Starting phenix.real_space_refine on Fri Dec 8 03:29:48 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mfe_23814/12_2023/7mfe_23814_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mfe_23814/12_2023/7mfe_23814.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mfe_23814/12_2023/7mfe_23814.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mfe_23814/12_2023/7mfe_23814.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mfe_23814/12_2023/7mfe_23814_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mfe_23814/12_2023/7mfe_23814_updated.pdb" } resolution = 4.07 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= 0.001 sd= 0.007 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 Zn 2 6.06 5 P 2 5.49 5 S 41 5.16 5 C 4333 2.51 5 N 1184 2.21 5 O 1282 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 538": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 6844 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 409, 3291 Classifications: {'peptide': 409} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 18, 'TRANS': 390} Chain breaks: 4 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 1785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1785 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 4, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 1766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1766 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 4, 'TRANS': 219} Chain breaks: 2 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 673 SG CYS A 248 50.552 27.800 52.225 1.00 14.22 S ATOM 808 SG CYS A 264 42.464 38.382 45.422 1.00 19.76 S Time building chain proxies: 4.20, per 1000 atoms: 0.61 Number of scatterers: 6844 At special positions: 0 Unit cell: (99.752, 74.14, 111.884, 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) Zn 2 29.99 S 41 16.00 P 2 15.00 O 1282 8.00 N 1184 7.00 C 4333 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: 2.90 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 901 " pdb="ZN ZN A 901 " - pdb=" ND1 HIS A 269 " pdb="ZN ZN A 901 " - pdb=" SG CYS A 248 " pdb=" ZN A 902 " pdb="ZN ZN A 902 " - pdb=" ND1 HIS A 235 " pdb="ZN ZN A 902 " - pdb=" SG CYS A 264 " 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1644 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 29 helices and 2 sheets defined 54.0% alpha, 1.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.27 Creating SS restraints... Processing helix chain 'A' and resid 177 through 188 removed outlier: 4.045A pdb=" N ALA A 184 " --> pdb=" O SER A 180 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N MET A 187 " --> pdb=" O LYS A 183 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N ARG A 188 " --> pdb=" O ALA A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 216 No H-bonds generated for 'chain 'A' and resid 214 through 216' Processing helix chain 'A' and resid 492 through 503 removed outlier: 3.918A pdb=" N GLN A 496 " --> pdb=" O PRO A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 541 Processing helix chain 'A' and resid 550 through 570 removed outlier: 3.566A pdb=" N ILE A 554 " --> pdb=" O MET A 550 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASP A 555 " --> pdb=" O ILE A 551 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA A 561 " --> pdb=" O ALA A 557 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU A 567 " --> pdb=" O GLY A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 625 No H-bonds generated for 'chain 'A' and resid 622 through 625' Processing helix chain 'A' and resid 637 through 650 removed outlier: 3.532A pdb=" N ALA A 641 " --> pdb=" O SER A 637 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU A 648 " --> pdb=" O ILE A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 670 removed outlier: 3.606A pdb=" N ILE A 666 " --> pdb=" O ARG A 662 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N PHE A 667 " --> pdb=" O ASP A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 680 No H-bonds generated for 'chain 'A' and resid 678 through 680' Processing helix chain 'A' and resid 687 through 696 removed outlier: 3.576A pdb=" N ALA A 694 " --> pdb=" O LYS A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 718 removed outlier: 3.610A pdb=" N ILE A 714 " --> pdb=" O ILE A 710 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU