Starting phenix.real_space_refine on Thu May 15 13:07:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xse_38617/05_2025/8xse_38617.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xse_38617/05_2025/8xse_38617.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xse_38617/05_2025/8xse_38617.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xse_38617/05_2025/8xse_38617.map" model { file = "/net/cci-nas-00/data/ceres_data/8xse_38617/05_2025/8xse_38617.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xse_38617/05_2025/8xse_38617.cif" } resolution = 2.5 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= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 6364 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 31 5.16 5 C 5117 2.51 5 N 1368 2.21 5 O 1604 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 8120 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1543 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 11, 'TRANS': 183} Chain: "H" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1658 Classifications: {'peptide': 223} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 210} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 1611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1611 Classifications: {'peptide': 212} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 201} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 2 Chain: "M" Number of atoms: 1673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1673 Classifications: {'peptide': 223} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 210} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 2 Chain: "N" Number of atoms: 1621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1621 Classifications: {'peptide': 212} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 199} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.00, per 1000 atoms: 0.74 Number of scatterers: 8120 At special positions: 0 Unit cell: (75.65, 107.95, 153, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 31 16.00 O 1604 8.00 N 1368 7.00 C 5117 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS H 150 " - pdb=" SG CYS H 206 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 96 " distance=2.03 Simple disulfide: pdb=" SG CYS M 150 " - pdb=" SG CYS M 206 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS N 134 " - pdb=" SG CYS N 194 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 Links applied NAG-ASN " NAG A 601 " - " ASN A 343 " Time building additional restraints: 2.01 Conformation dependent library (CDL) restraints added in 1.0 seconds 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1954 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 22 sheets defined 8.5% alpha, 39.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.26 Creating SS restraints... Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.581A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.139A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.281A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.823A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 163 through 168 removed outlier: 3.546A pdb=" N GLY H 167 " --> pdb=" O SER H 163 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ALA H 168 " --> pdb=" O TRP H 164 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 163 through 168' Processing helix chain 'L' and resid 121 through 128 removed outlier: 3.552A pdb=" N LYS L 126 " --> pdb=" O ASP L 122 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N SER L 127 " --> pdb=" O GLU L 123 " (cutoff:3.500A) Processing helix chain 'L' and resid 183 through 189 removed outlier: 3.658A pdb=" N LYS L 188 " --> pdb=" O ALA L 184 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N HIS L 189 " --> pdb=" O ASP L 185 " (cutoff:3.500A) Processing helix chain 'M' and resid 28 through 32 removed outlier: 3.722A pdb=" N SER M 31 " --> pdb=" O THR M 28 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N TYR M 32 " --> pdb=" O PHE M 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 28 through 32' Processing helix chain 'M' and resid 166 through 168 No H-bonds generated for 'chain 'M' and resid 166 through 168' Processing helix chain 'M' and resid 197 through 199 No H-bonds generated for 'chain 'M' and resid 197 through 199' Processing helix chain 'M' and resid 212 through 214 No H-bonds generated for 'chain 'M' and resid 212 through 214' Processing helix chain 'N' and resid 121 through 126 removed outlier: 3.671A pdb=" N LYS N 126 " --> pdb=" O ASP N 122 " (cutoff:3.500A) Processing helix chain 'N' and resid 183 through 187 removed outlier: 3.751A pdb=" N GLU N 187 " --> pdb=" O LYS N 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 183 through 187' Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.636A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA5, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.102A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 130 through 134 Processing sheet with id=AA7, first strand: chain 'H' and resid 130 through 134 Processing sheet with id=AA8, first strand: chain 'H' and resid 161 through 162 Processing sheet with id=AA9, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.784A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.465A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 114 through 118 removed outlier: 6.044A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 153 through 154 Processing sheet with id=AB4, first strand: chain 'M' and resid 3 through 7 Processing