb=" C13 GZO B 702 " pdb=" N06 GZO B 702 " ideal model delta sigma weight residual 1.327 1.535 -0.208 2.00e-02 2.50e+03 1.08e+02 bond pdb=" C17 GZO B 702 " pdb=" N07 GZO B 702 " ideal model delta sigma weight residual 1.322 1.476 -0.154 2.00e-02 2.50e+03 5.96e+01 bond pdb=" C17 GZO B 702 " pdb=" N08 GZO B 702 " ideal model delta sigma weight residual 1.321 1.473 -0.152 2.00e-02 2.50e+03 5.78e+01 bond pdb=" C12 GZO B 702 " pdb=" C18 GZO B 702 " ideal model delta sigma weight residual 1.397 1.536 -0.139 2.00e-02 2.50e+03 4.85e+01 bond pdb=" C25 GZO B 702 " pdb=" N06 GZO B 702 " ideal model delta sigma weight residual 1.319 1.456 -0.137 2.00e-02 2.50e+03 4.66e+01 ... (remaining 8615 not shown) Histogram of bond angle deviations from ideal: 85.86 - 103.92: 133 103.92 - 121.98: 9960 121.98 - 140.04: 1620 140.04 - 158.10: 0 158.10 - 176.17: 2 Bond angle restraints: 11715 Sorted by residual: angle pdb=" N ALA A 659 " pdb=" CA ALA A 659 " pdb=" C ALA A 659 " ideal model delta sigma weight residual 109.07 119.88 -10.81 1.52e+00 4.33e-01 5.06e+01 angle pdb=" N TRP A 467 " pdb=" CA TRP A 467 " pdb=" C TRP A 467 " ideal model delta sigma weight residual 111.07 103.85 7.22 1.07e+00 8.73e-01 4.56e+01 angle pdb=" C TRP A 467 " pdb=" CA TRP A 467 " pdb=" CB TRP A 467 " ideal model delta sigma weight residual 110.88 102.33 8.55 1.57e+00 4.06e-01 2.97e+01 angle pdb=" CA TRP A 467 " pdb=" CB TRP A 467 " pdb=" CG TRP A 467 " ideal model delta sigma weight residual 113.60 122.81 -9.21 1.90e+00 2.77e-01 2.35e+01 angle pdb=" N ASP A 658 " pdb=" CA ASP A 658 " pdb=" C ASP A 658 " ideal model delta sigma weight residual 111.36 116.26 -4.90 1.09e+00 8.42e-01 2.02e+01 ... (remaining 11710 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.19: 4494 17.19 - 34.38: 458 34.38 - 51.57: 154 51.57 - 68.75: 15 68.75 - 85.94: 13 Dihedral angle restraints: 5134 sinusoidal: 1956 harmonic: 3178 Sorted by residual: dihedral pdb=" CA ALA A 659 " pdb=" C ALA A 659 " pdb=" N TYR A 660 " pdb=" CA TYR A 660 " ideal model delta harmonic sigma weight residual 180.00 151.28 28.72 0 5.00e+00 4.00e-02 3.30e+01 dihedral pdb=" C TRP A 467 " pdb=" N TRP A 467 " pdb=" CA TRP A 467 " pdb=" CB TRP A 467 " ideal model delta harmonic sigma weight residual -122.60 -110.96 -11.64 0 2.50e+00 1.60e-01 2.17e+01 dihedral pdb=" CA HIS A 406 " pdb=" C HIS A 406 " pdb=" N ASN A 407 " pdb=" CA ASN A 407 " ideal model delta harmonic sigma weight residual -180.00 -157.00 -23.00 0 5.00e+00 4.00e-02 2.12e+01 ... (remaining 5131 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1122 0.061 - 0.121: 219 0.121 - 0.182: 20 0.182 - 0.242: 6 0.242 - 0.303: 2 Chirality restraints: 1369 Sorted by residual: chirality pdb=" CA LYS B 409 " pdb=" N LYS B 409 " pdb=" C LYS B 409 " pdb=" CB LYS B 409 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" CA ASN B 404 " pdb=" N ASN B 404 " pdb=" C ASN B 404 " pdb=" CB ASN B 404 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CA GLU B 405 " pdb=" N GLU B 405 " pdb=" C GLU B 405 " pdb=" CB GLU B 405 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 1366 not shown) Planarity restraints: 1471 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 657 " -0.017 2.00e-02 2.50e+03 3.29e-02 1.08e+01 pdb=" C LEU A 657 " 0.057 2.00e-02 2.50e+03 pdb=" O LEU A 657 " -0.021 2.00e-02 2.50e+03 pdb=" N ASP A 658 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG B 410 " -0.039 5.00e-02 4.00e+02 5.89e-02 5.56e+00 pdb=" N PRO B 411 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO B 411 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 411 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 574 " 0.038 5.00e-02 4.00e+02 5.75e-02 5.29e+00 pdb=" N PRO B 575 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO B 575 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 575 " 0.032 5.00e-02 4.00e+02 ... (remaining 1468 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 48 2.54 - 3.13: 6481 3.13 - 3.72: 12972 3.72 - 4.31: 18391 4.31 - 4.90: 31689 Nonbonded interactions: 69581 Sorted by model distance: nonbonded pdb=" O5' G2P A1001 " pdb="MG MG A1002 " model vdw 1.951 2.170 nonbonded pdb=" O3B G2P A1001 " pdb="MG MG A1003 " model vdw 2.050 2.170 nonbonded pdb=" O SER B 249 " pdb=" OG SER B 252 " model vdw 2.206 2.440 nonbonded pdb=" O GLY A 337 " pdb=" OG1 THR A 340 " model vdw 2.209 2.440 nonbonded pdb=" O ILE B 111 " pdb=" NH2 ARG B 360 " model vdw 2.214 2.520 ... (remaining 69576 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.960 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 29.180 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 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 : 0.010 0.219 8620 Z= 0.639 Angle : 0.845 12.335 11715 Z= 0.431 Chirality : 0.049 0.303 1369 Planarity : 0.005 0.059 1471 Dihedral : 15.942 85.944 3074 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.18 % Favored : 96.63 % Rotamer: Outliers : 0.46 % Allowed : 20.82 % Favored : 78.73 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 2.17 % 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: -0.23 (0.25), residues: 1069 helix: 0.46 (0.23), residues: 512 sheet: -0.11 (0.35), residues: 222 loop : -0.94 (0.32), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.004 TRP A 467 HIS 0.008 0.001 HIS A 578 PHE 0.018 0.002 PHE B 75 TYR 0.018 0.002 TYR B 112 ARG 0.005 0.000 ARG B 570 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 97 time to evaluate : 1.237 Fit side-chains REVERT: A 253 LEU cc_start: 0.8330 (mt) cc_final: 0.8077 (mp) outliers start: 4 outliers final: 2 residues processed: 100 average time/residue: 0.1679 time to fit residues: 25.0483 Evaluate side-chains 97 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 95 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain B residue 56 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 0.7980 chunk 82 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 chunk 44 optimal weight: 0.1980 chunk 85 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 chunk 51 optimal weight: 0.2980 chunk 63 optimal weight: 0.7980 chunk 98 optimal weight: 0.5980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 GLN A 470 GLN ** B 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.0582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8620 Z= 0.186 Angle : 0.538 7.908 11715 Z= 0.277 Chirality : 0.041 0.147 1369 Planarity : 0.004 0.054 1471 Dihedral : 6.774 87.517 1207 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.28 % Allowed : 20.14 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 0.43 (0.26), residues: 1069 helix: 1.34 (0.23), residues: 499 sheet: -0.16 (0.34), residues: 229 loop : -0.89 (0.32), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 602 HIS 0.004 0.001 HIS B 105 PHE 0.017 0.001 PHE B 75 TYR 0.016 0.001 TYR B 479 ARG 0.005 0.000 ARG B 570 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 107 time to evaluate : 0.984 Fit side-chains REVERT: A 335 PHE cc_start: 0.7789 (t80) cc_final: 0.7305 (t80) REVERT: A 458 PHE cc_start: 0.8497 (OUTLIER) cc_final: 0.6600 (p90) REVERT: B 93 ASN cc_start: 0.7725 (t0) cc_final: 0.7436 (t0) REVERT: B 570 ARG cc_start: 0.7279 (mtt90) cc_final: 0.6520 (mtt90) outliers start: 20 outliers final: 8 residues processed: 123 average time/residue: 0.1752 time to fit residues: 31.6827 Evaluate side-chains 108 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 99 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 467 TRP Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 541 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 82 optimal weight: 0.8980 chunk 67 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 107 optimal weight: 6.9990 chunk 88 optimal weight: 0.5980 chunk 98 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 600 ASN ** B 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.0813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8620 Z= 0.218 Angle : 0.534 7.926 11715 Z= 0.273 Chirality : 0.041 0.145 1369 Planarity : 0.004 0.053 1471 Dihedral : 6.587 78.357 1206 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.73 % Allowed : 20.59 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 0.60 (0.26), residues: 1069 helix: 1.53 (0.23), residues: 499 sheet: -0.11 (0.34), residues: 229 loop : -0.85 (0.32), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 