A 715 " --> pdb=" O LEU A 711 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 16 removed outlier: 3.909A pdb=" N ALA C 16 " --> pdb=" O LEU C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 30 removed outlier: 3.543A pdb=" N SER C 28 " --> pdb=" O ALA C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 67 removed outlier: 3.995A pdb=" N LEU C 43 " --> pdb=" O GLU C 39 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TYR C 48 " --> pdb=" O LEU C 44 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER C 64 " --> pdb=" O ARG C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 103 Processing helix chain 'C' and resid 112 through 131 removed outlier: 3.600A pdb=" N TYR C 118 " --> pdb=" O SER C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 159 removed outlier: 3.865A pdb=" N LYS C 138 " --> pdb=" O GLY C 135 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N GLY C 140 " --> pdb=" O ASP C 137 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL C 142 " --> pdb=" O LYS C 139 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ASP C 143 " --> pdb=" O GLY C 140 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN C 147 " --> pdb=" O GLN C 144 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR C 149 " --> pdb=" O GLN C 146 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLU C 151 " --> pdb=" O ALA C 148 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE C 153 " --> pdb=" O GLN C 150 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLU C 154 " --> pdb=" O GLU C 151 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LYS C 157 " --> pdb=" O GLU C 154 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU C 159 " --> pdb=" O SER C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 179 Processing helix chain 'C' and resid 185 through 198 Processing helix chain 'C' and resid 211 through 229 removed outlier: 3.522A pdb=" N ARG C 222 " --> pdb=" O MET C 218 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASN C 224 " --> pdb=" O LEU C 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 16 removed outlier: 3.573A pdb=" N ALA B 10 " --> pdb=" O LEU B 6 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ALA B 13 " --> pdb=" O LYS B 9 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLN B 15 " --> pdb=" O LYS B 11 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ALA B 16 " --> pdb=" O LEU B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 30 Processing helix chain 'B' and resid 38 through 66 removed outlier: 3.535A pdb=" N SER B 45 " --> pdb=" O ARG B 41 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG B 55 " --> pdb=" O VAL B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 103 removed outlier: 4.305A pdb=" N VAL B 97 " --> pdb=" O ILE B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 132 removed outlier: 3.573A pdb=" N GLY B 123 " --> pdb=" O LEU B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 159 removed outlier: 3.881A pdb=" N LYS B 158 " --> pdb=" O GLU B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 180 Processing helix chain 'B' and resid 185 through 202 Processing helix chain 'B' and resid 208 through 229 removed outlier: 4.006A pdb=" N LYS B 212 " --> pdb=" O GLU B 208 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N ASP B 213 " --> pdb=" O GLU B 209 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU B 216 " --> pdb=" O LYS B 212 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR B 229 " --> pdb=" O LEU B 225 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 197 through 199 removed outlier: 4.204A pdb=" N VAL A 197 " --> pdb=" O ILE A 208 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 238 through 241 removed outlier: 3.782A pdb=" N GLY A 258 " --> pdb=" O LYS A 240 " (cutoff:3.500A) 310 hydrogen bonds defined for protein. 891 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: 1.75 Time building geometry restraints manager: 3.