Starting phenix.real_space_refine on Fri Jul 19 11:20:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d9t_30620/07_2024/7d9t_30620.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d9t_30620/07_2024/7d9t_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_30620/07_2024/7d9t_30620.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d9t_30620/07_2024/7d9t_30620.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d9t_30620/07_2024/7d9t_30620.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d9t_30620/07_2024/7d9t_30620.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 7451 Number of models: 1 Model: "" Number of chains: 3 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: 4174 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 567, 4170 Classifications: {'peptide': 567} Incomplete info: {'truncation_to_alanine': 88} Link IDs: {'PTRANS': 23, 'TRANS': 543} 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: 567, 4170 Classifications: {'peptide': 567} Incomplete info: {'truncation_to_alanine': 88} Link IDs: {'PTRANS': 23, 'TRANS': 543} 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: 4249 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'Z90': 1} Classifications: {'undetermined': 1} 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: 9.59, per 1000 atoms: 1.29 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: 3.08 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... Secondary structure from input PDB file: 37 helices and 10 sheets defined 48.7% alpha, 18.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'A' and resid 70 through 83 Processing helix chain 'A' and resid 85 through 100 Processing helix chain 'A' and resid 115 through 122 Processing helix chain 'A' and resid 128 through 149 Processing helix chain 'A' and resid 158 through 171 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 208 through 227 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 278 through 286 Processing helix chain 'A' and resid 302 through 309 Processing helix chain 'A' and resid 319 through 324 removed outlier: 3.584A pdb=" N TYR A 323 " --> pdb=" O ASN A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 341 removed outlier: 3.642A pdb=" N MET A 341 " --> pdb=" O GLY A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 396 removed outlier: 4.091A pdb=" N GLY A 395 " --> pdb=" O GLU A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 418 removed outlier: 3.679A pdb=" N VAL A 412 " --> pdb=" O ALA A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 458 Processing helix chain 'A' and resid 459 through 469 Processing helix chain 'A' and resid 489 through 497 Processing helix chain 'A' and resid 498 through 521 Processing helix chain 'A' and resid 544 through 561 removed outlier: 3.790A pdb=" N ASP A 561 " --> pdb=" O MET A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 609 removed outlier: 3.762A pdb=" N THR A 602 " --> pdb=" O GLY A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 627 removed outlier: 3.788A pdb=" N LEU A 625 " --> pdb=" O THR A 621 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 29 removed outlier: 4.009A pdb=" N ASN B 6 " --> pdb=" O TYR B 2 " (cutoff:3.500A) 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 44 through 59 removed outlier: 3.923A pdb=" N THR B 48 " --> pdb=" O ASP B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 82 removed outlier: 3.734A pdb=" N ILE B 66 " --> pdb=" O ASN B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 90 Processing helix chain 'B' and resid 93 through 112 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 144 through 157 Processing helix chain 'B' and resid 209 through 217 Processing helix chain 'B' and resid 233 through 240 removed outlier: 3.848A pdb=" N ARG B 238 " --> pdb=" O ASN B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 271 Processing helix chain 'B' and resid 329 through 336 removed outlier: 3.796A pdb=" N LEU B 333 " --> pdb=" O ASN B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 355 Processing helix chain 'B' and resid 359 through 395 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 399 through 409 removed outlier: 3.969A pdb=" N HIS B 408 " --> pdb=" O ASN B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 437 Processing helix chain 'B' and resid 439 through 461 Processing helix chain 'B' and resid 491 through 508 removed outlier: 4.170A pdb=" N GLY B 508 " --> pdb=" O MET B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 557 removed outlier: 3.944A pdb=" N ASN B 548 " --> pdb=" O