467 HIS 0.004 0.001 HIS B 105 PHE 0.015 0.001 PHE B 75 TYR 0.014 0.001 TYR B 479 ARG 0.004 0.000 ARG B 570 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 106 time to evaluate : 1.017 Fit side-chains REVERT: A 258 HIS cc_start: 0.8210 (OUTLIER) cc_final: 0.7303 (m-70) REVERT: A 335 PHE cc_start: 0.7700 (t80) cc_final: 0.7299 (t80) REVERT: A 473 GLN cc_start: 0.8404 (OUTLIER) cc_final: 0.7599 (mp-120) REVERT: B 93 ASN cc_start: 0.7743 (t0) cc_final: 0.7449 (t0) REVERT: B 570 ARG cc_start: 0.7309 (mtt90) cc_final: 0.6583 (mtt90) outliers start: 24 outliers final: 13 residues processed: 124 average time/residue: 0.1670 time to fit residues: 30.9650 Evaluate side-chains 116 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 101 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 258 HIS Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 473 GLN Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 563 ASN Chi-restraints excluded: chain B residue 607 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 0.0170 chunk 74 optimal weight: 0.4980 chunk 51 optimal weight: 6.9990 chunk 10 optimal weight: 7.9990 chunk 47 optimal weight: 0.0470 chunk 66 optimal weight: 0.7980 chunk 99 optimal weight: 6.9990 chunk 105 optimal weight: 0.0270 chunk 94 optimal weight: 0.0670 chunk 28 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 overall best weight: 0.1312 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 ASN ** B 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.1230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 8620 Z= 0.135 Angle : 0.488 7.674 11715 Z= 0.248 Chirality : 0.040 0.138 1369 Planarity : 0.004 0.051 1471 Dihedral : 6.283 73.740 1206 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.93 % Allowed : 21.05 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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 (0.26), residues: 1069 helix: 1.83 (0.24), residues: 497 sheet: 0.02 (0.35), residues: 229 loop : -0.86 (0.32), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 602 HIS 0.003 0.000 HIS B 105 PHE 0.017 0.001 PHE B 223 TYR 0.013 0.001 TYR B 211 ARG 0.003 0.000 ARG B 570 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 111 time to evaluate : 0.900 Fit side-chains REVERT: A 258 HIS cc_start: 0.8222 (OUTLIER) cc_final: 0.7372 (m-70) REVERT: A 335 PHE cc_start: 0.7597 (t80) cc_final: 0.7119 (t80) REVERT: A 458 PHE cc_start: 0.8292 (OUTLIER) cc_final: 0.7385 (p90) REVERT: B 93 ASN cc_start: 0.7612 (t0) cc_final: 0.7337 (t0) outliers start: 17 outliers final: 9 residues processed: 122 average time/residue: 0.1907 time to fit residues: 33.3172 Evaluate side-chains 115 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 104 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 258 HIS Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 351 ASP Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 541 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 0.5980 chunk 1 optimal weight: 0.9980 chunk 78 optimal weight: 0.5980 chunk 43 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 72 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 53 optimal weight: 0.4980 chunk 94 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.1180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8620 Z= 0.202 Angle : 0.513 8.265 11715 Z= 0.259 Chirality : 0.041 0.150 1369 Planarity : 0.004 0.050 1471 Dihedral : 6.272 66.015 1206 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.39 % Allowed : 20.82 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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 (0.26), residues: 1069 helix: 1.79 (0.23), residues: 499 sheet: 0.08 (0.35), residues: 229 loop : -0.80 (0.32), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 467 HIS 0.004 0.001 HIS B 7 PHE 0.014 0.001 PHE B 75 TYR 0.015 0.001 TYR B 479 ARG 0.005 0.000 ARG B 570 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 103 time to evaluate : 0.987 Fit side-chains REVERT: A 258 HIS cc_start: 0.8215 (OUTLIER) cc_final: 0.7396 (m-70) REVERT: A 335 PHE cc_start: 0.7667 (t80) cc_final: 0.7201 (t80) REVERT: A 364 MET cc_start: 