Starting phenix.real_space_refine on Fri Dec 8 11:08:20 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d9u_30621/12_2023/7d9u_30621_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d9u_30621/12_2023/7d9u_30621.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d9u_30621/12_2023/7d9u_30621.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d9u_30621/12_2023/7d9u_30621.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d9u_30621/12_2023/7d9u_30621_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d9u_30621/12_2023/7d9u_30621_updated.pdb" } resolution = 3.8 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: 6 Type Number sf(0) Gaussians P 3 5.49 5 Mg 2 5.21 5 S 56 5.16 5 C 5264 2.51 5 N 1389 2.21 5 O 1476 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 68": "NH1" <-> "NH2" Residue "A GLU 138": "OE1" <-> "OE2" Residue "A GLU 149": "OE1" <-> "OE2" Residue "A ASP 161": "OD1" <-> "OD2" Residue "A TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 365": "OD1" <-> "OD2" Residue "A ASP 452": "OD1" <-> "OD2" Residue "A PHE 458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 486": "OD1" <-> "OD2" Residue "A TYR 532": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 583": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 614": "NH1" <-> "NH2" Residue "A PHE 632": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 24": "OD1" <-> "OD2" Residue "B ASP 44": "OD1" <-> "OD2" Residue "B ASP 45": "OD1" <-> "OD2" Residue "B GLU 65": "OE1" <-> "OE2" Residue "B PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 331": "OD1" <-> "OD2" Residue "B ASP 347": "OD1" <-> "OD2" Residue "B ARG 350": "NH1" <-> "NH2" Residue "B ARG 381": "NH1" <-> "NH2" Residue "B ASP 385": "OD1" <-> "OD2" Residue "B GLU 405": "OE1" <-> "OE2" Residue "B TYR 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 567": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 8190 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 3742 Classifications: {'peptide': 506} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PTRANS': 23, 'TRANS': 482} Chain breaks: 8 Unresolved non-hydrogen bonds: 261 Unresolved non-hydrogen angles: 319 Unresolved non-hydrogen dihedrals: 216 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 7, 'PHE:plan': 4, 'GLU:plan': 16, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 162 Chain: "B" Number of atoms: 4372 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 569, 4368 Classifications: {'peptide': 569} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 545} Chain breaks: 3 Unresolved non-hydrogen bonds: 182 Unresolved non-hydrogen angles: 218 Unresolved non-hydrogen dihedrals: 148 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 20, 'HIS:plan': 1, 'ARG:plan': 4, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 138 Conformer: "B" Number of residues, atoms: 569, 4368 Classifications: {'peptide': 569} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 545} Chain breaks: 3 Unresolved non-hydrogen bonds: 182 Unresolved non-hydrogen angles: 218 Unresolved non-hydrogen dihedrals: 148 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 20, 'HIS:plan': 1, 'ARG:plan': 4, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 138 bond proxies already assigned to first conformer: 4452 Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 34 Unusual residues: {' MG': 2, 'G2P': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 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: 1 residue: pdb=" N LEU A 254 " occ=0.92 ... (3 atoms not shown) pdb=" CB LEU A 254 " occ=0.92 Time building chain proxies: 6.81, per 1000 atoms: 0.83 Number of scatterers: 8190 At special positions: 0 Unit cell: (99.275, 137.94, 137.94, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 56 16.00 P 3 15.00 Mg 2 11.99 O 1476 8.00 N 1389 7.00 C 5264 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: 3.42 Conformation dependent library (CDL) restraints added in 2.5 seconds 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2026 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 38 helices and 10 sheets defined 43.8% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.72 Creating SS restraints... Processing helix chain 'A' and resid 71 through 82 Processing helix chain 'A' and resid 86 through 100 Processing helix chain 'A' and resid 115 through 125 Processing helix chain 'A' and resid 129 through 145 Processing helix chain 'A' and resid 159 through 170 removed outlier: 3.892A pdb=" N PHE A 166 " --> pdb=" O PHE A 162 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N SER A 167 " --> pdb=" O LEU A 163 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N THR A 168 " --> pdb=" O ASN A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 225 Processing helix chain 'A' and resid 279 through 285 Processing helix chain 'A' and resid 303 