Starting phenix.real_space_refine on Fri Dec 8 06:33:23 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d9t_30620/12_2023/7d9t_30620_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d9t_30620/12_2023/7d9t_30620.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d9t_30620/12_2023/7d9t_30620.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d9t_30620/12_2023/7d9t_30620.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d9t_30620/12_2023/7d9t_30620_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d9t_30620/12_2023/7d9t_30620_updated.pdb" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 35 5.16 5 C 4784 2.51 5 N 1279 2.21 5 O 1353 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 656": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 10": "OE1" <-> "OE2" Residue "B PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 116": "NH1" <-> "NH2" Residue "B TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 175": "OD1" <-> "OD2" Residue "B TYR 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 381": "NH1" <-> "NH2" Residue "B TYR 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 458": "OD1" <-> "OD2" Residue "B ASP 477": "OD1" <-> "OD2" Residue "B PHE 603": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 7451 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3235 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 512, 3232 Classifications: {'peptide': 512} Incomplete info: {'truncation_to_alanine': 226} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 486} Chain breaks: 9 Unresolved non-hydrogen bonds: 868 Unresolved non-hydrogen angles: 1075 Unresolved non-hydrogen dihedrals: 728 Unresolved non-hydrogen chiralities: 53 Planarities with less than four sites: {'GLN:plan1': 12, 'ASP:plan': 18, 'TYR:plan': 7, 'ASN:plan1': 7, 'HIS:plan': 9, 'PHE:plan': 14, 'GLU:plan': 33, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 518 Conformer: "B" Number of residues, atoms: 512, 3232 Classifications: {'peptide': 512} Incomplete info: {'truncation_to_alanine': 226} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 486} Chain breaks: 9 Unresolved non-hydrogen bonds: 868 Unresolved non-hydrogen angles: 1075 Unresolved non-hydrogen dihedrals: 728 Unresolved non-hydrogen chiralities: 53 Planarities with less than four sites: {'GLN:plan1': 12, 'ASP:plan': 18, 'TYR:plan': 7, 'ASN:plan1': 7, 'HIS:plan': 9, 'PHE:plan': 14, 'GLU:plan': 33, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 518 bond proxies already assigned to first conformer: 3276 Chain: "B" Number of atoms: 4216 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 568, 4212 Unusual residues: {'Z90': 1} Classifications: {'peptide': 567, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 88} Link IDs: {'PTRANS': 23, 'TRANS': 543, None: 1} Not linked: pdbres="LYS B 607 " pdbres="Z90 B 701 " Chain breaks: 3 Unresolved non-hydrogen bonds: 366 Unresolved non-hydrogen angles: 443 Unresolved non-hydrogen dihedrals: 303 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 9, 'PHE:plan': 2, 'GLU:plan': 29, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 263 Conformer: "B" Number of residues, atoms: 568, 4212 Unusual residues: {'Z90': 1} Classifications: {'peptide': 567, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 88} Link IDs: {'PTRANS': 23, 'TRANS': 543, None: 1} Not linked: pdbres="LYS B 607 " pdbres="Z90 B 701 " Chain breaks: 3 Unresolved non-hydrogen bonds: 366 Unresolved non-hydrogen angles: 443 Unresolved non-hydrogen dihedrals: 303 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 9, 'PHE:plan': 2, 'GLU:plan': 29, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 263 bond proxies already assigned to first conformer: 4294 Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N GLU A 147 " occ=0.91 ... (3 atoms not shown) pdb=" CB GLU A 147 " occ=0.91 residue: pdb=" N LEU A 254 " occ=0.92 ... (3 atoms not shown) pdb=" CB LEU A 254 " occ=0.92 residue: pdb=" N GLU A 325 " occ=0.75 ... (3 atoms not shown) pdb=" CB GLU A 325 " occ=0.75 residue: pdb=" N MET A 341 " occ=0.75 ... (3 atoms not shown) pdb=" CB MET A 341 " occ=0.75 Time building chain proxies: 8.77, per 1000 atoms: 1.18 Number of scatterers: 7451 At special positions: 0 Unit cell: (149.435, 71.06, 100.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 35 16.00 O 1353 8.00 N 1279 7.00 C 4784 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: 3.65 Conformation dependent library (CDL) restraints added in 3.0 seconds 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2038 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 37 helices and 10 sheets defined 42.7% alpha, 14.