Starting phenix.real_space_refine on Tue Feb 13 16:03:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mfe_23814/02_2024/7mfe_23814_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mfe_23814/02_2024/7mfe_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_23814/02_2024/7mfe_23814.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mfe_23814/02_2024/7mfe_23814.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mfe_23814/02_2024/7mfe_23814_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mfe_23814/02_2024/7mfe_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-dev-5238/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: 3.95, per 1000 atoms: 0.58 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: 2.69 Conformation dependent library (CDL) restraints added in 1.1 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: 1.19 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: 1.52 Time building geometry restraints manager: 2.85 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: 0.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.820 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 22.400 Find NCS groups from input model: 0.300 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.530 ------------------------------------------------------------------------------- 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 : 0.712 Fit side-chains revert: symmetry clash REVERT: A 190 LEU cc_start: 0.8438 (mt) cc_final: 0.8101 (mt) REVERT: A 254 LEU cc_start: 0.6824 (tp) cc_final: 0.6526 (tp) REVERT: C 160 MET cc_start: 0.6214 (tpt) cc_final: 0.5870 (tpt) outliers start: 3 outliers final: 1 residues processed: 166 average time/residue: 0.1818 time to fit residues: 40.2344 Evaluate side-chains 125 residues out of total 755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 124 time to evaluate : 0.833 ------------------------------------------------------------------------------- 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: 0.6495 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6961 Z= 0.218 Angle : 0.630 9.797 9385 Z= 0.333 Chirality : 0.041 0.151 1045 Planarity : 0.005 0.060 1198 Dihedral : 5.479 34.256 938 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % 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: -1.71 (0.28), residues: 833 helix: 0.05 (0.23), residues: 452 sheet: -3.28 (1.19), residues: 18 loop : -2.62 (0.31), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 59 HIS 0.008 0.001 HIS A 542 PHE 0.025 0.002 PHE B 174 TYR 0.021 0.002 TYR C 125 ARG 0.003 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 144 residues out of total 755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 0.708 Fit side-chains REVERT: A 190 LEU cc_start: 0.8235 (mt) cc_final: 0.7771 (mt) REVERT: A 564 MET cc_start: 0.7343 (ttm) cc_final: 0.7013 (mtt) REVERT: B 40 GLU cc_start: 0.6482 (pm20) cc_final: 0.6142 (pm20) REVERT: B 149 TYR cc_start: 0.7003 (m-80) cc_final: 0.6327 (m-80) REVERT: B 155 ILE cc_start: 0.8042 (tp) cc_final: 0.7601 (tp) outliers start: 0 outliers final: 0 residues processed: 144 average time/residue: 0.1693 time to fit residues: 33.4746 Evaluate side-chains 122 residues out of total 755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 0.724 ------------------------------------------------------------------------------- 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: 10.0000 chunk 23 optimal weight: 9.9990 chunk 63 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 chunk 76 optimal weight: 7.9990 chunk 82 optimal weight: 10.0000 chunk 68 optimal weight: 10.0000 chunk 75 optimal weight: 0.0170 chunk 26 optimal weight: 0.0980 chunk 61 optimal weight: 0.9990 overall best weight: 0.8224 ------------------------------------------------------------------------------- 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** ** C 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 ASN B 224 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6395 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6961 Z= 0.156 Angle : 0.577 9.617 9385 Z= 0.300 Chirality : 0.040 0.140 1045 Planarity : 0.004 0.056 1198 Dihedral : 5.213 34.181 938 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % 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: -1.32 (0.28), residues: 833 helix: 0.39 (0.24), residues: 455 sheet: -3.33 (0.77), residues: 29 loop : -2.42 (0.32), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 59 HIS 0.005 0.001 HIS A 540 PHE 0.044 0.002 PHE C 174 TYR 0.027 0.002 TYR B 126 ARG 0.003 0.000 ARG A 172 *********************** 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 164 residues out of total 755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 LEU cc_start: 0.8045 (mt) cc_final: 0.7653 (mt) REVERT: A 636 GLN cc_start: 0.8651 (mm-40) cc_final: 0.8398 (mm-40) REVERT: B 40 GLU cc_start: 0.6456 (pm20) cc_final: 0.6156 (pm20) REVERT: B 59 TRP cc_start: 0.5838 (t60) cc_final: 0.5629 (t60) REVERT: B 149 TYR cc_start: 0.6798 (m-80) cc_final: 0.6368 (m-80) outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.1736 time to fit residues: 38.5531 Evaluate side-chains 122 residues out of total 755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 0.807 ------------------------------------------------------------------------------- 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: 0.7980 chunk 39 optimal weight: 10.0000 chunk 8 optimal weight: 7.9990 chunk 36 optimal weight: 0.8980 chunk 51 optimal weight: 8.9990 chunk 76 optimal weight: 2.9990 chunk 81 optimal weight: 6.9990 chunk 40 optimal weight: 0.6980 chunk 72 optimal weight: 9.9990 chunk 21 optimal weight: 7.9990 overall best weight: 2.4784 ------------------------------------------------------------------------------- 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 585 HIS ** C 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 GLN B 150 GLN B 224 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6517 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6961 Z= 0.258 Angle : 0.657 11.042 9385 Z= 0.340 Chirality : 0.042 0.158 1045 Planarity : 0.005 0.058 1198 Dihedral : 5.613 39.847 938 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 16.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % 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: -1.58 (0.28), residues: 833 helix: 0.18 (0.23), residues: 458 sheet: -3.52 (0.68), residues: 35 loop : -2.53 (0.32), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 59 HIS 0.005 0.001 HIS A 510 PHE 0.056 0.003 PHE C 174 TYR 0.023 0.002 TYR A 640 ARG 0.008 0.001 ARG C 56 *********************** 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 157 residues out of total 755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 190 LEU cc_start: 0.8103 (mt) cc_final: 0.7651 (mt) REVERT: A 595 PHE cc_start: 0.6240 (p90) cc_final: 0.6028 (p90) REVERT: A 636 GLN cc_start: 0.8554 (mm-40) cc_final: 0.8221 (mm-40) REVERT: C 223 ASP cc_start: 0.7501 (p0) cc_final: 0.7228 (p0) REVERT: B 40 GLU cc_start: 0.6662 (pm20) cc_final: 0.6442 (pm20) REVERT: B 59 TRP cc_start: 0.5998 (t60) cc_final: 0.5658 (t60) REVERT: B 149 TYR cc_start: 0.6861 (m-80) cc_final: 0.6337 (m-80) REVERT: B 218 MET cc_start: 0.5630 (mtp) cc_final: 0.5394 (mtp) outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.1779 time to fit residues: 37.6945 Evaluate side-chains 125 residues out of total 755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 0.786 ------------------------------------------------------------------------------- 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: 2.9990 chunk 46 optimal weight: 7.9990 chunk 1 optimal weight: 6.9990 chunk 60 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 69 optimal weight: 7.9990 chunk 56 optimal weight: 2.9990 chunk 0 optimal weight: 0.9980 chunk 41 optimal weight: 0.5980 chunk 72 optimal weight: 9.9990 chunk 20 optimal weight: 10.0000 overall best weight: 1.7184 ------------------------------------------------------------------------------- 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** B 224 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6451 moved from start: 0.2759 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 : 0.614 10.756 9385 Z= 0.317 Chirality : 0.041 0.160 1045 Planarity : 0.005 0.054 1198 Dihedral : 5.421 35.966 938 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % 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 (0.28), residues: 833 helix: 0.29 (0.23), residues: 457 sheet: -2.87 (0.82), residues: 28 loop : -2.43 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 59 HIS 0.006 0.001 HIS A 540 PHE 0.059 0.003 PHE C 174 TYR 0.018 0.002 TYR C 82 ARG 0.004 0.000 ARG C 56 *********************** 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 149 residues out of total 755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 186 MET cc_start: 0.5439 (mmt) cc_final: 0.5220 (mmm) REVERT: A 636 GLN cc_start: 0.8470 (mm-40) cc_final: 0.8172 (mm-40) REVERT: C 160 MET cc_start: 0.6555 (tpp) cc_final: 0.6151 (tpp) REVERT: C 223 ASP cc_start: 0.7303 (p0) cc_final: 0.7054 (p0) REVERT: B 40 GLU cc_start: 0.6568 (pm20) cc_final: 0.5961 (pp20) REVERT: B 59 TRP cc_start: 0.5890 (t60) cc_final: 0.5656 (t60) REVERT: B 149 TYR cc_start: 0.6690 (m-80) cc_final: 0.6318 (m-80) REVERT: B 191 LEU cc_start: 0.7141 (mt) cc_final: 0.6926 (mt) outliers start: 0 outliers final: 0 residues processed: 149 average time/residue: 0.1830 time to fit residues: 36.4744 Evaluate side-chains 117 residues out of total 755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 0.802 ------------------------------------------------------------------------------- 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: 2.9990 chunk 73 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 20 optimal weight: 9.9990 chunk 81 optimal weight: 6.9990 chunk 67 optimal weight: 6.9990 chunk 37 optimal weight: 4.9990 chunk 6 optimal weight: 6.9990 chunk 26 optimal weight: 0.0770 chunk 42 optimal weight: 9.9990 overall best weight: 2.0144 ------------------------------------------------------------------------------- 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 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: 0.6473 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6961 Z= 0.224 Angle : 0.622 11.055 9385 Z= 0.320 Chirality : 0.041 0.176 1045 Planarity : 0.005 0.054 1198 Dihedral : 5.472 37.584 938 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % 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: -1.39 (0.28), residues: 833 helix: 0.25 (0.23), residues: 458 sheet: -2.92 (0.79), residues: 28 loop : -2.38 (0.32), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 59 HIS 0.003 0.001 HIS A 510 PHE 0.039 0.002 PHE B 174 TYR 0.023 0.002 TYR A 640 ARG 0.005 0.000 ARG A 506 *********************** 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 159 residues out of total 755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 MET cc_start: 0.5485 (mmt) cc_final: 0.5245 (mmm) REVERT: A 636 GLN cc_start: 0.8580 (mm-40) cc_final: 0.8227 (mm-40) REVERT: C 31 GLU cc_start: 0.6429 (mt-10) cc_final: 0.5699 (mt-10) REVERT: C 160 MET cc_start: 0.6654 (tpp) cc_final: 0.6294 (tpp) REVERT: C 223 ASP cc_start: 0.7371 (p0) cc_final: 0.7100 (p0) REVERT: B 40 GLU cc_start: 0.6661 (pm20) cc_final: 0.6285 (mm-30) REVERT: B 59 TRP cc_start: 0.5950 (t60) cc_final: 0.5630 (t60) outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.1909 time to fit residues: 39.9083 Evaluate side-chains 122 residues out of total 755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 0.815 ------------------------------------------------------------------------------- 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: 3.9990 chunk 9 optimal weight: 4.9990 chunk 46 optimal weight: 6.9990 chunk 59 optimal weight: 0.8980 chunk 45 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 80 optimal weight: 6.9990 chunk 50 optimal weight: 9.9990 chunk 49 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- 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 368 ASN A 540 HIS A 585 HIS ** C 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6490 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6961 Z= 0.249 Angle : 0.667 11.485 9385 Z= 0.341 Chirality : 0.042 0.193 1045 Planarity : 0.005 0.054 1198 Dihedral : 5.625 38.372 938 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 17.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % 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: -1.45 (0.28), residues: 833 helix: 0.13 (0.23), residues: 454 sheet: -3.01 (0.79), residues: 29 loop : -2.26 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 59 HIS 0.009 0.002 HIS A 568 PHE 0.037 0.003 PHE C 174 TYR 0.020 0.002 TYR C 125 ARG 0.005 0.001 ARG A 506 *********************** 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 157 residues out of total 755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 0.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 160 MET cc_start: 0.6594 (tpp) cc_final: 0.6277 (tpp) REVERT: C 223 ASP cc_start: 0.7458 (p0) cc_final: 0.7183 (p0) outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.1931 time to fit residues: 40.2108 Evaluate side-chains 124 residues out of total 755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 0.835 ------------------------------------------------------------------------------- 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: 7.9990 chunk 24 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 51 optimal weight: 6.9990 chunk 55 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 63 optimal weight: 0.9990 chunk 73 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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 585 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6472 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6961 Z= 0.231 Angle : 0.666 11.815 9385 Z= 0.339 Chirality : 0.042 0.210 1045 Planarity : 0.005 0.074 1198 Dihedral : 5.606 38.354 938 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 17.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 0.14 % Allowed : 1.10 % Favored : 98.77 % 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: -1.44 (0.28), residues: 833 helix: 0.14 (0.23), residues: 455 sheet: -2.97 (0.77), residues: 29 loop : -2.28 (0.33), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 59 HIS 0.006 0.001 HIS A 568 PHE 0.038 0.002 PHE C 174 TYR 0.023 0.002 TYR A 640 ARG 0.006 0.001 ARG C 56 *********************** 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 155 residues out of total 755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 154 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 160 MET cc_start: 0.6558 (tpp) cc_final: 0.6301 (tpp) REVERT: C 223 ASP cc_start: 0.7395 (p0) cc_final: 0.7114 (p0) REVERT: B 59 TRP cc_start: 0.5863 (t60) cc_final: 0.5617 (t60) REVERT: B 198 GLU cc_start: 0.5991 (tm-30) cc_final: 0.5671 (tm-30) outliers start: 1 outliers final: 0 residues processed: 154 average time/residue: 0.1820 time to fit residues: 37.3729 Evaluate side-chains 125 residues out of total 755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 0.705 ------------------------------------------------------------------------------- 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: 0.9980 chunk 77 optimal weight: 0.0030 chunk 45 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 59 optimal weight: 8.9990 chunk 23 optimal weight: 6.9990 chunk 68 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 chunk 49 optimal weight: 3.9990 chunk 79 optimal weight: 0.4980 chunk 48 optimal weight: 0.7980 overall best weight: 0.5790 ------------------------------------------------------------------------------- 