through 308 Processing helix chain 'A' and resid 335 through 340 Processing helix chain 'A' and resid 400 through 402 No H-bonds generated for 'chain 'A' and resid 400 through 402' Processing helix chain 'A' and resid 409 through 457 Processing helix chain 'A' and resid 460 through 467 Processing helix chain 'A' and resid 490 through 496 Processing helix chain 'A' and resid 499 through 518 Processing helix chain 'A' and resid 545 through 562 removed outlier: 3.623A pdb=" N GLU A 562 " --> pdb=" O GLU A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 609 Processing helix chain 'A' and resid 620 through 626 Processing helix chain 'B' and resid 3 through 28 Proline residue: B 19 - end of helix removed outlier: 3.820A 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: 4.597A pdb=" N ASP B 102 " --> pdb=" O LEU B 98 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N ALA B 103 " --> pdb=" O GLN B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 157 Processing helix chain 'B' and resid 210 through 216 Processing helix chain 'B' and resid 236 through 239 No H-bonds generated for 'chain 'B' and resid 236 through 239' Processing helix chain 'B' and resid 241 through 244 No H-bonds generated for 'chain 'B' and resid 241 through 244' Processing helix chain 'B' and resid 250 through 253 No H-bonds generated for 'chain 'B' and resid 250 through 253' Processing helix chain 'B' and resid 265 through 270 Processing helix chain 'B' and resid 282 through 284 No H-bonds generated for 'chain 'B' and resid 282 through 284' Processing helix chain 'B' and resid 330 through 334 Processing helix chain 'B' and resid 340 through 342 No H-bonds generated for 'chain 'B' and resid 340 through 342' Processing helix chain 'B' and resid 348 through 397 removed outlier: 4.188A pdb=" N VAL B 353 " --> pdb=" O ARG B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 407 Processing helix chain 'B' and resid 430 through 436 Processing helix chain 'B' and resid 443 through 460 Processing helix chain 'B' and resid 492 through 506 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 202 through 204 Processing sheet with id= B, first strand: chain 'A' and resid 289 through 292 removed outlier: 3.745A pdb=" N PHE A 290 " --> pdb=" O PHE A 381 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE A 292 " --> pdb=" O ILE A 379 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLY A 368 " --> pdb=" O PHE A 346 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 575 through 580 removed outlier: 3.546A pdb=" N PHE A 484 " --> pdb=" O GLY A 576 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR A 481 " --> pdb=" O GLY A 536 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N CYS A 533 " --> pdb=" O VAL A 525 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 583 through 586 Processing sheet with id= E, first strand: chain 'B' and resid 119 through 124 removed outlier: 3.617A pdb=" N ARG B 121 " --> pdb=" O HIS B 134 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 162 through 164 removed outlier: 3.941A pdb=" N ASP B 163 " --> pdb=" O GLU B 182 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLU B 182 " --> pdb=" O ASP B 163 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'B' and resid 220 through 223 removed outlier: 3.658A pdb=" N PHE B 223 " --> pdb=" O ILE B 319 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE B 319 " --> pdb=" O PHE B 223 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 415 through 417 removed outlier: 3.686A pdb=" N GLY B 531 " --> pdb=" O CYS B 541 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N CYS B 541 " --> pdb=" O GLY B 531 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 478 through 482 removed outlier: 3.591A pdb=" N ILE B 422 " --> pdb=" O HIS B 524 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N HIS B 524 " --> pdb=" O ILE B 422 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 563 through 565 383 hydrogen bonds defined for protein. 972 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: 2.30 Time building geometry restraints manager: 3.61 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: 2635 1.34 - 1.46: 1766 1.46 - 1.58: 3858 1.58 - 1.69: 5 1.69 - 1.81: 86 Bond restraints: 8350 Sorted by residual: bond pdb=" O3B G2P A1001 " pdb=" PG G2P A1001 " ideal model delta sigma weight residual 1.716 1.606 0.110 2.00e-02 2.50e+03 3.02e+01 bond pdb=" O1A G2P A1001 " pdb=" PA G2P A1001 " ideal model delta sigma weight residual 1.507 1.608 -0.101 2.00e-02 2.50e+03 2.57e+01 bond pdb=" O1B G2P A1001 " pdb=" PB G2P A1001 " ideal model delta sigma weight residual 1.510 1.608 -0.098 2.00e-02 2.50e+03 2.43e+01 bond pdb=" C4 G2P A1001 " pdb=" C5 G2P A1001 " ideal model delta sigma weight residual 1.384 1.467 -0.083 2.00e-02 2.50e+03 1.72e+01 bond pdb=" CBN Z90 B 701 " pdb=" CBO Z90 B 701 " ideal model