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2248 1.34 - 1.46: 1537 1.46 - 1.58: 3103 1.58 - 1.70: 8 1.70 - 1.82: 65 Bond restraints: 6961 Sorted by residual: bond pdb=" N VAL B 97 " pdb=" CA VAL B 97 " ideal model delta sigma weight residual 1.460 1.493 -0.034 1.21e-02 6.83e+03 7.76e+00 bond pdb=" N LEU B 98 " pdb=" CA LEU B 98 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.21e-02 6.83e+03 7.39e+00 bond pdb=" N CYS B 94 " pdb=" CA CYS B 94 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.30e-02 5.92e+03 7.18e+00 bond pdb=" N SER B 99 " pdb=" CA SER B 99 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.23e-02 6.61e+03 5.45e+00 bond pdb=" N ASN B 95 " pdb=" CA ASN B 95 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.33e-02 5.65e+03 5.17e+00 ... (remaining 6956 not shown) Histogram of bond angle deviations from ideal: 99.74 - 106.59: 154 106.59 - 113.44: 3807 113.44 - 120.29: 2589 120.29 - 127.14: 2780 127.14 - 133.99: 55 Bond angle restraints: 9385 Sorted by residual: angle pdb=" N ASP B 96 " pdb=" CA ASP B 96 " pdb=" C ASP B 96 " ideal model delta sigma weight residual 111.07 105.23 5.84 1.07e+00 8.73e-01 2.98e+01 angle pdb=" N CYS B 94 " pdb=" CA CYS B 94 " pdb=" C CYS B 94 " ideal model delta sigma weight residual 113.55 108.64 4.91 1.26e+00 6.30e-01 1.52e+01 angle pdb=" N ASN B 95 " pdb=" CA ASN B 95 " pdb=" C ASN B 95 " ideal model delta sigma weight residual 112.54 107.85 4.69 1.22e+00 6.72e-01 1.48e+01 angle pdb=" CA VAL B 97 " pdb=" C VAL B 97 " pdb=" O VAL B 97 " ideal model delta sigma weight residual 120.85 117.20 3.65 1.06e+00 8.90e-01 1.19e+01 angle pdb=" N LEU B 100 " pdb=" CA LEU B 100 " pdb=" C LEU B 100 " ideal model delta sigma weight residual 111.28 107.75 3.53 1.09e+00 8.42e-01 1.05e+01 ... (remaining 9380 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 3782 17.94 - 35.88: 384 35.88 - 53.82: 63 53.82 - 71.76: 19 71.76 - 89.69: 8 Dihedral angle restraints: 4256 sinusoidal: 1730 harmonic: 2526 Sorted by residual: dihedral pdb=" CA GLU C 209 " pdb=" C GLU C 209 " pdb=" N SER C 210 " pdb=" CA SER C 210 " ideal model delta harmonic sigma weight residual -180.00 -154.10 -25.90 0 5.00e+00 4.00e-02 2.68e+01 dihedral pdb=" CA MET A 620 " pdb=" C MET A 620 " pdb=" N ALA A 621 " pdb=" CA ALA A 621 " ideal model delta harmonic sigma weight residual -180.00 -158.09 -21.91 0 5.00e+00 4.00e-02 1.92e+01 dihedral pdb=" CA GLN C 15 " pdb=" C GLN C 15 " pdb=" N ALA C 16 " pdb=" CA ALA C 16 " ideal model delta harmonic sigma weight residual -180.00 -160.48 -19.52 0 5.00e+00 4.00e-02 1.52e+01 ... (remaining 4253 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 832 0.045 - 0.090: 173 0.090 - 0.134: 36 0.134 - 0.179: 2 0.179 - 0.224: 2 Chirality restraints: 1045 Sorted by residual: chirality pdb=" CA LEU B 100 " pdb=" N LEU B 100 " pdb=" C LEU B 100 " pdb=" CB LEU B 100 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CA ASP B 96 " pdb=" N ASP B 96 " pdb=" C ASP B 96 " pdb=" CB ASP B 96 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA CYS B 94 " pdb=" N CYS B 94 " pdb=" C CYS B 94 " pdb=" CB CYS B 94 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.96e-01 ... (remaining 1042 not shown) Planarity restraints: 1198 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 191 " -0.036 5.00e-02 4.00e+02 5.46e-02 4.78e+00 pdb=" N PRO A 192 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 192 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 192 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 621 " 0.035 5.00e-02 4.00e+02 5.32e-02 4.52e+00 pdb=" N PRO A 622 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 622 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 622 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 707 " 0.033 5.00e-02 4.00e+02 5.02e-02 4.04e+00 pdb=" N PRO A 708 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 708 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 708 " 0.028 5.00e-02 4.00e+02 ... (remaining 1195 not shown) Histogram of nonbonded interaction distances: 1.39 - 2.09: 2 2.09 - 2.79: 1701 2.79 - 3.49: 10097 3.49 - 4.20: 15373 4.20 - 4.90: 26767 Nonbonded interactions: 53940 Sorted by model distance: nonbonded pdb=" ND2 ASN A 163 " pdb=" O SER A 679 " model vdw 1.387 2.520 nonbonded pdb=" O TYR A 647 " pdb=" OG1 THR A 651 " model vdw 2.044 2.440 nonbonded pdb=" O PHE A 268 " pdb=" NE2 GLN A 270 " model vdw 2.155 2.520 nonbonded pdb=" OG1 THR C 163 " pdb=" OE2 GLU C 209 " model vdw 2.155 2.440 nonbonded pdb=" CD2 HIS A 235 " pdb="ZN ZN A 902 " model vdw 2.168 1.960 ... (remaining 53935 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'B' and (resid 2 or (resid 3 and (name N or name CA or name C or name O o \ r name