0.7829 (ttp) cc_final: 0.7554 (ptm) REVERT: B 93 ASN cc_start: 0.7687 (t0) cc_final: 0.7394 (t0) outliers start: 21 outliers final: 13 residues processed: 120 average time/residue: 0.1889 time to fit residues: 32.7612 Evaluate side-chains 115 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 101 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 258 HIS Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 541 CYS Chi-restraints excluded: chain B residue 563 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 0.0980 chunk 20 optimal weight: 0.8980 chunk 61 optimal weight: 0.0670 chunk 26 optimal weight: 0.9990 chunk 105 optimal weight: 0.2980 chunk 87 optimal weight: 0.8980 chunk 48 optimal weight: 4.9990 chunk 8 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 55 optimal weight: 0.0670 chunk 101 optimal weight: 1.9990 overall best weight: 0.2456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8620 Z= 0.146 Angle : 0.488 7.926 11715 Z= 0.246 Chirality : 0.040 0.142 1369 Planarity : 0.004 0.049 1471 Dihedral : 5.884 63.726 1204 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.73 % Allowed : 21.27 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 0.97 (0.26), residues: 1069 helix: 1.86 (0.23), residues: 502 sheet: 0.14 (0.35), residues: 229 loop : -0.80 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 602 HIS 0.004 0.001 HIS B 7 PHE 0.014 0.001 PHE B 223 TYR 0.015 0.001 TYR B 211 ARG 0.004 0.000 ARG B 570 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 107 time to evaluate : 0.960 Fit side-chains REVERT: A 258 HIS cc_start: 0.8196 (OUTLIER) cc_final: 0.7461 (m-70) REVERT: A 335 PHE cc_start: 0.7643 (t80) cc_final: 0.7213 (t80) REVERT: A 364 MET cc_start: 0.7838 (ttp) cc_final: 0.7541 (ptm) REVERT: A 458 PHE cc_start: 0.8320 (OUTLIER) cc_final: 0.7698 (p90) REVERT: A 590 LYS cc_start: 0.8036 (OUTLIER) cc_final: 0.7657 (ttmm) REVERT: B 93 ASN cc_start: 0.7638 (t0) cc_final: 0.7355 (t0) REVERT: B 600 GLN cc_start: 0.7633 (mt0) cc_final: 0.7035 (mm-40) outliers start: 24 outliers final: 17 residues processed: 125 average time/residue: 0.1757 time to fit residues: 32.0377 Evaluate side-chains 123 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 103 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 258 HIS Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 468 GLN Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 590 LYS Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 351 ASP Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 541 CYS Chi-restraints excluded: chain B residue 563 ASN Chi-restraints excluded: chain B residue 607 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 10.0000 chunk 60 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 88 optimal weight: 0.6980 chunk 58 optimal weight: 0.5980 chunk 105 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 41 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.1265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8620 Z= 0.231 Angle : 0.525 9.124 11715 Z= 0.264 Chirality : 0.041 0.148 1369 Planarity : 0.004 0.048 1471 Dihedral : 5.956 63.229 1204 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.73 % Allowed : 21.16 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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 (0.26), residues: 1069 helix: 1.81 (0.23), residues: 502 sheet: 0.16 (0.35), residues: 229 loop : -0.81 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 467 HIS 0.004 0.001 HIS B 492 PHE 0.013 0.001 PHE B 4 TYR 0.015 0.001 TYR B 479 ARG 0.006 0.000 ARG B 570 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 102 time to evaluate : 0.915 Fit side-chains REVERT: A 258 HIS cc_start: 0.8204 (OUTLIER) cc_final: 0.7437 (m-70) REVERT: A 335 PHE cc_start: 0.7679 (t80) cc_final: 0.7214 (t80) REVERT: A 364 MET cc_start: 0.7963 (ttp) cc_final: 0.7673 (ptm) REVERT: A 590 LYS cc_start: 0.8054 (OUTLIER) cc_final: 0.7653 (ttmm) REVERT: B 93 ASN cc_start: 0.7719 (t0) cc_final: 0.7413 (t0) REVERT: B 362 GLU cc_start: 0.8013 (mm-30) cc_final: 0.7708 (mm-30) REVERT: B 600 GLN cc_start: 0.7646 (mt0) cc_final: 0.7063 (mm-40) outliers start: 24 outliers final: 