delta sigma weight residual 1.405 1.480 -0.075 2.00e-02 2.50e+03 1.39e+01 ... (remaining 8345 not shown) Histogram of bond angle deviations from ideal: 100.46 - 107.58: 300 107.58 - 114.70: 5029 114.70 - 121.82: 4310 121.82 - 128.94: 1662 128.94 - 136.06: 42 Bond angle restraints: 11343 Sorted by residual: angle pdb=" C3A G2P A1001 " pdb=" PB G2P A1001 " pdb=" O3B G2P A1001 " ideal model delta sigma weight residual 99.71 111.00 -11.29 3.00e+00 1.11e-01 1.42e+01 angle pdb=" PA G2P A1001 " pdb=" C3A G2P A1001 " pdb=" PB G2P A1001 " ideal model delta sigma weight residual 120.83 110.32 10.51 3.00e+00 1.11e-01 1.23e+01 angle pdb=" C3A G2P A1001 " pdb=" PA G2P A1001 " pdb=" O5' G2P A1001 " ideal model delta sigma weight residual 99.14 109.41 -10.27 3.00e+00 1.11e-01 1.17e+01 angle pdb=" C5 G2P A1001 " pdb=" C4 G2P A1001 " pdb=" N3 G2P A1001 " ideal model delta sigma weight residual 128.08 118.68 9.40 3.00e+00 1.11e-01 9.81e+00 angle pdb=" N3 G2P A1001 " pdb=" C4 G2P A1001 " pdb=" N9 G2P A1001 " ideal model delta sigma weight residual 126.73 134.95 -8.22 3.00e+00 1.11e-01 7.51e+00 ... (remaining 11338 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.93: 4833 24.93 - 49.86: 153 49.86 - 74.80: 11 74.80 - 99.73: 2 99.73 - 124.66: 2 Dihedral angle restraints: 5001 sinusoidal: 1878 harmonic: 3123 Sorted by residual: 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 -55.93 -124.66 1 3.00e+01 1.11e-03 1.67e+01 dihedral pdb=" CAW Z90 B 701 " pdb=" CBB Z90 B 701 " pdb=" NBP Z90 B 701 " pdb=" CBC Z90 B 701 " ideal model delta sinusoidal sigma weight residual -158.43 -36.24 -122.19 1 3.00e+01 1.11e-03 1.63e+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 180.00 164.21 15.79 0 5.00e+00 4.00e-02 9.97e+00 ... (remaining 4998 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 875 0.032 - 0.063: 316 0.063 - 0.095: 101 0.095 - 0.127: 46 0.127 - 0.158: 4 Chirality restraints: 1342 Sorted by residual: chirality pdb=" C1' G2P A1001 " pdb=" C2' G2P A1001 " pdb=" N9 G2P A1001 " pdb=" O4' G2P A1001 " both_signs ideal model delta sigma weight residual False 2.36 2.52 -0.16 2.00e-01 2.50e+01 6.26e-01 chirality pdb=" CA PRO B 210 " pdb=" N PRO B 210 " pdb=" C PRO B 210 " pdb=" CB PRO B 210 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 5.10e-01 chirality pdb=" C2' G2P A1001 " pdb=" C1' G2P A1001 " pdb=" C3' G2P A1001 " pdb=" O2' G2P A1001 " both_signs ideal model delta sigma weight residual False -2.48 -2.62 0.14 2.00e-01 2.50e+01 5.01e-01 ... (remaining 1339 not shown) Planarity restraints: 1431 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 565 " -0.022 5.00e-02 4.00e+02 3.38e-02 1.83e+00 pdb=" N PRO A 566 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 566 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 566 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER A 485 " 0.005 2.00e-02 2.50e+03 1.09e-02 1.19e+00 pdb=" C SER A 485 " -0.019 2.00e-02 2.50e+03 pdb=" O SER A 485 " 0.007 2.00e-02 2.50e+03 pdb=" N ASP A 486 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 642 " 0.018 5.00e-02 4.00e+02 2.72e-02 1.19e+00 pdb=" N PRO A 643 " -0.047 5.00e-02 4.00e+02 pdb=" CA PRO A 643 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 643 " 0.015 5.00e-02 4.00e+02 ... (remaining 1428 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 506 2.73 - 3.27: 8642 3.27 - 3.81: 13447 3.81 - 4.36: 15306 4.36 - 4.90: 26692 Nonbonded interactions: 64593 Sorted by model distance: nonbonded pdb=" O1A G2P A1001 " pdb=" O3B G2P A1001 " model vdw 2.187 3.040 nonbonded pdb=" OG SER B 280 " pdb=" O CYS B 303 " model vdw 2.213 2.440 nonbonded pdb=" O LEU A 520 " pdb=" NE2 GLN A 548 " model vdw 2.239 2.520 nonbonded pdb=" OD1 ASN B 6 " pdb=" OG1 THR B 48 " model vdw 2.243 2.440 nonbonded pdb=" OD1 ASP A 486 " pdb="MG MG A1003 " model vdw 2.245 2.170 ... (remaining 64588 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: 0.910 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: 3.320 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 28.860 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 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 : 0.004 0.110 8350 Z= 0.272 Angle : 0.592 11.289 11343 Z= 0.292 Chirality : 0.040 0.158 1342 Planarity : 0.003 0.034 1431 Dihedral : 12.325 124.661 2975 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.43 % Favored : 96.47 % Rotamer: Outliers : 0.12 % Allowed : 4.72 % Favored : 95.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.24), residues: 1049 helix: -0.18 (0.21), residues: 476 sheet: -2.02 (0.35), residues: 189 loop : -2.55 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 22 HIS 0.002 0.001 HIS A 539 PHE 0.012 0.001 PHE A 607 TYR 0.011 0.001 TYR B 2 ARG 0.001 0.000 ARG A 88 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 144 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 145 average time/residue: 0.1883 time to fit residues: 38.0613 Evaluate side-chains 98 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 0.954 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 0.6980 chunk 80 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 54 optimal weight: 4.9990 chunk 42 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 96 optimal weight: 3.