Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 21 16:43:55 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wbv_21599/04_2023/6wbv_21599_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wbv_21599/04_2023/6wbv_21599.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wbv_21599/04_2023/6wbv_21599.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wbv_21599/04_2023/6wbv_21599.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wbv_21599/04_2023/6wbv_21599_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wbv_21599/04_2023/6wbv_21599_updated.pdb" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= -0.013 sd= 0.959 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3344 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Co 2 6.85 5 P 2 5.49 5 S 47 5.16 5 C 4398 2.51 5 N 1114 2.21 5 O 1297 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 40": "NH1" <-> "NH2" Residue "A TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 178": "NH1" <-> "NH2" Residue "A ASP 181": "OD1" <-> "OD2" Residue "A GLU 219": "OE1" <-> "OE2" Residue "A TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 296": "NH1" <-> "NH2" Residue "A ARG 371": "NH1" <-> "NH2" Residue "A ARG 466": "NH1" <-> "NH2" Residue "A GLU 518": "OE1" <-> "OE2" Residue "L ASP 1": "OD1" <-> "OD2" Residue "L GLU 83": "OE1" <-> "OE2" Residue "L GLU 84": "OE1" <-> "OE2" Residue "L ARG 96": "NH1" <-> "NH2" Residue "L GLU 97": "OE1" <-> "OE2" Residue "L ARG 112": "NH1" <-> "NH2" Residue "L ASP 188": "OD1" <-> "OD2" Residue "L GLU 191": "OE1" <-> "OE2" Residue "L PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 6860 Number of models: 1 Model: "" Number of chains: 7 Chain: "B" Number of atoms: 181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 181 Classifications: {'peptide': 25} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 23} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 3262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3262 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 10, 'TRANS': 418} Chain breaks: 2 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "L" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1670 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 4, 'PTRANS': 10, 'TRANS': 203} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "H" Number of atoms: 1674 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 220, 1666 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 205} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Conformer: "B" Number of residues, atoms: 220, 1666 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 205} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 bond proxies already assigned to first conformer: 1703 Chain: "A" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 62 Unusual residues: {' CO': 2, 'AGA': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2181 SG CYS A 326 78.631 63.845 45.666 1.00 49.12 S Time building chain proxies: 4.99, per 1000 atoms: 0.73 Number of scatterers: 6860 At special positions: 0 Unit cell: (113.424, 110.088, 111.756, 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) Co 2 26.99 S 47 16.00 P 2 15.00 O 1297 8.00 N 1114 7.00 C 4398 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS B 7 " - pdb=" SG CYS B 23 " distance=2.03 Simple disulfide: pdb=" SG CYS B 10 " - pdb=" SG CYS B 13 " distance=2.02 Simple disulfide: pdb=" SG CYS B 11 " - pdb=" SG CYS B 19 " distance=2.03 Simple disulfide: pdb=" SG CYS B 14 " - pdb=" SG CYS B 22 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 92 " distance=2.05 Simple disulfide: pdb=" SG CYS L 138 " - pdb=" SG CYS L 198 " distance=2.04 Simple disulfide: pdb=" SG CYS L 218 " - pdb=" SG CYS H 133 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.04 Simple disulfide: pdb=" SG CYS H 145 " - pdb=" SG CYS H 200 " distance=2.04 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: 2.66 Conformation dependent library (CDL) restraints added in 1.2 seconds 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1650 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 24 helices and 11 sheets defined 43.8% alpha, 21.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 17 through 22 removed outlier: 3.876A pdb=" N THR A 22 " --> pdb=" O ALA A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 53 Processing helix chain 'A' and resid 59 through 84 removed outlier: 5.850A pdb=" N ALA A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N ILE A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 115 Processing helix chain 'A' and resid 117 through 122 Processing helix chain 'A' and resid 126 through 155 Processing helix chain 'A' and resid 158 through 162 Processing helix chain 'A' and resid 167 through 198 removed outlier: 3.956A pdb=" N ILE A 186 " --> pdb=" O GLN A 182 " (cutoff:3.500A) Proline residue: A 189 - end of helix Processing helix chain 'A' and