GLY B 544 " (cutoff:3.500A) Processing helix chain 'B' and resid 566 through 573 Processing sheet with id=AA1, 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=AA2, first strand: chain 'A' and resid 298 through 300 removed outlier: 6.931A pdb=" N MET A 291 " --> pdb=" O LEU A 299 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 523 through 524 removed outlier: 4.529A pdb=" N ASN A 479 " --> pdb=" O GLY A 580 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N GLY A 580 " --> pdb=" O ASN A 479 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 485 through 487 Processing sheet with id=AA5, 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) Processing sheet with id=AA6, first strand: chain 'B' and resid 120 through 124 Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 232 removed outlier: 6.881A pdb=" N ILE B 222 " --> pdb=" O THR B 230 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N CYS B 232 " --> pdb=" O HIS B 220 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N HIS B 220 " --> pdb=" O CYS B 232 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N PHE B 223 " --> pdb=" O ILE B 319 " (cutoff:3.500A) Processing sheet with id=AA8, 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: 3.505A pdb=" N ASN B 419 " --> pdb=" O GLY B 526 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N GLY B 526 " --> pdb=" O ASN B 419 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N THR B 421 " --> pdb=" O HIS B 524 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N HIS B 524 " --> pdb=" O THR B 421 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N LEU B 423 " --> pdb=" O GLY B 522 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N GLY B 522 " --> pdb=" O LEU B 423 " (cutoff:3.500A) Processing sheet with id=AA9, 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: 3.505A pdb=" N ASN B 419 " --> pdb=" O GLY B 526 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N GLY B 526 " --> pdb=" O ASN B 419 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N THR B 421 " --> pdb=" O HIS B 524 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N HIS B 524 " --> pdb=" O THR B 421 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N LEU B 423 " --> pdb=" O GLY B 522 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N GLY B 522 " --> pdb=" O LEU B 423 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N ILE B 521 " --> pdb=" O ASN B 563 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N SER B 565 " --> pdb=" O ILE B 521 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N ILE B 523 " --> 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: 6.070A pdb=" N MET B 599 " --> pdb=" O PRO B 589 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N VAL B 601 " --> pdb=" O ARG B 587 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG B 587 " --> pdb=" O VAL B 601 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 511 through 512 469 hydrogen bonds defined for protein. 1343 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: 2.41 Time building geometry restraints manager: 3.31 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: 1366 2.76 - 3.30: 7435 3.30 - 3.83: 12064 3.83 - 4.37: 12847 4.37 - 4.90: 22726 Nonbonded interactions: 56438 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 56433 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: 4.810 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: 0.000 Extract box with map and model: 1.540 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 30.160 Find NCS groups from input model: 0.120 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:2.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.070 ------------------------------------------------------------------------------- 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= 0.184 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 : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 319 ASN cc_start: 0.8093 (t0) cc_final: 0.7783 (t0) REVERT: A 321 GLU cc_start: 0.7944 (pm20) cc_final: 0.7084 (pm20) REVERT: A 333 GLN cc_start: 0.8954 (pt0) cc_final: 0.8561 (pt0) REVERT: A 455 CYS cc_start: 0.8622 (p) cc_final: 0.8380 (p) REVERT: A 524 LYS cc_start: 0.9199 (tttt) cc_final: 0.8982 (ttmt) REVERT: B 38 LEU cc_start: 0.8927 (tt) cc_final: 0.8496 (mp) REVERT: B 65 GLU cc_start: 0.8831 (tp30) cc_final: 0.8579 (tp30) REVERT: B 69 MET cc_start: 0.8682 (mtp) cc_final: 0.8143 (mtm) REVERT: B 96 GLU cc_start: 0.9008 (mp0) cc_final: 0.8646 (mp0) REVERT: B 406 LEU cc_start: 0.9541 (tp) cc_final: 