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.74 Creating SS restraints... Processing helix chain 'A' and resid 71 through 82 Processing helix chain 'A' and resid 86 through 99 Processing helix chain 'A' and resid 115 through 121 Processing helix chain 'A' and resid 129 through 148 Processing helix chain 'A' and resid 159 through 170 removed outlier: 4.432A pdb=" N SER A 167 " --> pdb=" O LEU A 163 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N THR A 168 " --> pdb=" O ASN A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 226 removed outlier: 4.228A pdb=" N LEU A 213 " --> pdb=" O ARG A 209 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE A 214 " --> pdb=" O THR A 210 " (cutoff:3.500A) 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 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 390 through 395 removed outlier: 3.563A pdb=" N GLY A 395 " --> pdb=" O ASP A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 417 Processing helix chain 'A' and resid 427 through 457 Processing helix chain 'A' and resid 460 through 468 Processing helix chain 'A' and resid 490 through 495 Processing helix chain 'A' and resid 499 through 520 Processing helix chain 'A' and resid 545 through 560 Processing helix chain 'A' and resid 599 through 610 Processing helix chain 'A' and resid 620 through 626 removed outlier: 3.788A pdb=" N LEU A 625 " --> pdb=" O THR A 621 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 28 Proline residue: B 19 - end of helix removed outlier: 4.153A pdb=" N TRP B 22 " --> pdb=" O GLY B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 58 Processing helix chain 'B' and resid 63 through 81 Processing helix chain 'B' and resid 84 through 89 Processing helix chain 'B' and resid 94 through 111 removed outlier: 4.580A pdb=" N ASP B 102 " --> pdb=" O LEU B 98 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N ALA B 103 " --> pdb=" O GLN B 99 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE B 111 " --> pdb=" O HIS B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 156 Processing helix chain 'B' and resid 210 through 216 Processing helix chain 'B' and resid 234 through 239 removed outlier: 3.848A pdb=" N ARG B 238 " --> pdb=" O ASN B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 270 Processing helix chain 'B' and resid 330 through 335 Processing helix chain 'B' and resid 348 through 354 removed outlier: 3.574A pdb=" N LEU B 354 " --> pdb=" O ASP B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 394 removed outlier: 3.759A pdb=" N LEU B 365 " --> pdb=" O GLU B 361 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR B 366 " --> pdb=" O GLU B 362 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLN B 367 " --> pdb=" O TYR B 363 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLU B 368 " --> pdb=" O LYS B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 408 removed outlier: 3.969A pdb=" N HIS B 408 " --> pdb=" O ASN B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 436 Processing helix chain 'B' and resid 440 through 460 Processing helix chain 'B' and resid 492 through 509 removed outlier: 4.170A pdb=" N GLY B 508 " --> pdb=" O MET B 504 " (cutoff:3.500A) removed outlier: 4.559A 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 573 Processing sheet with id= A, first strand: chain 'A' and resid 189 through 193 removed outlier: 3.679A pdb=" N SER A 189 " --> pdb=" O PHE A 205 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU A 232 " --> pdb=" O HIS A 258 " (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 481 through 483 Processing sheet with id= E, first strand: chain 'A' and resid 485 through 487 Processing sheet with id= F, first strand: chain 'A' and resid 616 through 618 removed outlier: 4.299A pdb=" N ILE A 616 " --> pdb=" O LEU A 657 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL A 633 " --> pdb=" O ASP A 658 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 120 through 124 Processing sheet with id= H, first strand: chain 'B' and resid 254 through 256 removed outlier: 3.796A pdb=" N PHE B 223 " --> pdb=" O ILE B 319 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ASP B 224 " --> pdb=" O VAL B 229 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N VAL B 229 " --> pdb=" O ASP B 224 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 415 through 417 Processing sheet with id= J, first strand: chain 'B' and resid 470 through 472 removed outlier: 4.484A pdb=" N MET B 480 " --> pdb=" O VAL B 472 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N THR B 421 " --> pdb=" O SER B 483 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N