resid 201 through 229 removed outlier: 3.975A pdb=" N CYS A 217 " --> pdb=" O LEU A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 234 Processing helix chain 'A' and resid 290 through 303 Processing helix chain 'A' and resid 308 through 318 removed outlier: 3.900A pdb=" N TYR A 318 " --> pdb=" O LEU A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 334 Processing helix chain 'A' and resid 339 through 366 Processing helix chain 'A' and resid 369 through 392 removed outlier: 3.540A pdb=" N LEU A 374 " --> pdb=" O VAL A 370 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N LEU A 386 " --> pdb=" O SER A 382 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N CYS A 387 " --> pdb=" O CYS A 383 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N PHE A 392 " --> pdb=" O VAL A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 483 removed outlier: 4.491A pdb=" N ILE A 467 " --> pdb=" O ILE A 463 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N GLY A 468 " --> pdb=" O ALA A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 513 removed outlier: 5.157A pdb=" N GLY A 490 " --> pdb=" O SER A 487 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE A 491 " --> pdb=" O GLU A 488 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ILE A 492 " --> pdb=" O ARG A 489 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N TYR A 501 " --> pdb=" O SER A 498 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU A 505 " --> pdb=" O LEU A 502 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU A 506 " --> pdb=" O LEU A 503 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N VAL A 511 " --> pdb=" O PHE A 508 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU A 513 " --> pdb=" O MET A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 545 removed outlier: 3.573A pdb=" N GLY A 521 " --> pdb=" O PRO A 517 " (cutoff:3.500A) Processing helix chain 'L' and resid 84 through 86 No H-bonds generated for 'chain 'L' and resid 84 through 86' Processing helix chain 'L' and resid 126 through 130 Processing helix chain 'L' and resid 187 through 192 removed outlier: 3.669A pdb=" N ARG L 192 " --> pdb=" O ASP L 188 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 89 No H-bonds generated for 'chain 'H' and resid 87 through 89' Processing helix chain 'H' and resid 160 through 162 No H-bonds generated for 'chain 'H' and resid 160 through 162' Processing helix chain 'H' and resid 205 through 207 No H-bonds generated for 'chain 'H' and resid 205 through 207' Processing sheet with id= A, first strand: chain 'B' and resid 7 through 11 Processing sheet with id= B, first strand: chain 'L' and resid 4 through 7 Processing sheet with id= C, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.623A pdb=" N LYS L 107 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N VAL L 13 " --> pdb=" O LYS L 107 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N GLU L 109 " --> pdb=" O VAL L 13 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N GLN L 41 " --> pdb=" O PRO L 50 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'L' and resid 118 through 122 removed outlier: 5.815A pdb=" N TYR L 177 " --> pdb=" O ASN L 142 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'L' and resid 157 through 159 removed outlier: 4.240A pdb=" N TRP L 152 " --> pdb=" O ARG L 159 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'H' and resid 3 through 7 removed outlier: 4.616A pdb=" N GLN H 66 " --> pdb=" O ASN H 83 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'H' and resid 112 through 114 removed outlier: 3.599A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ARG H 38 " --> pdb=" O TYR H 47 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N TYR H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N PHE H 40 " --> pdb=" O LEU H 45 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N LEU H 45 " --> pdb=" O PHE H 40 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'H' and resid 125 through 129 removed outlier: 5.573A pdb=" N TYR H 180 " --> pdb=" O GLY H 149 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'H' and resid 156 through 159 Processing sheet with id= J, first strand: chain 'H' and resid 174 through 176 Processing sheet with id= K, first strand: chain 'H' and resid 96 through 98 removed outlier: 3.987A pdb=" N VAL H 107 " --> pdb=" O ARG H 97 " (cutoff:3.500A) 410 hydrogen bonds defined for protein. 1122 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.96 Time building geometry restraints manager: 2.