0.9294 (tt) REVERT: B 473 GLU cc_start: 0.8071 (pp20) cc_final: 0.7822 (tp30) outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.1934 time to fit residues: 27.3393 Evaluate side-chains 70 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 0.869 ------------------------------------------------------------------------------- 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: 0.9990 chunk 81 optimal weight: 0.0020 chunk 45 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 54 optimal weight: 0.0670 chunk 43 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 50 optimal weight: 20.0000 chunk 62 optimal weight: 0.9980 chunk 97 optimal weight: 8.9990 overall best weight: 0.5926 ------------------------------------------------------------------------------- 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 7 HIS 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.1201 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= 0.156 Angle : 0.541 8.049 10390 Z= 0.277 Chirality : 0.040 0.142 1298 Planarity : 0.004 0.034 1334 Dihedral : 6.370 135.475 1137 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.15 % Allowed : 3.05 % Favored : 96.80 % 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: -0.78 (0.26), residues: 1052 helix: 0.70 (0.23), residues: 512 sheet: -1.27 (0.33), residues: 213 loop : -1.83 (0.34), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 602 HIS 0.004 0.001 HIS B 437 PHE 0.027 0.001 PHE A 162 TYR 0.015 0.001 TYR A 399 ARG 0.007 0.001 ARG A 306 *********************** 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 88 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 87 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 319 ASN cc_start: 0.7992 (t0) cc_final: 0.7623 (t0) REVERT: A 321 GLU cc_start: 0.7996 (pm20) cc_final: 0.6995 (pm20) REVERT: B 65 GLU cc_start: 0.8821 (tp30) cc_final: 0.8473 (tp30) REVERT: B 69 MET cc_start: 0.8718 (mtp) cc_final: 0.8136 (mtm) REVERT: B 96 GLU cc_start: 0.9095 (mp0) cc_final: 0.8639 (mp0) REVERT: B 473 GLU cc_start: 0.8047 (pp20) cc_final: 0.7787 (tp30) REVERT: B 480 MET cc_start: 0.9267 (ttp) cc_final: 0.8441 (ttp) outliers start: 1 outliers final: 0 residues processed: 88 average time/residue: 0.1644 time to fit residues: 20.9216 Evaluate side-chains 67 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 0.961 ------------------------------------------------------------------------------- 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: 10.0000 chunk 30 optimal weight: 0.9980 chunk 80 optimal weight: 0.0570 chunk 66 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 97 optimal weight: 4.9990 chunk 105 optimal weight: 6.9990 chunk 86 optimal weight: 0.0670 chunk 96 optimal weight: 0.9980 chunk 33 optimal weight: 8.9990 chunk 78 optimal weight: 1.9990 overall best weight: 0.5636 ------------------------------------------------------------------------------- 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: 0.8145 moved from start: 0.1527 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= 0.152 Angle : 0.533 8.221 10390 Z= 0.268 Chirality : 0.040 0.156 1298 Planarity : 0.003 0.031 1334 Dihedral : 6.300 134.073 1137 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % 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: -0.22 (0.27), residues: 1052 helix: 1.18 (0.23), residues: 513 sheet: -0.95 (0.33), residues: 221 loop : -1.64 (0.36), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 602 HIS 0.004 0.001 HIS B 437 PHE 0.021 0.001 PHE A 162 TYR 0.017 0.001 TYR A 399 ARG 0.004 0.000 ARG A 349 *********************** 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 : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 65 GLU cc_start: 0.8843 (tp30) cc_final: 0.8372 (tp30) REVERT: B 69 MET cc_start: 0.8711 (mtp) cc_final: 0.8081 (mtm) REVERT: B 96 GLU cc_start: 0.9093 (mp0) cc_final: 0.8538 (mp0) REVERT: B 473 GLU cc_start: 0.8115 (pp20) cc_final: 0.7730 (tp30) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.1286 time to fit residues: 17.5335 Evaluate side-chains 63 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 0.861 ------------------------------------------------------------------------------- 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: 7.9990 chunk 73 optimal weight: 7.9990 chunk 50 optimal weight: 0.0020 chunk 10 optimal weight: 5.9990 chunk 46 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 97 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 overall best weight: 1.7792 ------------------------------------------------------------------------------- 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: 0.8187 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 7586 Z= 0.239 Angle : 0.582 8.678 10390 Z= 0.298 Chirality : 0.042 0.161 1298 Planarity : 0.004 0.041 1334 Dihedral : 6.450 136.416 1137 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % 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: 0.09 (0.27), residues: 1052 helix: 1.46 (0.24), residues: 509 sheet: -0.95 (0.34), residues: 223 loop : -1.39 (0.37), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 22 HIS 0.005 0.001 HIS B 437 PHE 0.023 0.002 PHE A 162 TYR 0.016 0.002 TYR A 399 ARG 0.005 0.001 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 77 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 319 ASN cc_start: 0.8211 (t0) cc_final: 0.7688 (t0) REVERT: A 321 GLU cc_start: 0.8106 (pm20) cc_final: 0.7736 (pm20) REVERT: A 339 MET cc_start: 0.9448 (tpp) cc_final: 0.9077 (tpp) REVERT: B 65 GLU cc_start: 0.8910 (tp30) cc_final: 0.8434 (tp30) REVERT: B 69 MET cc_start: 0.8714 (mtp) cc_final: 0.8102 (mtm) REVERT: B 96 GLU cc_start: 0.9102 (mp0) cc_final: 0.8632 (mp0) REVERT: B 473 GLU cc_start: 0.8132 (pp20) cc_final: 0.7839 (tp30) REVERT: B 480 MET cc_start: 0.9212 (ttp) cc_final: 0.8673 (ttp) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.1310 time to fit residues: 15.7068 Evaluate side-chains 62 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 0.834 ------------------------------------------------------------------------------- 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: 0.0470 chunk 58 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 chunk 77 optimal weight: 0.6980 chunk 42 optimal weight: 0.0470 chunk 88 optimal weight: 6.9990 chunk 71 optimal weight: 4.9990 chunk 0 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 26 optimal weight: 0.4980 overall best weight: 0.3976 ------------------------------------------------------------------------------- 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: 0.8133 moved from start: 0.1935 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= 0.148 Angle : 0.544 8.677 10390 Z= 0.273 Chirality : 0.040 0.141 1298 Planarity : 0.003 0.032 1334 Dihedral : 6.410 132.712 1137 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % 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: 0.35 (0.27), residues: 1052 helix: 1.68 (0.24), residues: 502 sheet: -0.70 (0.34), residues: 224 loop : -1.32 (0.36), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 22 HIS 0.003 0.001 HIS B 437 PHE 0.040 0.002 PHE A 162 TYR 0.020 0.001 TYR A 399 ARG 0.003 0.000 ARG B 238 *********************** 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 79 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 192 CYS cc_start: 0.9109 (t) cc_final: 0.8224 (p) REVERT: A 319 ASN cc_start: 0.8152 (t0) cc_final: 0.7679 (t0) REVERT: B 65 GLU cc_start: 0.8821 (tp30) cc_final: 0.8453 (tp30) REVERT: B 69 MET cc_start: 0.8693 (mtp) cc_final: 0.8121 (mtm) REVERT: B 96 GLU cc_start: 0.9082 (mp0) cc_final: 0.8541 (mp0) REVERT: B 473 GLU cc_start: 0.8247 (pp20) cc_final: 0.7944 (tp30) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.1334 time to fit residues: 16.2870 Evaluate side-chains 66 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 0.838 ------------------------------------------------------------------------------- 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: 4.9990 chunk 93 optimal weight: 4.9990 chunk 20 optimal weight: 0.0030 chunk 60 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 103 optimal weight: 0.6980 chunk 85 optimal weight: 5.9990 chunk 47 optimal weight: 0.8980 chunk 8 optimal weight: 0.4980 chunk 54 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 overall best weight: 0.8192 ------------------------------------------------------------------------------- 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: 0.8142 moved from start: 0.2027 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= 0.163 Angle : 0.545 8.980 10390 Z= 0.276 Chirality : 0.041 0.178 1298 Planarity : 0.003 0.034 1334 Dihedral : 6.411 132.746 1137 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % 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: 0.53 (0.27), residues: 1052 helix: 1.79 (0.24), residues: 504 sheet: -0.61 (0.34), residues: 226 loop : -1.18 (0.37), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 22 HIS 0.004 0.001 HIS B 437 PHE 0.035 0.001 PHE A 162 TYR 0.018 