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 540 HIS A 585 HIS B 224 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6353 moved from start: 0.3239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6961 Z= 0.154 Angle : 0.602 11.170 9385 Z= 0.306 Chirality : 0.040 0.199 1045 Planarity : 0.004 0.054 1198 Dihedral : 5.108 29.761 938 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 0.14 % Allowed : 0.82 % Favored : 99.04 % 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: -0.92 (0.29), residues: 833 helix: 0.62 (0.24), residues: 457 sheet: -2.61 (0.80), residues: 28 loop : -2.17 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 59 HIS 0.007 0.001 HIS A 540 PHE 0.034 0.002 PHE C 174 TYR 0.021 0.002 TYR C 125 ARG 0.004 0.000 ARG A 178 *********************** 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 154 residues out of total 755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 153 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 GLN cc_start: 0.7478 (OUTLIER) cc_final: 0.7278 (mp10) REVERT: A 477 HIS cc_start: 0.5270 (m170) cc_final: 0.4637 (t-170) REVERT: C 223 ASP cc_start: 0.7208 (p0) cc_final: 0.6953 (p0) REVERT: B 198 GLU cc_start: 0.5982 (tm-30) cc_final: 0.5754 (tm-30) outliers start: 1 outliers final: 0 residues processed: 154 average time/residue: 0.1727 time to fit residues: 36.1177 Evaluate side-chains 125 residues out of total 755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 124 time to evaluate : 0.803 ------------------------------------------------------------------------------- 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: 0.9990 chunk 55 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 77 optimal weight: 0.0770 chunk 66 optimal weight: 0.9990 chunk 6 optimal weight: 7.9990 chunk 51 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 chunk 20 optimal weight: 9.9990 overall best weight: 0.9744 ------------------------------------------------------------------------------- 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 368 ASN A 494 GLN A 585 HIS ** C 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 GLN B 224 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6368 moved from start: 0.3382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6961 Z= 0.170 Angle : 0.612 11.314 9385 Z= 0.310 Chirality : 0.040 0.182 1045 Planarity : 0.004 0.054 1198 Dihedral : 5.052 32.396 938 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % 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: -0.79 (0.29), residues: 833 helix: 0.78 (0.24), residues: 451 sheet: -2.53 (0.83), residues: 28 loop : -2.14 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 59 HIS 0.007 0.001 HIS C 164 PHE 0.043 0.002 PHE C 174 TYR 0.015 0.002 TYR B 48 ARG 0.005 0.000 ARG A 178 ********************** 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 154 residues out of total 755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 477 HIS cc_start: 0.5276 (m170) cc_final: 0.4655 (t-170) REVERT: C 83 ARG cc_start: 0.6827 (ttp-110) cc_final: 0.6311 (ttp80) REVERT: C 223 ASP cc_start: 0.7386 (p0) cc_final: 0.7058 (p0) REVERT: B 198 GLU cc_start: 0.6094 (tm-30) cc_final: 0.5849 (tm-30) outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.1979 time to fit residues: 39.9262 Evaluate side-chains 125 residues out of total 755 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 0.730 ------------------------------------------------------------------------------- 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: 7.9990 chunk 9 optimal weight: 4.9990 chunk 18 optimal weight: 9.9990 chunk 66 optimal weight: 5.9990 chunk 27 optimal weight: 10.0000 chunk 68 optimal weight: 10.0000 chunk 8 optimal weight: 6.9990 chunk 12 optimal weight: 10.0000 chunk 58 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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 368 ASN A 370 HIS ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.169980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.148095 restraints weight = 10416.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.149388 restraints weight = 9028.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.151306 restraints weight = 7584.558| |-----------------------------------------------------------------------------| r_work (final): 0.4016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6595 moved from start: 0.3246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 6961 Z= 0.441 Angle : 0.858 14.777 9385 Z= 0.437 Chirality : 0.048 0.196 1045 Planarity : 0.006 0.052 1198 Dihedral : 6.327 41.856 938 Min Nonbonded Distance : 1.566 Molprobity Statistics. All-atom Clashscore : 20.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 0.14 % Allowed : 0.27 % 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: -1.88 (0.28), residues: 833 helix: -0.30 (0.22), residues: 460 sheet: -3.23 (0.85), residues: 24 loop : -2.40 (0.33), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP C 59 HIS 0.009 0.002 HIS A 568 PHE 0.062 0.004 PHE C 174 TYR 0.020 0.003 TYR A 266 ARG 0.009 0.001 ARG A 691 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1513.36 seconds wall clock time: 28 minutes 38.36 seconds (1718.36 seconds total)