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.11 - 1.26: 1060 1.26 - 1.40: 1747 1.40 - 1.55: 4118 1.55 - 1.69: 12 1.69 - 1.83: 68 Bond restraints: 7005 Sorted by residual: bond pdb=" C SER L 32 " pdb=" O SER L 32 " ideal model delta sigma weight residual 1.243 1.122 0.121 9.50e-03 1.11e+04 1.63e+02 bond pdb=" C TYR L 34 " pdb=" O TYR L 34 " ideal model delta sigma weight residual 1.234 1.114 0.120 1.28e-02 6.10e+03 8.84e+01 bond pdb=" CA ALA L 31 " pdb=" C ALA L 31 " ideal model delta sigma weight residual 1.520 1.427 0.093 1.16e-02 7.43e+03 6.44e+01 bond pdb=" CA TYR L 34 " pdb=" C TYR L 34 " ideal model delta sigma weight residual 1.523 1.429 0.094 1.21e-02 6.83e+03 6.10e+01 bond pdb=" C ALA L 31 " pdb=" O ALA L 31 " ideal model delta sigma weight residual 1.235 1.175 0.059 1.13e-02 7.83e+03 2.77e+01 ... (remaining 7000 not shown) Histogram of bond angle deviations from ideal: 99.75 - 106.60: 215 106.60 - 113.46: 3970 113.46 - 120.31: 2600 120.31 - 127.16: 2674 127.16 - 134.02: 88 Bond angle restraints: 9547 Sorted by residual: angle pdb=" C ASN A 516 " pdb=" N PRO A 517 " pdb=" CA PRO A 517 " ideal model delta sigma weight residual 119.28 127.37 -8.09 1.10e+00 8.26e-01 5.41e+01 angle pdb=" C ALA L 55 " pdb=" CA ALA L 55 " pdb=" CB ALA L 55 " ideal model delta sigma weight residual 110.04 100.16 9.88 1.51e+00 4.39e-01 4.28e+01 angle pdb=" O5 AGA A 701 " pdb=" P1 AGA A 701 " pdb=" O6 AGA A 701 " ideal model delta sigma weight residual 93.68 110.17 -16.49 3.00e+00 1.11e-01 3.02e+01 angle pdb=" O5 AGA A 702 " pdb=" P1 AGA A 702 " pdb=" O6 AGA A 702 " ideal model delta sigma weight residual 93.68 109.83 -16.15 3.00e+00 1.11e-01 2.90e+01 angle pdb=" N PRO A 515 " pdb=" CA PRO A 515 " pdb=" C PRO A 515 " ideal model delta sigma weight residual 112.47 121.47 -9.00 2.06e+00 2.36e-01 1.91e+01 ... (remaining 9542 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.21: 3717 17.21 - 34.42: 274 34.42 - 51.63: 85 51.63 - 68.84: 27 68.84 - 86.05: 13 Dihedral angle restraints: 4116 sinusoidal: 1539 harmonic: 2577 Sorted by residual: dihedral pdb=" C SER L 32 " pdb=" N SER L 32 " pdb=" CA SER L 32 " pdb=" CB SER L 32 " ideal model delta harmonic sigma weight residual -122.60 -135.46 12.86 0 2.50e+00 1.60e-01 2.65e+01 dihedral pdb=" C ALA L 55 " pdb=" N ALA L 55 " pdb=" CA ALA L 55 " pdb=" CB ALA L 55 " ideal model delta harmonic sigma weight residual -122.60 -110.94 -11.66 0 2.50e+00 1.60e-01 2.17e+01 dihedral pdb=" CA TYR H 50 " pdb=" C TYR H 50 " pdb=" N ILE H 51 " pdb=" CA ILE H 51 " ideal model delta harmonic sigma weight residual 180.00 158.54 21.46 0 5.00e+00 4.00e-02 1.84e+01 ... (remaining 4113 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 1086 0.111 - 0.221: 33 0.221 - 0.331: 2 0.331 - 0.442: 2 0.442 - 0.552: 1 Chirality restraints: 1124 Sorted by residual: chirality pdb=" CA SER L 32 " pdb=" N SER L 32 " pdb=" C SER L 32 " pdb=" CB SER L 32 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.55 2.00e-01 2.50e+01 7.63e+00 chirality pdb=" CA TRP H 103 " pdb=" N TRP H 103 " pdb=" C TRP H 103 " pdb=" CB TRP H 103 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.20e+00 chirality pdb=" CA PRO A 515 " pdb=" N PRO A 515 " pdb=" C PRO A 515 " pdb=" CB PRO A 515 " both_signs ideal model delta sigma weight residual False 2.72 2.36 0.36 2.00e-01 2.50e+01 3.19e+00 ... (remaining 1121 not shown) Planarity restraints: 1176 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 516 " -0.015 2.00e-02 2.50e+03 2.99e-02 8.95e+00 pdb=" C ASN A 516 " 0.052 2.00e-02 2.50e+03 pdb=" O ASN A 516 " -0.020 2.00e-02 2.50e+03 pdb=" N PRO A 517 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER L 71 " -0.013 2.00e-02 2.50e+03 2.74e-02 7.52e+00 pdb=" C SER L 71 " 0.047 2.00e-02 2.50e+03 pdb=" O SER L 71 " -0.018 2.00e-02 2.50e+03 pdb=" N GLY L 72 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN H 35 " 0.013 2.00e-02 2.50e+03 2.72e-02 7.42e+00 pdb=" C ASN H 35 " -0.047 2.00e-02 2.50e+03 pdb=" O ASN H 35 " 0.018 2.00e-02 2.50e+03 pdb=" N TRP H 36 " 0.016 2.00e-02 2.50e+03 ... (remaining 1173 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.42: 25 2.42 - 3.04: 4172 3.04 - 3.66: 10406 3.66 - 4.28: 16114 4.28 - 4.90: 26538 Nonbonded interactions: 57255 Sorted by model distance: nonbonded pdb="CO CO A 704 " pdb=" O HOH A 806 " model vdw 1.797 2.220 nonbonded pdb=" O THR B 25 " pdb="CO CO A 704 " model vdw 1.798 2.220 nonbonded pdb=" ND2 ASN L 95 " pdb=" O TRP H 103 " model vdw 1.887 2.520 nonbonded pdb=" NE2 HIS A 507 " pdb="CO CO A 704 " model vdw 2.111 2.300 nonbonded pdb=" OG SER A 35 " pdb=" OE1 GLU A 219 " model vdw 2.113 2.440 ... (remaining 57250 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 6.490 Check model and map are aligned: 0.110 Set scattering table: 0.060 Process input model: 22.170 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 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:12.