THR B 525 " --> pdb=" O SER B 565 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N ILE B 562 " --> pdb=" O LEU B 604 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL B 601 " --> pdb=" O GLY B 588 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N GLY B 588 " --> pdb=" O VAL B 601 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N PHE B 603 " --> pdb=" O HIS B 586 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N HIS B 586 " --> pdb=" O PHE B 603 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N SER B 605 " --> pdb=" O LEU B 584 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N LEU B 584 " --> pdb=" O SER B 605 " (cutoff:3.500A) 407 hydrogen bonds defined for protein. 1145 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: 2.46 Time building geometry restraints manager: 3.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2452 1.34 - 1.46: 1489 1.46 - 1.58: 3597 1.58 - 1.69: 0 1.69 - 1.81: 48 Bond restraints: 7586 Sorted by residual: bond pdb=" CBN Z90 B 701 " pdb=" CBO Z90 B 701 " ideal model delta sigma weight residual 1.405 1.483 -0.078 2.00e-02 2.50e+03 1.54e+01 bond pdb=" CAX Z90 B 701 " pdb=" CBG Z90 B 701 " ideal model delta sigma weight residual 1.542 1.506 0.036 2.00e-02 2.50e+03 3.16e+00 bond pdb=" CBE Z90 B 701 " pdb=" NBP Z90 B 701 " ideal model delta sigma weight residual 1.449 1.477 -0.028 2.00e-02 2.50e+03 1.99e+00 bond pdb=" CBH Z90 B 701 " pdb=" CBM Z90 B 701 " ideal model delta sigma weight residual 1.522 1.496 0.026 2.00e-02 2.50e+03 1.74e+00 bond pdb=" CBB Z90 B 701 " pdb=" NBP Z90 B 701 " ideal model delta sigma weight residual 1.454 1.472 -0.018 2.00e-02 2.50e+03 7.91e-01 ... (remaining 7581 not shown) Histogram of bond angle deviations from ideal: 100.44 - 107.14: 235 107.14 - 113.84: 4442 113.84 - 120.55: 2862 120.55 - 127.25: 2781 127.25 - 133.95: 70 Bond angle restraints: 10390 Sorted by residual: angle pdb=" N VAL A 155 " pdb=" CA VAL A 155 " pdb=" C VAL A 155 " ideal model delta sigma weight residual 111.88 108.21 3.67 1.06e+00 8.90e-01 1.20e+01 angle pdb=" C LEU A 398 " pdb=" N TYR A 399 " pdb=" CA TYR A 399 " ideal model delta sigma weight residual 121.54 127.61 -6.07 1.91e+00 2.74e-01 1.01e+01 angle pdb=" C LEU B 338 " pdb=" N TYR B 339 " pdb=" CA TYR B 339 " ideal model delta sigma weight residual 121.54 127.49 -5.95 1.91e+00 2.74e-01 9.70e+00 angle pdb=" N VAL B 239 " pdb=" CA VAL B 239 " pdb=" C VAL B 239 " ideal model delta sigma weight residual 113.16 108.88 4.28 1.49e+00 4.50e-01 8.24e+00 angle pdb=" N LYS A 555 " pdb=" CA LYS A 555 " pdb=" C LYS A 555 " ideal model delta sigma weight residual 111.36 108.32 3.04 1.09e+00 8.42e-01 7.80e+00 ... (remaining 10385 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.30: 4404 28.30 - 56.59: 70 56.59 - 84.89: 4 84.89 - 113.18: 1 113.18 - 141.48: 1 Dihedral angle restraints: 4480 sinusoidal: 1348 harmonic: 3132 Sorted by residual: dihedral pdb=" CA LEU A 398 " pdb=" C LEU A 398 " pdb=" N TYR A 399 " pdb=" CA TYR A 399 " ideal model delta harmonic sigma weight residual 180.00 158.03 21.97 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" CAX Z90 B 701 " pdb=" CAV Z90 B 701 " pdb=" CAW Z90 B 701 " pdb=" CBB Z90 B 701 " ideal model delta sinusoidal sigma weight residual 179.41 37.93 141.48 1 3.00e+01 1.11e-03 1.90e+01 dihedral pdb=" CA LEU B 338 " pdb=" C LEU B 338 " pdb=" N TYR B 339 " pdb=" CA TYR B 339 " ideal model delta harmonic sigma weight residual 180.00 159.70 20.30 0 5.00e+00 4.00e-02 1.65e+01 ... (remaining 4477 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 844 0.030 - 0.060: 302 0.060 - 0.090: 85 0.090 - 0.120: 59 0.120 - 0.149: 8 Chirality restraints: 1298 Sorted by residual: chirality pdb=" CB THR A 511 " pdb=" CA THR A 511 " pdb=" OG1 THR A 511 " pdb=" CG2 THR A 511 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 5.58e-01 chirality pdb=" CA ILE A 528 " pdb=" N ILE A 528 " pdb=" C ILE A 528 " pdb=" CB ILE A 528 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.85e-01 chirality pdb=" CA ILE A 403 " pdb=" N ILE A 403 " pdb=" C ILE A 403 " pdb=" CB ILE A 403 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.67e-01 ... (remaining 1295 not shown) Planarity restraints: 1334 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 554 " 0.010 2.00e-02 2.50e+03 2.03e-02 4.11e+00 pdb=" C VAL A 554 " -0.035 2.00e-02 2.50e+03 pdb=" O VAL A 554 " 0.013 2.00e-02 2.50e+03 pdb=" N LYS A 555 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 4 " 0.007 2.00e-02 2.50e+03 8.69e-03 1.32e+00 pdb=" CG PHE B 4 " -0.019 2.00e-02 2.50e+03 pdb=" CD1 PHE B 4 