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS A 303 ASN A 422 GLN B 99 GLN B 242 GLN B 266 HIS B 346 HIS B 408 HIS ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 451 ASN B 466 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.1303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8350 Z= 0.200 Angle : 0.559 8.654 11343 Z= 0.287 Chirality : 0.041 0.148 1342 Planarity : 0.005 0.039 1431 Dihedral : 8.648 127.172 1189 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.06 % Allowed : 14.17 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.25), residues: 1049 helix: 0.44 (0.23), residues: 479 sheet: -1.72 (0.37), residues: 182 loop : -2.07 (0.31), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.004 TRP B 602 HIS 0.012 0.001 HIS B 266 PHE 0.019 0.002 PHE A 458 TYR 0.037 0.001 TYR B 569 ARG 0.003 0.000 ARG B 139 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 107 time to evaluate : 1.026 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 3 residues processed: 111 average time/residue: 0.1398 time to fit residues: 24.4127 Evaluate side-chains 102 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 99 time to evaluate : 0.994 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0764 time to fit residues: 1.6165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 53 optimal weight: 10.0000 chunk 29 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 chunk 104 optimal weight: 8.9990 chunk 85 optimal weight: 0.4980 chunk 95 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 HIS B 99 GLN ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8350 Z= 0.248 Angle : 0.560 8.006 11343 Z= 0.284 Chirality : 0.041 0.147 1342 Planarity : 0.004 0.040 1431 Dihedral : 8.704 130.745 1189 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.77 % Allowed : 15.47 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.26), residues: 1049 helix: 0.51 (0.23), residues: 479 sheet: -1.45 (0.37), residues: 183 loop : -1.90 (0.31), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP B 602 HIS 0.003 0.001 HIS B 105 PHE 0.023 0.002 PHE B 433 TYR 0.023 0.001 TYR B 569 ARG 0.003 0.000 ARG B 139 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 94 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 6 residues processed: 102 average time/residue: 0.1341 time to fit residues: 21.6468 Evaluate side-chains 96 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 90 time to evaluate : 0.769 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0770 time to fit residues: 1.9796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 4.9990 chunk 72 optimal weight: 0.6980 chunk 50 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 46 optimal weight: 0.0870 chunk 64 optimal weight: 0.8980 chunk 96 optimal weight: 0.9990 chunk 102 optimal weight: 0.3980 chunk 91 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 chunk 85 optimal weight: 1.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 464 GLN B 99 GLN ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8350 Z= 0.163 Angle : 0.534 9.134 11343 Z= 0.269 Chirality : 0.041 0.155 1342 Planarity : 0.004 0.040 1431 Dihedral : 8.726 130.249 1189 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.53 % Allowed : 16.17 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.26), residues: 1049 helix: 0.61 (0.23), residues: 479 sheet: -1.20 (0.38), residues: 183 loop : -1.76 (0.31), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP B 602 HIS 0.005 0.001 HIS B 437 PHE 0.030 0.001 PHE B 433 TYR 0.020 0.001 TYR B 479 ARG 0.002 0.000 ARG B 139 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 99 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 3 residues processed: 104 average time/residue: 0.1431 time to fit residues: 23.4830 Evaluate side-chains 93 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 90 time to evaluate : 0.973 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0843 time to fit residues: 1.7959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 58 optimal weight: 0.0270 chunk 1 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 chunk 42 optimal weight: 0.9990 chunk 87 optimal weight: 4.9990 chunk 70 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 91 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 34 optimal weight: 10.0000 overall best weight: 0.7240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 GLN ** B 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8350 Z= 0.186 Angle : 0.546 8.430 11343 Z= 0.277 Chirality : 0.041 0.227 1342 Planarity : 0.004 0.040 1431 Dihedral : 8.727 129.435 1189 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.06 % Allowed : 17.12 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.26), residues: 1049 helix: 0.71 (0.24), residues: 478 sheet: -1.06 (0.38), residues: 183 loop : -1.66 (0.31), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP B 602 HIS 0.002 0.001 HIS B 524 PHE 0.018 0.001 PHE A 458 TYR 0.018 0.001 TYR B 479 ARG 0.001 0.000 ARG B 139 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 95 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 3 residues processed: 101 average time/residue: 0.1378 time to fit residues: 22.2758 Evaluate side-chains 91 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 88 time to evaluate : 0.969 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0829 time to fit residues: 1.7579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 92 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 chunk 102 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 53 optimal weight: 0.0170 chunk 98 optimal weight: 4.9990 overall best weight: 2.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 HIS A 406 HIS B 99 GLN ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 8350 Z= 0.404 Angle : 0.635 8.268 11343 Z= 0.327 Chirality : 0.044 0.165 1342 Planarity : 0.004 0.040 1431 Dihedral : 9.049 128.269 1189 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 1.42 % Allowed : 18.30 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.26), residues: 1049 helix: 0.73 (0.24), residues: 477 sheet: -1.01 (0.38), residues: 186 loop : -1.69 (0.32), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP B 602 HIS 0.006 0.001 HIS A 289 PHE 0.030 0.002 PHE A 458 TYR 0.017 0.002 TYR A 203 ARG 0.004 0.000 ARG B 139 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 83 time to evaluate : 0.965 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 8 residues processed: 88 average time/residue: 0.1411 time to fit residues: 19.9531 Evaluate side-chains 90 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 82 time to evaluate : 0.875 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0788 time to fit residues: 2.3235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 11 optimal weight: 0.0370 chunk 58 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 chunk 57 optimal weight: 0.6980 chunk 102 optimal weight: 6.9990 chunk 63 optimal weight: 0.8980 chunk 62 optimal weight: 0.7980 chunk 47 optimal weight: 4.9990 chunk 40 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 GLN B 437 HIS ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8350 Z= 0.177 Angle : 0.555 8.373 11343 Z= 0.281 Chirality : 0.041 0.156 1342 Planarity : 0.004 0.040 1431 Dihedral : 8.798 129.181 1189 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.59 % Allowed : 19.01 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.26), residues: 1049 helix: 0.83 (0.24), residues: 477 sheet: -0.87 (0.38), residues: 185 loop : -1.53 (0.32), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP B 602 HIS 0.005 0.001 HIS B 437 PHE 0.034 0.002 PHE B 433 TYR 0.017 0.001 TYR B 479 ARG 0.001 0.000 ARG B 539 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 90 time to evaluate : 1.154 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 93 average time/residue: 0.1628 time to fit residues: 24.3503 Evaluate side-chains 82 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 81 time to evaluate : 0.985 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1785 time to fit residues: 2.3330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 30 optimal weight: 0.4980 chunk 20 optimal weight: 4.9990 chunk 19 optimal weight: 0.0570 chunk 64 optimal weight: 0.2980 chunk 69 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 97 optimal weight: 0.6980 chunk 89 optimal weight: 0.9980 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 GLN ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8350 Z= 0.164 Angle : 0.545 8.205 11343 Z= 0.276 Chirality : 0.040 0.147 1342 Planarity : 0.004 0.039 1431 Dihedral : 8.605 129.224 1189 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 0.59 % Allowed : 19.60 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.26), residues: 1049 helix: 0.90 (0.24), residues: 476 sheet: -0.59 (0.39), residues: 178 loop : -1.48 (0.32), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 602 HIS 0.002 0.000 HIS A 539 PHE 0.028 0.001 PHE A 458 TYR 0.016 0.001 TYR B 479 ARG 0.001 0.000 ARG B 539 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 88 time to evaluate : 0.998 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 90 average time/residue: 0.1433 time to fit residues: 20.4297 Evaluate side-chains 86 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 83 time