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 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 : 0.006 0.121 7005 Z= 0.410 Angle : 0.935 16.494 9547 Z= 0.501 Chirality : 0.054 0.552 1124 Planarity : 0.007 0.067 1176 Dihedral : 15.295 86.050 2439 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer Outliers : 4.26 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 18.42 % 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: 879 helix: -0.19 (0.22), residues: 382 sheet: 0.01 (0.33), residues: 226 loop : -0.63 (0.37), residues: 271 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 133 time to evaluate : 0.822 Fit side-chains revert: symmetry clash outliers start: 32 outliers final: 11 residues processed: 157 average time/residue: 0.9530 time to fit residues: 159.2161 Evaluate side-chains 120 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 109 time to evaluate : 0.800 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 9 residues processed: 2 average time/residue: 0.8998 time to fit residues: 3.0494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 73 optimal weight: 9.9990 chunk 65 optimal weight: 6.9990 chunk 36 optimal weight: 0.9980 chunk 22 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 41 optimal weight: 0.0670 chunk 50 optimal weight: 8.9990 chunk 79 optimal weight: 6.9990 overall best weight: 2.0124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 15 HIS A 86 ASN A 99 GLN A 141 ASN A 155 GLN ** A 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 ASN ** A 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 496 GLN A 516 ASN L 141 ASN L 149 ASN L 194 ASN L 216 ASN H 3 GLN H 77 HIS H 83 ASN ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 196 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 7005 Z= 0.257 Angle : 0.622 8.759 9547 Z= 0.326 Chirality : 0.044 0.180 1124 Planarity : 0.006 0.056 1176 Dihedral : 7.877 90.481 979 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer Outliers : 3.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.28), residues: 879 helix: 1.52 (0.25), residues: 389 sheet: 0.69 (0.34), residues: 223 loop : -0.21 (0.38), residues: 267 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 108 time to evaluate : 0.824 Fit side-chains revert: symmetry clash outliers start: 30 outliers final: 16 residues processed: 130 average time/residue: 1.0385 time to fit residues: 143.2920 Evaluate side-chains 120 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 104 time to evaluate : 0.745 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 13 residues processed: 3 average time/residue: 0.5887 time to fit residues: 2.9085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 43 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 chunk 85 optimal weight: 5.9990 chunk 70 optimal weight: 0.9990 chunk 78 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 63 optimal weight: 20.0000 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 7005 Z= 0.231 Angle : 0.586 9.760 9547 Z= 0.303 Chirality : 0.042 0.174 1124 Planarity : 0.005 0.056 1176 Dihedral : 7.576 81.933 979 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer Outliers : 4.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.42 % 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: 1.69 (0.29), residues: 879 helix: 2.06 (0.26), residues: 389 sheet: 1.13 (0.35), residues: 213 loop : -0.20 (0.38), residues: 277 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 105 time to evaluate : 0.825 Fit side-chains revert: symmetry clash outliers start: 33 outliers final: 20 residues processed: 126 average time/residue: 1.0975 time to fit residues: 146.5132 Evaluate side-chains 120 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 100 time to evaluate : 0.799 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 17 residues processed: 3 average time/residue: 1.4571 time to fit residues: 5.5587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 78 optimal weight: 20.0000 chunk 59 optimal weight: 5.9990 chunk 41 optimal weight: 0.9990 chunk 8 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 79 optimal weight: 9.9990 chunk 84 optimal weight: 20.0000 chunk 75 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 chunk 70 optimal weight: 3.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 7005 Z= 0.262 Angle : 0.599 9.828 9547 Z= 0.311 Chirality : 0.043 0.193 1124 Planarity : 0.005 0.055 1176 Dihedral : 7.563 79.909 979 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer Outliers : 3.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.42 % 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: 1.73 (0.29), residues: 879 helix: 2.15 (0.26), residues: 388 sheet: 1.16 (0.35), residues: 213 loop : -0.28 (0.38), residues: 278 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 103 time to evaluate : 0.913 Fit side-chains revert: symmetry clash outliers start: 28 outliers final: 22 residues processed: 124 average time/residue: 1.0963 time to fit residues: 144.2334 Evaluate side-chains 123 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 101 time to evaluate : 0.797 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 18 residues processed: 4 average time/residue: 1.5196 time to fit residues: 7.3955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 47 optimal weight: 10.0000 chunk 1 optimal weight: 0.0040 chunk 62 optimal weight: 30.0000 chunk 34 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 42 optimal weight: 0.3980 chunk 75 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 GLN ** A 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN H 98 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.045 7005 Z= 0.134 Angle : 0.501 9.848 9547 Z= 0.258 Chirality : 0.039 0.149 1124 Planarity : 0.004 0.051 1176 Dihedral : 7.138 72.298 979 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer Outliers : 3.