CB or name CG or name CD or name CE )) or resid 4 through 67 or (resid 68 \ and (name N or name CA or name C or name O or name CB )) or resid 69 or resid 7 \ 3 through 74 or (resid 75 and (name N or name CA or name C or name O or name CB \ or name CG )) or (resid 76 and (name N or name CA or name C or name O or name CB \ )) or resid 77 through 102 or (resid 103 and (name N or name CA or name C or na \ me O or name CB or name CG )) or resid 104 through 138 or (resid 139 and (name N \ or name CA or name C or name O or name CB or name CG )) or resid 140 through 15 \ 7 or (resid 158 and (name N or name CA or name C or name O or name CB or name CG \ or name CD or name CE )) or resid 159 through 230)) selection = (chain 'C' and (resid 2 through 4 or (resid 5 and (name N or name CA or name C o \ r name O or name CB or name CG )) or resid 6 through 102 or (resid 103 and (name \ N or name CA or name C or name O or name CB or name CG )) or resid 104 through \ 133 or (resid 137 and (name N or name CA or name C or name O or name CB )) or re \ sid 138 through 156 or (resid 157 through 158 and (name N or name CA or name C o \ r name O or name CB or name CG or name CD or name CE )) or resid 159 through 207 \ or (resid 208 through 209 and (name N or name CA or name C or name O or name CB \ )) or resid 210 through 211 or (resid 212 and (name N or name CA or name C or n \ ame O or name CB )) or resid 213 through 229 or (resid 230 and (name N or name C \ A or name C or name O or name CB )))) } 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=1.00 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: 0.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.890 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 23.940 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6509 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 : 0.002 0.035 6961 Z= 0.158 Angle : 0.592 6.843 9385 Z= 0.353 Chirality : 0.039 0.224 1045 Planarity : 0.004 0.055 1198 Dihedral : 15.258 89.694 2612 Min Nonbonded Distance : 1.387 Molprobity Statistics. All-atom Clashscore : 18.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 0.41 % Allowed : 0.27 % Favored : 99.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.56 (0.28), residues: 833 helix: -0.73 (0.24), residues: 457 sheet: -3.50 (1.08), residues: 18 loop : -2.92 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 228 HIS 0.007 0.001 HIS A 542 PHE 0.022 0.002 PHE B 117 TYR 0.021 0.002 TYR A 266 ARG 0.004 0.000 ARG A 252 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 164 time to evaluate : 0.795 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 166 average time/residue: 0.1827 time to fit residues: 40.6664 Evaluate side-chains 125 residues out of total 755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 124 time to evaluate : 0.850 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0658 time to fit residues: 1.4035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 35 optimal weight: 8.9990 chunk 21 optimal weight: 2.9990 chunk 42 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 chunk 65 optimal weight: 9.9990 chunk 25 optimal weight: 10.0000 chunk 40 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 76 optimal weight: 0.6980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 585 HIS ** C 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 224 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6494 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6961 Z= 0.208 Angle : 0.627 10.157 9385 Z= 0.329 Chirality : 0.041 0.149 1045 Planarity : 0.005 0.060 1198 Dihedral : 5.487 34.313 938 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 15.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.70 (0.28), residues: 833 helix: 0.04 (0.23), residues: 454 sheet: -3.31 (1.17), residues: 18 loop : -2.60 (0.31), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 59 HIS 0.008 0.002 HIS A 542 PHE 0.027 0.002 PHE B 174 TYR 0.022 0.002 TYR C 125 ARG 0.005 0.000 ARG A 178 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 0.850 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 145 average time/residue: 0.1665 time to fit residues: 33.2692 Evaluate side-chains 121 residues out of total 755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 0.771 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 42 optimal weight: 9.9990 chunk 23 optimal weight: 6.9990 chunk 63 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 21 optimal weight: 5.9990 chunk 76 optimal weight: 7.9990 chunk 82 optimal weight: 0.9980 chunk 68 optimal weight: 9.9990 chunk 75 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 61 optimal weight: 7.