to evaluate : 0.941 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0848 time to fit residues: 1.7266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 0.0050 chunk 97 optimal weight: 6.9990 chunk 57 optimal weight: 0.5980 chunk 41 optimal weight: 0.0770 chunk 74 optimal weight: 0.6980 chunk 29 optimal weight: 0.7980 chunk 86 optimal weight: 0.8980 chunk 90 optimal weight: 0.0870 chunk 94 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 overall best weight: 0.2930 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 GLN ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 8350 Z= 0.152 Angle : 0.552 9.449 11343 Z= 0.276 Chirality : 0.040 0.167 1342 Planarity : 0.004 0.040 1431 Dihedral : 8.445 130.256 1189 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.47 % Allowed : 20.07 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.26), residues: 1049 helix: 0.88 (0.24), residues: 476 sheet: -0.48 (0.39), residues: 178 loop : -1.42 (0.32), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP B 602 HIS 0.002 0.000 HIS A 539 PHE 0.028 0.002 PHE B 433 TYR 0.016 0.001 TYR B 479 ARG 0.001 0.000 ARG A 624 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 96 time to evaluate : 1.177 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 97 average time/residue: 0.1417 time to fit residues: 22.0239 Evaluate side-chains 88 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 86 time to evaluate : 1.050 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0904 time to fit residues: 1.6450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 61 optimal weight: 0.0870 chunk 47 optimal weight: 4.9990 chunk 69 optimal weight: 0.0170 chunk 105 optimal weight: 5.9990 chunk 97 optimal weight: 0.0370 chunk 84 optimal weight: 0.8980 chunk 8 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 51 optimal weight: 0.5980 chunk 66 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 overall best weight: 0.3274 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 645 ASN B 99 GLN ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 8350 Z= 0.172 Angle : 0.610 12.638 11343 Z= 0.300 Chirality : 0.042 0.251 1342 Planarity : 0.004 0.039 1431 Dihedral : 8.360 131.407 1189 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.12 % Allowed : 21.02 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.26), residues: 1049 helix: 0.83 (0.24), residues: 476 sheet: -0.38 (0.40), residues: 178 loop : -1.41 (0.31), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP B 602 HIS 0.004 0.001 HIS B 7 PHE 0.038 0.001 PHE B 433 TYR 0.017 0.001 TYR B 479 ARG 0.001 0.000 ARG B 15 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 90 time to evaluate : 1.033 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 90 average time/residue: 0.1368 time to fit residues: 19.7520 Evaluate side-chains 89 residues out of total 955 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 88 time to evaluate : 0.897 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0893 time to fit residues: 1.3834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 25 optimal weight: 0.6980 chunk 77 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 84 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 86 optimal weight: 0.0270 chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 73 optimal weight: 4.9990 chunk 4 optimal weight: 20.0000 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 GLN B 105 HIS ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.083892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.068212 restraints weight = 28380.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.070645 restraints weight = 14363.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.072297 restraints weight = 9010.376| |-----------------------------------------------------------------------------| r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3072 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3072 r_free = 0.3072 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3071 r_free = 0.3071 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| r_final: 0.3071 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8350 Z= 0.185 Angle : 0.616 10.920 11343 Z= 0.300 Chirality : 0.042 0.261 1342 Planarity : 0.004 0.039 1431 Dihedral : 8.417 130.501 1189 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 0.12 % Allowed : 21.61 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.26), residues: 1049 helix: 0.82 (0.24), residues: 476 sheet: -0.51 (0.39), residues: 180 loop : -1.37 (0.31), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP B 602 HIS 0.002 0.001 HIS A 539 PHE 0.044 0.002 PHE A 513 TYR 0.014 0.001 TYR A 203 ARG 0.004 0.000 ARG A 512 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1656.49 seconds wall clock time: 31 minutes 8.93 seconds (1868.93 seconds total)