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.42 % 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: 2.19 (0.29), residues: 879 helix: 2.59 (0.27), residues: 389 sheet: 1.28 (0.35), residues: 215 loop : -0.06 (0.39), residues: 275 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 106 time to evaluate : 0.816 Fit side-chains revert: symmetry clash outliers start: 27 outliers final: 17 residues processed: 128 average time/residue: 1.1197 time to fit residues: 152.1780 Evaluate side-chains 115 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 98 time to evaluate : 0.801 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 16 residues processed: 1 average time/residue: 1.5267 time to fit residues: 2.6488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 75 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 84 optimal weight: 0.3980 chunk 69 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 chunk 44 optimal weight: 6.9990 chunk 81 optimal weight: 20.0000 overall best weight: 3.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 141 ASN L 170 GLN ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 160 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.062 7005 Z= 0.355 Angle : 0.645 10.472 9547 Z= 0.334 Chirality : 0.046 0.224 1124 Planarity : 0.005 0.052 1176 Dihedral : 7.578 75.691 979 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer Outliers : 4.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.42 % 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: 1.78 (0.28), residues: 879 helix: 2.12 (0.26), residues: 388 sheet: 1.30 (0.35), residues: 213 loop : -0.23 (0.38), residues: 278 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 105 time to evaluate : 0.801 Fit side-chains revert: symmetry clash outliers start: 34 outliers final: 26 residues processed: 127 average time/residue: 1.1988 time to fit residues: 161.1924 Evaluate side-chains 127 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 101 time to evaluate : 0.755 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 20 residues processed: 6 average time/residue: 0.9832 time to fit residues: 7.2617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 9 optimal weight: 0.6980 chunk 47 optimal weight: 8.9990 chunk 61 optimal weight: 9.9990 chunk 70 optimal weight: 1.9990 chunk 83 optimal weight: 10.0000 chunk 52 optimal weight: 7.9990 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.058 7005 Z= 0.304 Angle : 0.621 10.458 9547 Z= 0.321 Chirality : 0.044 0.191 1124 Planarity : 0.005 0.051 1176 Dihedral : 7.572 76.779 979 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer Outliers : 4.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.42 % 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: 1.72 (0.28), residues: 879 helix: 2.02 (0.26), residues: 389 sheet: 1.27 (0.35), residues: 215 loop : -0.22 (0.38), residues: 275 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 105 time to evaluate : 0.771 Fit side-chains revert: symmetry clash outliers start: 32 outliers final: 24 residues processed: 129 average time/residue: 1.0407 time to fit residues: 142.4645 Evaluate side-chains 126 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 102 time to evaluate : 0.769 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 20 residues processed: 4 average time/residue: 1.1417 time to fit residues: 5.8360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 16 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 57 optimal weight: 8.9990 chunk 41 optimal weight: 0.0470 chunk 7 optimal weight: 0.7980 chunk 65 optimal weight: 5.9990 chunk 76 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 78 optimal weight: 0.9990 chunk 47 optimal weight: 4.9990 overall best weight: 1.3684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 7005 Z= 0.195 Angle : 0.563 10.599 9547 Z= 0.288 Chirality : 0.041 0.153 1124 Planarity : 0.005 0.050 1176 Dihedral : 7.307 73.738 979 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer Outliers : 3.