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE B 4 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE B 4 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE B 4 " 0.006 2.00e-02 2.50e+03 pdb=" CZ PHE B 4 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 458 " 0.017 5.00e-02 4.00e+02 2.62e-02 1.10e+00 pdb=" N PRO A 459 " -0.045 5.00e-02 4.00e+02 pdb=" CA PRO A 459 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 459 " 0.015 5.00e-02 4.00e+02 ... (remaining 1331 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1383 2.76 - 3.30: 7459 3.30 - 3.83: 12142 3.83 - 4.37: 12909 4.37 - 4.90: 22745 Nonbonded interactions: 56638 Sorted by model distance: nonbonded pdb=" O VAL B 397 " pdb=" OH TYR B 470 " model vdw 2.230 2.440 nonbonded pdb=" NH2 ARG B 238 " pdb=" OD2 ASP B 342 " model vdw 2.260 2.520 nonbonded pdb=" OH TYR B 454 " pdb=" O GLY B 476 " model vdw 2.296 2.440 nonbonded pdb=" O PHE B 223 " pdb=" OG SER B 318 " model vdw 2.308 2.440 nonbonded pdb=" NH1 ARG B 121 " pdb=" O SER B 270 " model vdw 2.310 2.520 ... (remaining 56633 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=0.30 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.790 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: 3.150 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 31.200 Find NCS groups from input model: 0.270 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: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 7586 Z= 0.193 Angle : 0.567 8.938 10390 Z= 0.320 Chirality : 0.039 0.149 1298 Planarity : 0.003 0.026 1334 Dihedral : 11.031 141.481 2442 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: -1.91 (0.25), residues: 1052 helix: -0.27 (0.22), residues: 496 sheet: -1.81 (0.31), residues: 220 loop : -2.18 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 467 HIS 0.001 0.001 HIS B 271 PHE 0.019 0.001 PHE B 4 TYR 0.017 0.001 TYR A 399 ARG 0.001 0.000 ARG B 207 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 0.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.1951 time to fit residues: 27.6146 Evaluate side-chains 67 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 0.875 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 1.9990 chunk 81 optimal weight: 0.6980 chunk 45 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 chunk 32 optimal weight: 0.2980 chunk 50 optimal weight: 20.0000 chunk 62 optimal weight: 0.0980 chunk 97 optimal weight: 8.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 HIS ** A 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 377 GLN B 548 ASN ** B 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.1111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 7586 Z= 0.163 Angle : 0.523 7.762 10390 Z= 0.268 Chirality : 0.040 0.136 1298 Planarity : 0.003 0.034 1334 Dihedral : 6.392 136.665 1137 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.15 % Allowed : 3.20 % Favored : 96.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: -0.71 (0.26), residues: 1052 helix: 0.81 (0.23), residues: 496 sheet: -1.23 (0.33), residues: 219 loop : -1.76 (0.35), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 602 HIS 0.003 0.001 HIS B 524 PHE 0.026 0.001 PHE A 162 TYR 0.011 0.001 TYR A 227 ARG 0.007 0.001 ARG B 207 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 84 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 85 average time/residue: 0.1590 time to fit residues: 19.8604 Evaluate side-chains 62 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 0.860 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 54 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 chunk 80 optimal weight: 0.0670 chunk 66 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 97 optimal weight: 5.9990 chunk 105 optimal weight: 8.9990 chunk 86 optimal weight: 0.7980 chunk 96 optimal weight: 0.7980 chunk 33 optimal weight: 0.0050 chunk 78 optimal weight: 1.9990 overall best weight: 0.4532 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 7586 Z= 0.140 Angle : 0.521 8.048 10390 Z= 0.262 Chirality : 0.040 0.146 1298 Planarity : 0.003 0.029 1334 Dihedral : 6.356 135.891 1137 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: -0.24 (0.27), residues: 1052 helix: 1.21 (0.24), residues: 495 sheet: -1.00 (0.33), residues: 227 loop : -1.54 (0.36), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 602 HIS 0.002 0.000 HIS A 289 PHE 0.021 0.001 PHE A 162 TYR 0.032 0.001 TYR A 399 ARG 0.004 0.000 ARG A 306 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.1361 time to fit residues: 18.4559 Evaluate side-chains 64 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 0.835 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 