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 494 GLN A 585 HIS ** C 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 150 GLN B 224 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6568 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 6961 Z= 0.302 Angle : 0.693 10.760 9385 Z= 0.360 Chirality : 0.043 0.163 1045 Planarity : 0.005 0.057 1198 Dihedral : 5.954 40.405 938 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 17.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.95 (0.28), residues: 833 helix: -0.23 (0.23), residues: 461 sheet: -3.38 (1.12), residues: 18 loop : -2.65 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 59 HIS 0.005 0.001 HIS A 540 PHE 0.044 0.003 PHE C 174 TYR 0.023 0.002 TYR B 126 ARG 0.004 0.001 ARG A 691 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 0.817 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 144 average time/residue: 0.1695 time to fit residues: 33.9108 Evaluate side-chains 114 residues out of total 755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 0.867 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 10.0000 chunk 57 optimal weight: 0.6980 chunk 39 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 51 optimal weight: 7.9990 chunk 76 optimal weight: 0.9990 chunk 81 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 72 optimal weight: 6.9990 chunk 21 optimal weight: 5.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 512 ASN A 585 HIS ** C 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 224 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6483 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6961 Z= 0.211 Angle : 0.618 10.067 9385 Z= 0.323 Chirality : 0.040 0.153 1045 Planarity : 0.005 0.057 1198 Dihedral : 5.587 35.348 938 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.64 (0.28), residues: 833 helix: 0.07 (0.24), residues: 457 sheet: -3.38 (0.79), residues: 29 loop : -2.50 (0.33), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 59 HIS 0.004 0.001 HIS A 510 PHE 0.060 0.003 PHE C 174 TYR 0.021 0.002 TYR C 125 ARG 0.003 0.000 ARG A 178 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 0.831 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 149 average time/residue: 0.1847 time to fit residues: 37.3387 Evaluate side-chains 116 residues out of total 755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 0.892 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 67 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 1 optimal weight: 7.9990 chunk 60 optimal weight: 10.0000 chunk 33 optimal weight: 3.9990 chunk 69 optimal weight: 7.9990 chunk 56 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 41 optimal weight: 7.9990 chunk 72 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 585 HIS C 42 ASN B 144 GLN B 224 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6675 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 6961 Z= 0.473 Angle : 0.856 11.271 9385 Z= 0.446 Chirality : 0.048 0.195 1045 Planarity : 0.007 0.058 1198 Dihedral : 6.762 42.637 938 Min Nonbonded Distance : 1.680 Molprobity Statistics. All-atom Clashscore : 23.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.04 % Favored : 88.96 % Rotamer: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.49 (0.27), residues: 833 helix: -0.71 (0.22), residues: 459 sheet: -3.23 (1.04), residues: 18 loop : -2.85 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 619 HIS 0.006 0.002 HIS A 510 PHE 0.055 0.004 PHE C 174 TYR 0.027 0.003 TYR A 472 ARG 0.008 0.001 ARG A 691 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 145 average time/residue: 0.1727 time to fit residues: 34.5305 Evaluate side-chains 111 residues out of total 755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 0.819 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 27 optimal weight: 6.9990 chunk 73 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 47 optimal weight: 6.9990 chunk 20 optimal weight: 7.9990 chunk 81 optimal weight: 5.9990 chunk 67 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 chunk 6 optimal weight: 0.9990 chunk 26 optimal weight: 7.9990 chunk 42 optimal weight: 6.