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.42 % 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: 1.99 (0.29), residues: 879 helix: 2.26 (0.26), residues: 389 sheet: 1.32 (0.35), residues: 213 loop : -0.01 (0.39), residues: 277 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 104 time to evaluate : 0.803 Fit side-chains revert: symmetry clash outliers start: 26 outliers final: 20 residues processed: 125 average time/residue: 1.1138 time to fit residues: 147.6245 Evaluate side-chains 123 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 103 time to evaluate : 0.852 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 18 residues processed: 2 average time/residue: 2.2547 time to fit residues: 5.8222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 34 optimal weight: 3.9990 chunk 61 optimal weight: 10.0000 chunk 23 optimal weight: 0.5980 chunk 70 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 77 optimal weight: 20.0000 chunk 51 optimal weight: 4.9990 chunk 82 optimal weight: 4.9990 chunk 50 optimal weight: 0.0010 chunk 39 optimal weight: 3.9990 chunk 57 optimal weight: 6.9990 overall best weight: 2.3192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 7005 Z= 0.285 Angle : 0.619 10.340 9547 Z= 0.320 Chirality : 0.044 0.208 1124 Planarity : 0.005 0.050 1176 Dihedral : 7.463 74.643 979 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer Outliers : 3.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.42 % 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: 1.81 (0.28), residues: 879 helix: 2.12 (0.26), residues: 388 sheet: 1.23 (0.35), residues: 213 loop : -0.09 (0.38), residues: 278 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 104 time to evaluate : 0.790 Fit side-chains revert: symmetry clash outliers start: 28 outliers final: 23 residues processed: 123 average time/residue: 1.0696 time to fit residues: 139.4009 Evaluate side-chains 125 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 102 time to evaluate : 0.799 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 18 residues processed: 5 average time/residue: 0.6995 time to fit residues: 4.8385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 86 optimal weight: 10.0000 chunk 79 optimal weight: 6.9990 chunk 69 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 63 optimal weight: 8.9990 chunk 10 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 128 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.039 7005 Z= 0.154 Angle : 0.540 9.970 9547 Z= 0.275 Chirality : 0.040 0.154 1124 Planarity : 0.005 0.049 1176 Dihedral : 7.150 70.770 979 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer Outliers : 2.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.42 % 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: 2.17 (0.29), residues: 879 helix: 2.42 (0.26), residues: 388 sheet: 1.42 (0.35), residues: 213 loop : 0.06 (0.39), residues: 278 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1758 Ramachandran restraints generated. 879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 102 time to evaluate : 0.717 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 19 residues processed: 120 average time/residue: 1.1117 time to fit residues: 141.1858 Evaluate side-chains 120 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 101 time to evaluate : 0.904 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 18 residues processed: 1 average time/residue: 1.6965 time to fit residues: 2.8300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 19 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 chunk 70 optimal weight: 0.5980 chunk 8 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 chunk 60 optimal weight: 10.0000 chunk 3 optimal weight: 0.6980 chunk 49 optimal weight: 0.0570 chunk 79 optimal weight: 5.9990 chunk 46 optimal weight: 10.0000 overall best weight: 1.0702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.162249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.111975 restraints weight = 13021.906| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 2.13 r_work: 0.3383 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3290 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3295 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3295 r_free = 0.3295 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3295 r_free = 0.3295 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3295 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 7005 Z= 0.172 Angle : 0.552 10.182 9547 Z= 0.283 Chirality : 0.041 0.155 1124 Planarity : 0.005 0.049 1176 Dihedral : 7.081 68.098 979 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer Outliers : 2.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.42 % 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: 2.21 (0.29), residues: 879 helix: 2.41 (0.26), residues: 388 sheet: 1.49 (0.35), residues: 213 loop : 0.12 (0.39), residues: 278 =============================================================================== Job complete usr+sys time: 3183.31 seconds wall clock time: 56 minutes 59.92 seconds (3419.92 seconds total)