96 optimal weight: 0.8980 chunk 73 optimal weight: 0.0070 chunk 50 optimal weight: 0.0370 chunk 10 optimal weight: 0.0980 chunk 46 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 chunk 92 optimal weight: 0.9990 chunk 27 optimal weight: 0.1980 overall best weight: 0.2476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 7586 Z= 0.136 Angle : 0.517 8.272 10390 Z= 0.259 Chirality : 0.040 0.151 1298 Planarity : 0.003 0.034 1334 Dihedral : 6.342 134.360 1137 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 0.07 (0.27), residues: 1052 helix: 1.43 (0.24), residues: 497 sheet: -0.70 (0.33), residues: 223 loop : -1.48 (0.36), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 22 HIS 0.001 0.000 HIS B 176 PHE 0.029 0.001 PHE A 162 TYR 0.022 0.001 TYR A 399 ARG 0.004 0.000 ARG B 238 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.1402 time to fit residues: 18.4970 Evaluate side-chains 64 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 0.801 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 86 optimal weight: 0.0870 chunk 58 optimal weight: 0.8980 chunk 1 optimal weight: 0.5980 chunk 77 optimal weight: 7.9990 chunk 42 optimal weight: 0.3980 chunk 88 optimal weight: 6.9990 chunk 71 optimal weight: 0.7980 chunk 0 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 chunk 92 optimal weight: 3.9990 chunk 26 optimal weight: 0.0970 overall best weight: 0.3956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 7586 Z= 0.133 Angle : 0.523 11.916 10390 Z= 0.258 Chirality : 0.040 0.152 1298 Planarity : 0.003 0.033 1334 Dihedral : 6.307 133.490 1137 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 0.28 (0.27), residues: 1052 helix: 1.52 (0.24), residues: 499 sheet: -0.51 (0.34), residues: 221 loop : -1.32 (0.36), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 602 HIS 0.003 0.000 HIS B 524 PHE 0.040 0.001 PHE A 162 TYR 0.021 0.001 TYR A 399 ARG 0.003 0.000 ARG B 552 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.1504 time to fit residues: 19.6001 Evaluate side-chains 67 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 0.872 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 34 optimal weight: 8.9990 chunk 93 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 25 optimal weight: 0.0570 chunk 103 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 47 optimal weight: 0.0270 chunk 8 optimal weight: 0.6980 chunk 54 optimal weight: 8.9990 chunk 99 optimal weight: 5.9990 overall best weight: 0.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 7586 Z= 0.153 Angle : 0.513 9.297 10390 Z= 0.257 Chirality : 0.040 0.141 1298 Planarity : 0.003 0.025 1334 Dihedral : 6.302 133.505 1137 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 0.47 (0.28), residues: 1052 helix: 1.64 (0.24), residues: 501 sheet: -0.35 (0.35), residues: 221 loop : -1.23 (0.37), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 22 HIS 0.002 0.000 HIS B 524 PHE 0.033 0.001 PHE A 162 TYR 0.022 0.001 TYR A 399 ARG 0.004 0.000 ARG B 238 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.1540 time to fit residues: 19.4491 Evaluate side-chains 64 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 0.891 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 11 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 75 optimal weight: 0.8980 chunk 87 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 chunk 103 optimal weight: 10.0000 chunk 64 optimal weight: 0.7980 chunk 62 optimal weight: 0.7980 chunk 47 optimal weight: 0.0050 chunk 63 optimal weight: 0.7980 chunk 41 optimal weight: 7.9990 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 7586 Z= 0.146 Angle : 0.523 9.148 10390 Z= 0.261 Chirality : 0.041 0.167 1298 Planarity : 0.003 0.029 1334 Dihedral : 6.317 133.331 1137 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.27), residues: 1052 helix: 1.80 (0.24), residues: 493 sheet: -0.25 (0.35), residues: 221 loop : -1.10 (0.37), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 22 HIS 0.002 0.000 HIS B 524 PHE 0.027 0.001 PHE A 162 TYR 0.023 0.001 TYR A 399 ARG 0.003 0.000 ARG B 238 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.1537 time to fit residues: 19.2989 Evaluate side-chains 64 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 0.873 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 61 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 70 optimal weight: 0.7980 chunk 50 optimal weight: 0.0030 chunk 9 optimal weight: 7.9990 chunk 81 optimal weight: 0.0970 chunk 93 optimal weight: 4.9990 chunk 98 optimal weight: 0.5980 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 7586 