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 GLN ** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 ASN A 585 HIS B 224 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6512 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6961 Z= 0.226 Angle : 0.667 10.802 9385 Z= 0.345 Chirality : 0.041 0.172 1045 Planarity : 0.005 0.055 1198 Dihedral : 5.913 36.474 938 Min Nonbonded Distance : 1.693 Molprobity Statistics. All-atom Clashscore : 16.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 0.14 % Allowed : 2.88 % Favored : 96.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.89 (0.28), residues: 833 helix: -0.21 (0.23), residues: 452 sheet: -3.06 (0.82), residues: 28 loop : -2.51 (0.33), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 59 HIS 0.009 0.001 HIS A 568 PHE 0.062 0.003 PHE C 174 TYR 0.022 0.002 TYR C 125 ARG 0.003 0.000 ARG A 704 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 152 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 153 average time/residue: 0.1864 time to fit residues: 38.3568 Evaluate side-chains 125 residues out of total 755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 0.781 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 78 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 46 optimal weight: 8.9990 chunk 59 optimal weight: 5.9990 chunk 45 optimal weight: 4.9990 chunk 68 optimal weight: 8.9990 chunk 80 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 494 GLN A 585 HIS B 144 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6650 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 6961 Z= 0.427 Angle : 0.858 17.440 9385 Z= 0.438 Chirality : 0.048 0.195 1045 Planarity : 0.006 0.057 1198 Dihedral : 6.708 42.969 938 Min Nonbonded Distance : 1.548 Molprobity Statistics. All-atom Clashscore : 22.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.68 % Favored : 89.32 % Rotamer: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.46 (0.27), residues: 833 helix: -0.73 (0.22), residues: 454 sheet: -3.24 (0.86), residues: 26 loop : -2.71 (0.32), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 619 HIS 0.011 0.002 HIS A 568 PHE 0.041 0.004 PHE B 174 TYR 0.034 0.003 TYR A 640 ARG 0.007 0.001 ARG C 18 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 143 average time/residue: 0.1914 time to fit residues: 36.5338 Evaluate side-chains 110 residues out of total 755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 0.862 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 48 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 15 optimal weight: 20.0000 chunk 51 optimal weight: 3.9990 chunk 55 optimal weight: 7.9990 chunk 40 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 63 optimal weight: 6.9990 chunk 73 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 70 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 HIS ** A 574 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 585 HIS B 144 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6449 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6961 Z= 0.183 Angle : 0.653 10.989 9385 Z= 0.336 Chirality : 0.041 0.175 1045 Planarity : 0.005 0.058 1198 Dihedral : 5.648 33.269 938 Min Nonbonded Distance : 1.675 Molprobity Statistics. All-atom Clashscore : 16.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.61 (0.29), residues: 833 helix: -0.03 (0.24), residues: 454 sheet: -2.90 (0.82), residues: 29 loop : -2.30 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 450 HIS 0.008 0.001 HIS A 540 PHE 0.039 0.002 PHE C 174 TYR 0.020 0.002 TYR C 82 ARG 0.004 0.000 ARG B 18 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 150 average time/residue: 0.1904 time to fit residues: 38.8109 Evaluate side-chains 120 residues out of total 755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 0.867 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 4.9990 chunk 77 optimal weight: 9.9990 chunk 45 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 23 optimal weight: 6.9990 chunk 68 optimal weight: 7.9990 chunk 71 optimal weight: 0.9990 chunk 49 optimal weight: 5.9990 chunk 79 optimal weight: 0.0270 chunk 48 optimal weight: 1.9990 overall best weight: 1.1844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 HIS A 494 GLN ** A 574 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 585 HIS ** C 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6437 moved from start: 0.3125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6961 Z= 0.194 Angle : 0.642 10.078 9385 Z= 0.329 Chirality : 0.042 0.187 1045 Planarity : 0.005 0.065 1198 Dihedral : 5.508 34.247 938 Min Nonbonded Distance : 1.607 Molprobity Statistics. All-atom Clashscore : 16.