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 79 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 1.332 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 192 CYS cc_start: 0.9087 (t) cc_final: 0.8244 (p) REVERT: A 319 ASN cc_start: 0.8264 (t0) cc_final: 0.7854 (t0) REVERT: B 65 GLU cc_start: 0.8826 (tp30) cc_final: 0.8455 (tp30) REVERT: B 69 MET cc_start: 0.8692 (mtp) cc_final: 0.8133 (mtm) REVERT: B 96 GLU cc_start: 0.9083 (mp0) cc_final: 0.8542 (mp0) REVERT: B 473 GLU cc_start: 0.8222 (pp20) cc_final: 0.7924 (tp30) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.1462 time to fit residues: 17.9865 Evaluate side-chains 65 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 0.872 ------------------------------------------------------------------------------- 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: 3.9990 chunk 58 optimal weight: 0.8980 chunk 75 optimal weight: 5.9990 chunk 87 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 chunk 103 optimal weight: 4.9990 chunk 64 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 47 optimal weight: 0.0770 chunk 63 optimal weight: 0.9980 chunk 41 optimal weight: 0.2980 overall best weight: 0.6538 ------------------------------------------------------------------------------- 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: 0.8131 moved from start: 0.2163 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= 0.152 Angle : 0.533 9.187 10390 Z= 0.270 Chirality : 0.040 0.166 1298 Planarity : 0.003 0.033 1334 Dihedral : 6.407 132.029 1137 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % 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: 0.74 (0.28), residues: 1052 helix: 1.96 (0.24), residues: 498 sheet: -0.44 (0.35), residues: 224 loop : -1.09 (0.37), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 22 HIS 0.003 0.001 HIS B 437 PHE 0.029 0.002 PHE A 162 TYR 0.018 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 82 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 CYS cc_start: 0.9124 (t) cc_final: 0.8329 (p) REVERT: A 319 ASN cc_start: 0.8303 (t0) cc_final: 0.7892 (t0) REVERT: B 65 GLU cc_start: 0.8821 (tp30) cc_final: 0.8315 (tp30) REVERT: B 69 MET cc_start: 0.8685 (mtp) cc_final: 0.8082 (mtm) REVERT: B 96 GLU cc_start: 0.9071 (mp0) cc_final: 0.8547 (mp0) REVERT: B 473 GLU cc_start: 0.8230 (pp20) cc_final: 0.7894 (tp30) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1354 time to fit residues: 17.4168 Evaluate side-chains 63 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 1.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 51.5396 > 50: distance: 12 - 17: 6.780 distance: 17 - 18: 12.856 distance: 17 - 137: 8.563 distance: 18 - 19: 9.559 distance: 18 - 21: 22.666 distance: 19 - 20: 11.286 distance: 19 - 22: 20.442 distance: 20 - 134: 4.723 distance: 22 - 23: 8.740 distance: 23 - 24: 21.103 distance: 23 - 26: 13.802 distance: 24 - 25: 20.577 distance: 24 - 30: 17.342 distance: 26 - 27: 31.129 distance: 26 - 28: 16.487 distance: 27 - 29: 31.324 distance: 30 - 31: 8.027 distance: 31 - 32: 16.259 distance: 31 - 34: 12.022 distance: 32 - 33: 9.615 distance: 32 - 38: 9.514 distance: 34 - 35: 18.457 distance: 35 - 36: 19.880 distance: 35 - 37: 16.244 distance: 38 - 39: 20.609 distance: 39 - 40: 17.482 distance: 39 - 42: 18.078 distance: 40 - 41: 19.783 distance: 40 - 45: 23.362 distance: 42 - 43: 19.616 distance: 42 - 44: 23.280 distance: 45 - 46: 14.558 distance: 45 - 51: 13.945 distance: 46 - 47: 14.447 distance: 46 - 49: 12.572 distance: 47 - 48: 19.721 distance: 47 - 52: 16.645 distance: 49 - 50: 9.804 distance: 50 - 51: 19.624 distance: 52 - 53: 13.284 distance: 53 - 54: 13.827 distance: 53 - 56: 16.572 distance: 54 - 55: 12.502 distance: 54 - 57: 10.666 distance: 57 - 58: 9.042 distance: 58 - 59: 7.161 distance: 58 - 61: 3.995 distance: 59 - 60: 10.195 distance: 59 - 65: 16.983 distance: 61 - 62: 17.268 distance: 61 - 63: 14.099 distance: 62 - 64: 15.089 distance: 65 - 66: 13.894 distance: 66 - 67: 10.125 distance: 66 - 69: 8.458 distance: 67 - 68: 13.791 distance: 67 - 73: 7.080 distance: 69 - 70: 14.427 distance: 70 - 71: 9.735 distance: 70 - 72: 18.279 distance: 73 - 74: 8.487 distance: 74 - 75: 12.681 distance: 75 - 76: 18.119 distance: 75 - 82: 11.607 distance: 77 - 78: 9.439 distance: 78 - 79: 7.143 distance: 79 - 80: 6.295 distance: 79 - 81: 9.026 distance: 82 - 83: 8.377 distance: 83 - 84: 9.133 distance: 83 - 86: 17.718 distance: 84 - 85: 8.789 distance: 84 - 89: 12.069 distance: 85 - 103: 18.642 distance: 86 - 87: 8.355 distance: 86 - 88: 13.773