16 residues processed: 121 average time/residue: 0.1769 time to fit residues: 31.0533 Evaluate side-chains 115 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 97 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 258 HIS Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 590 LYS Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 351 ASP Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 541 CYS Chi-restraints excluded: chain B residue 563 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 71 optimal weight: 0.6980 chunk 51 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 82 optimal weight: 0.5980 chunk 95 optimal weight: 0.5980 chunk 100 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.1293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8620 Z= 0.217 Angle : 0.524 9.265 11715 Z= 0.262 Chirality : 0.041 0.151 1369 Planarity : 0.004 0.048 1471 Dihedral : 5.951 63.026 1204 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.84 % Allowed : 21.39 % Favored : 75.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 0.91 (0.26), residues: 1069 helix: 1.78 (0.23), residues: 503 sheet: 0.15 (0.35), residues: 229 loop : -0.81 (0.33), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 467 HIS 0.004 0.001 HIS B 492 PHE 0.013 0.001 PHE B 75 TYR 0.014 0.001 TYR B 479 ARG 0.005 0.000 ARG B 570 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 100 time to evaluate : 0.930 Fit side-chains REVERT: A 220 LYS cc_start: 0.8408 (ttmt) cc_final: 0.7988 (ttpp) REVERT: A 258 HIS cc_start: 0.8213 (OUTLIER) cc_final: 0.7502 (m-70) REVERT: A 335 PHE cc_start: 0.7668 (t80) cc_final: 0.7177 (t80) REVERT: A 364 MET cc_start: 0.7982 (ttp) cc_final: 0.7695 (ptm) REVERT: A 590 LYS cc_start: 0.8018 (OUTLIER) cc_final: 0.7633 (ttmm) REVERT: B 93 ASN cc_start: 0.7691 (t0) cc_final: 0.7383 (t0) REVERT: B 362 GLU cc_start: 0.8010 (mm-30) cc_final: 0.7697 (mm-30) REVERT: B 600 GLN cc_start: 0.7630 (mt0) cc_final: 0.7061 (mm-40) outliers start: 25 outliers final: 18 residues processed: 120 average time/residue: 0.1873 time to fit residues: 32.4816 Evaluate side-chains 119 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 99 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 258 HIS Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 349 ARG Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 468 GLN Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 590 LYS Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 351 ASP Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 541 CYS Chi-restraints excluded: chain B residue 563 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 0.9990 chunk 100 optimal weight: 0.0070 chunk 58 optimal weight: 0.5980 chunk 42 optimal weight: 0.5980 chunk 76 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 88 optimal weight: 0.0980 chunk 92 optimal weight: 0.7980 chunk 64 optimal weight: 0.5980 chunk 103 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 overall best weight: 0.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8620 Z= 0.158 Angle : 0.497 9.015 11715 Z= 0.248 Chirality : 0.040 0.147 1369 Planarity : 0.004 0.048 1471 Dihedral : 5.822 63.106 1204 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.28 % Allowed : 21.84 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 1.05 (0.26), residues: 1069 helix: 1.95 (0.23), residues: 501 sheet: 0.20 (0.35), residues: 229 loop : -0.80 (0.32), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 602 HIS 0.003 0.001 HIS B 105 PHE 0.014 0.001 PHE B 75 TYR 0.018 0.001 TYR A 145 ARG 0.005 0.000 ARG B 570 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 103 time to evaluate : 1.044 Fit side-chains REVERT: A 258 HIS cc_start: 0.8273 (OUTLIER) cc_final: 0.7626 (m-70) REVERT: A 335 PHE cc_start: 0.7638 (t80) cc_final: 0.7168 (t80) REVERT: A 364 MET cc_start: 0.7941 (ttp) cc_final: 0.7666 (ptm) REVERT: A 458 PHE cc_start: 0.8386 (OUTLIER) cc_final: 0.7592 (p90) REVERT: A 590 LYS cc_start: 0.7829 (OUTLIER) cc_final: 0.7432 (ttmm) REVERT: A 661 GLN cc_start: 0.7857 (mm110) cc_final: 0.7656 (mm-40) REVERT: B 93 ASN cc_start: 0.7633 (t0) cc_final: 0.7345 (t0) REVERT: B 362 GLU