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.37 (0.29), residues: 833 helix: 0.15 (0.24), residues: 454 sheet: -2.42 (0.83), residues: 28 loop : -2.22 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 450 HIS 0.008 0.001 HIS C 164 PHE 0.035 0.002 PHE B 174 TYR 0.025 0.002 TYR C 125 ARG 0.005 0.000 ARG A 704 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 147 average time/residue: 0.2064 time to fit residues: 40.4133 Evaluate side-chains 121 residues out of total 755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 0.832 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 37 optimal weight: 0.4980 chunk 55 optimal weight: 0.9980 chunk 83 optimal weight: 4.9990 chunk 77 optimal weight: 9.9990 chunk 66 optimal weight: 4.9990 chunk 6 optimal weight: 9.9990 chunk 51 optimal weight: 7.9990 chunk 40 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 574 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 585 HIS ** C 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6454 moved from start: 0.3192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6961 Z= 0.205 Angle : 0.664 8.821 9385 Z= 0.335 Chirality : 0.042 0.171 1045 Planarity : 0.005 0.058 1198 Dihedral : 5.460 36.324 938 Min Nonbonded Distance : 1.589 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.29 (0.29), residues: 833 helix: 0.25 (0.24), residues: 453 sheet: -2.53 (0.84), residues: 29 loop : -2.22 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 59 HIS 0.004 0.001 HIS A 585 PHE 0.035 0.002 PHE B 174 TYR 0.019 0.002 TYR C 125 ARG 0.008 0.000 ARG C 83 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 139 time to evaluate : 1.160 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 139 average time/residue: 0.3027 time to fit residues: 55.2729 Evaluate side-chains 117 residues out of total 755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 0.720 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 61 optimal weight: 3.9990 chunk 9 optimal weight: 0.0870 chunk 18 optimal weight: 9.9990 chunk 66 optimal weight: 4.9990 chunk 27 optimal weight: 0.1980 chunk 68 optimal weight: 9.9990 chunk 8 optimal weight: 0.9990 chunk 12 optimal weight: 9.9990 chunk 58 optimal weight: 2.9990 chunk 3 optimal weight: 9.9990 chunk 48 optimal weight: 6.9990 overall best weight: 1.6564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 494 GLN ** A 574 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 585 HIS ** C 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 HIS ** 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 = 0.4310 r_free = 0.4310 target = 0.177396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.157162 restraints weight = 9975.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.157481 restraints weight = 9029.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.160051 restraints weight = 7671.502| |-----------------------------------------------------------------------------| r_work (final): 0.4124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6428 moved from start: 0.3309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6961 Z= 0.214 Angle : 0.651 8.599 9385 Z= 0.334 Chirality : 0.043 0.179 1045 Planarity : 0.005 0.056 1198 Dihedral : 5.507 36.375 938 Min Nonbonded Distance : 1.576 Molprobity Statistics. All-atom Clashscore : 16.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.25 (0.29), residues: 833 helix: 0.29 (0.24), residues: 453 sheet: -2.12 (0.91), residues: 29 loop : -2.25 (0.32), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 450 HIS 0.004 0.001 HIS A 585 PHE 0.039 0.002 PHE B 174 TYR 0.022 0.003 TYR A 640 ARG 0.004 0.001 ARG A 178 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1496.25 seconds wall clock time: 28 minutes 24.67 seconds (1704.67 seconds total)