Z= 0.136 Angle : 0.522 8.703 10390 Z= 0.258 Chirality : 0.040 0.166 1298 Planarity : 0.003 0.031 1334 Dihedral : 6.297 131.804 1137 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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 (0.27), residues: 1052 helix: 1.84 (0.24), residues: 495 sheet: -0.15 (0.36), residues: 219 loop : -0.92 (0.37), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 22 HIS 0.002 0.000 HIS B 524 PHE 0.030 0.001 PHE B 4 TYR 0.022 0.001 TYR A 399 ARG 0.002 0.000 ARG B 238 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.1335 time to fit residues: 17.7667 Evaluate side-chains 65 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 0.790 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 98 optimal weight: 0.4980 chunk 57 optimal weight: 0.8980 chunk 41 optimal weight: 0.0670 chunk 75 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 86 optimal weight: 0.0070 chunk 95 optimal weight: 0.7980 chunk 63 optimal weight: 5.9990 chunk 101 optimal weight: 2.9990 overall best weight: 0.4536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 7586 Z= 0.134 Angle : 0.522 8.853 10390 Z= 0.259 Chirality : 0.040 0.159 1298 Planarity : 0.003 0.029 1334 Dihedral : 6.304 131.306 1137 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.28), residues: 1052 helix: 1.90 (0.24), residues: 494 sheet: -0.10 (0.36), residues: 219 loop : -0.84 (0.37), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 22 HIS 0.003 0.000 HIS B 524 PHE 0.036 0.001 PHE A 162 TYR 0.023 0.001 TYR B 2 ARG 0.002 0.000 ARG B 238 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.1545 time to fit residues: 20.8391 Evaluate side-chains 62 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 0.769 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 62 optimal weight: 0.9990 chunk 48 optimal weight: 0.0970 chunk 70 optimal weight: 1.9990 chunk 106 optimal weight: 0.0170 chunk 98 optimal weight: 0.7980 chunk 84 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 67 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 7586 Z= 0.139 Angle : 0.531 10.858 10390 Z= 0.261 Chirality : 0.040 0.155 1298 Planarity : 0.003 0.025 1334 Dihedral : 6.327 131.441 1137 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 0.96 (0.27), residues: 1052 helix: 2.01 (0.24), residues: 488 sheet: -0.08 (0.36), residues: 219 loop : -0.85 (0.36), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 22 HIS 0.003 0.000 HIS B 524 PHE 0.036 0.001 PHE A 162 TYR 0.020 0.001 TYR A 399 ARG 0.003 0.000 ARG B 238 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2104 Ramachandran restraints generated. 1052 Oldfield, 0 Emsley, 1052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.1400 time to fit residues: 18.1380 Evaluate side-chains 63 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 0.908 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 26 optimal weight: 0.0070 chunk 78 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 87 optimal weight: 0.0370 chunk 10 optimal weight: 8.9990 chunk 15 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 4 optimal weight: 20.0000 overall best weight: 0.8080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 577 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 600 GLN ** 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 = 0.3158 r_free = 0.3158 target = 0.062836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.052639 restraints weight = 43987.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.054254 restraints weight = 23981.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.055546 restraints weight = 15939.715| |-----------------------------------------------------------------------------| r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2960 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2960 r_free = 0.2960 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2953 r_free = 0.2953 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.2953 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 7586 Z= 0.154 Angle : 0.533 10.123 10390 Z= 0.265 Chirality : 0.041 0.161 1298 Planarity : 0.003 0.028 1334 Dihedral : 6.424 131.965 1137 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 0.98 (0.28), residues: 1052 helix: 1.94 (0.24), residues: 501 sheet: -0.11 (0.36), residues: 219 loop : -0.78 (0.37), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 22 HIS 0.003 0.001 HIS B 524 PHE 0.034 0.001 PHE A 162 TYR 0.023 0.001 TYR A 399 ARG 0.003 0.000 ARG A 306 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1658.55 seconds wall clock time: 30 minutes 55.76 seconds (1855.76 seconds total)