cc_start: 0.7971 (mm-30) cc_final: 0.7676 (mm-30) REVERT: B 600 GLN cc_start: 0.7608 (mt0) cc_final: 0.7099 (mm-40) outliers start: 20 outliers final: 15 residues processed: 119 average time/residue: 0.1920 time to fit residues: 32.6444 Evaluate side-chains 121 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 103 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 HIS Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 468 GLN Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 590 LYS Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 351 ASP Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 541 CYS Chi-restraints excluded: chain B residue 563 ASN Chi-restraints excluded: chain B residue 607 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 0.7980 chunk 71 optimal weight: 0.7980 chunk 108 optimal weight: 0.7980 chunk 99 optimal weight: 0.0010 chunk 86 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 66 optimal weight: 0.4980 chunk 53 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8620 Z= 0.193 Angle : 0.514 9.255 11715 Z= 0.256 Chirality : 0.041 0.149 1369 Planarity : 0.004 0.048 1471 Dihedral : 5.846 63.374 1204 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.16 % Allowed : 22.18 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 1.02 (0.26), residues: 1069 helix: 1.88 (0.23), residues: 503 sheet: 0.23 (0.35), residues: 229 loop : -0.80 (0.32), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 602 HIS 0.004 0.001 HIS B 105 PHE 0.013 0.001 PHE B 75 TYR 0.014 0.001 TYR B 479 ARG 0.005 0.000 ARG B 570 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 101 time to evaluate : 1.029 Fit side-chains REVERT: A 258 HIS cc_start: 0.8279 (OUTLIER) cc_final: 0.7655 (m-70) REVERT: A 364 MET cc_start: 0.7983 (ttp) cc_final: 0.7709 (ptm) REVERT: A 590 LYS cc_start: 0.7874 (OUTLIER) cc_final: 0.7468 (ttmm) REVERT: B 93 ASN cc_start: 0.7659 (t0) cc_final: 0.7371 (t0) REVERT: B 362 GLU cc_start: 0.7987 (mm-30) cc_final: 0.7713 (mm-30) REVERT: B 600 GLN cc_start: 0.7576 (mt0) cc_final: 0.7087 (mm-40) outliers start: 19 outliers final: 15 residues processed: 116 average time/residue: 0.1737 time to fit residues: 29.5080 Evaluate side-chains 116 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 99 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 HIS Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 468 GLN Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 547 VAL Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 590 LYS Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 541 CYS Chi-restraints excluded: chain B residue 563 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 24 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 88 optimal weight: 0.0270 chunk 10 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 76 optimal weight: 0.1980 chunk 4 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 overall best weight: 0.4438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.166296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.138064 restraints weight = 12251.639| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 2.00 r_work: 0.3410 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3285 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3285 r_free = 0.3285 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3285 r_free = 0.3285 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3285 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8620 Z= 0.170 Angle : 0.507 9.135 11715 Z= 0.253 Chirality : 0.040 0.148 1369 Planarity : 0.004 0.048 1471 Dihedral : 5.818 63.365 1204 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.50 % Allowed : 21.73 % Favored : 75.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 1.05 (0.26), residues: 1069 helix: 1.91 (0.23), residues: 501 sheet: 0.30 (0.35), residues: 227 loop : -0.84 (0.32), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 602 HIS 0.004 0.001 HIS B 105 PHE 0.013 0.001 PHE B 75 TYR 0.029 0.001 TYR A 372 ARG 0.006 0.000 ARG B 570 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2042.83 seconds wall clock time: 37 minutes 45.00 seconds (2265.00 seconds total)