sheet with id=AB5, first strand: chain 'M' and resid 10 through 12 removed outlier: 6.027A pdb=" N GLY M 10 " --> pdb=" O THR M 120 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N MET M 34 " --> pdb=" O VAL M 50 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N VAL M 50 " --> pdb=" O MET M 34 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N TRP M 36 " --> pdb=" O VAL M 48 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'M' and resid 130 through 134 removed outlier: 4.031A pdb=" N GLY M 149 " --> pdb=" O LEU M 134 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N TYR M 186 " --> pdb=" O ASP M 154 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'M' and resid 130 through 134 removed outlier: 4.031A pdb=" N GLY M 149 " --> pdb=" O LEU M 134 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N TYR M 186 " --> pdb=" O ASP M 154 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'M' and resid 160 through 164 Processing sheet with id=AB9, first strand: chain 'M' and resid 160 through 164 removed outlier: 4.510A pdb=" N TYR M 204 " --> pdb=" O VAL M 221 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'N' and resid 4 through 7 Processing sheet with id=AC2, first strand: chain 'N' and resid 10 through 13 removed outlier: 6.496A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'N' and resid 114 through 118 removed outlier: 5.965A pdb=" N TYR N 173 " --> pdb=" O ASN N 138 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'N' and resid 145 through 149 321 hydrogen bonds defined for protein. 828 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.61 Time building geometry restraints manager: 2.37 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: 2607 1.34 - 1.46: 2123 1.46 - 1.58: 3548 1.58 - 1.70: 1 1.70 - 1.82: 38 Bond restraints: 8317 Sorted by residual: bond pdb=" CB PRO L 113 " pdb=" CG PRO L 113 " ideal model delta sigma weight residual 1.492 1.663 -0.171 5.00e-02 4.00e+02 1.17e+01 bond pdb=" C ASP M 111 " pdb=" N PRO M 112 " ideal model delta sigma weight residual 1.333 1.354 -0.021 1.20e-02 6.94e+03 2.92e+00 bond pdb=" CB PRO L 120 " pdb=" CG PRO L 120 " ideal model delta sigma weight residual 1.492 1.577 -0.085 5.00e-02 4.00e+02 2.88e+00 bond pdb=" CB PRO N 204 " pdb=" CG PRO N 204 " ideal model delta sigma weight residual 1.492 1.572 -0.080 5.00e-02 4.00e+02 2.59e+00 bond pdb=" CG PRO N 204 " pdb=" CD PRO N 204 " ideal model delta sigma weight residual 1.503 1.553 -0.050 3.40e-02 8.65e+02 2.20e+00 ... (remaining 8312 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 11190 2.49 - 4.98: 103 4.98 - 7.47: 15 7.47 - 9.96: 4 9.96 - 12.45: 1 Bond angle restraints: 11313 Sorted by residual: angle pdb=" CA PRO L 113 " pdb=" N PRO L 113 " pdb=" CD PRO L 113 " ideal model delta sigma weight residual 112.00 99.55 12.45 1.40e+00 5.10e-01 7.91e+01 angle pdb=" N PRO L 113 " pdb=" CD PRO L 113 " pdb=" CG PRO L 113 " ideal model delta sigma weight residual 103.20 95.54 7.66 1.50e+00 4.44e-01 2.61e+01 angle pdb=" CA PRO N 204 " pdb=" N PRO N 204 " pdb=" CD PRO N 204 " ideal model delta sigma weight residual 112.00 106.89 5.11 1.40e+00 5.10e-01 1.33e+01 angle pdb=" CA PRO L 120 " pdb=" N PRO L 120 " pdb=" CD PRO L 120 " ideal model delta sigma weight residual 112.00 107.20 4.80 1.40e+00 5.10e-01 1.17e+01 angle pdb=" CA ILE H 205 " pdb=" CB ILE H 205 " pdb=" CG1 ILE H 205 " ideal model delta sigma weight residual 110.40 116.00 -5.60 1.70e+00 3.46e-01 1.08e+01 ... (remaining 11308 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 4205 17.93 - 35.87: 547 35.87 - 53.80: 165 53.80 - 71.73: 31 71.73 - 89.66: 12 Dihedral angle restraints: 4960 sinusoidal: 1893 harmonic: 3067 Sorted by residual: dihedral pdb=" CA PRO M 212 " pdb=" C PRO M 212 " pdb=" N SER M 213 " pdb=" CA SER M 213 " ideal model delta harmonic sigma weight residual 180.00 161.38 18.62 0 5.00e+00 4.00e-02 1.39e+01 dihedral pdb=" CA SER H 52 " pdb=" C SER H 52 " pdb=" N GLY H 53 " pdb=" CA GLY H 53 " ideal model delta harmonic sigma weight residual 180.00 163.63 16.37 0 5.00e+00 4.00e-02 1.07e+01 dihedral pdb=" CB GLU N 187 " pdb=" CG GLU N 187 " pdb=" CD GLU N 187 " pdb=" OE1 GLU N 187 " ideal model delta sinusoidal sigma weight residual 0.00 89.66 -89.66 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 4957 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 926 0.043 - 0.085: 239 0.085 - 0.127: 81 0.127 - 0.170: 10 0.170 - 0.212: 1 Chirality restraints: 1257 Sorted by residual: chirality pdb=" CA PRO L 113 " pdb=" N PRO L 113 " pdb=" C PRO L 113 " pdb=" CB PRO L 113 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA ILE L 21 " pdb=" N ILE L 21 " pdb=" C ILE L 21 " pdb=" CB ILE L 21 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.44e-01 chirality pdb=" CB ILE L 2 " pdb=" CA ILE L 2 " pdb=" CG1 ILE L 2 " pdb=" CG2 ILE L 2 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.15 2.00e-01 2.50e+01 5.34e-01 ... (remaining 1254 not shown) Planarity restraints: 1459 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER N 203 " -0.064 5.00e-02 4.00e+02 9.43e-02 1.42e+01 pdb=" N PRO N 204 " 0.163 5.00e-02 4.00e+02 pdb=" CA PRO N 204 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO N 204 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA L 112 " -0.059 5.00e-02 4.00e+02 8.22e-02 1.08e+01 pdb=" N PRO L 113 " 0.142 5.00e-02 4.00e+02 pdb=" CA PRO L 113 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO L 113 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO L 119 " -0.038 5.00e-02 4.00e+02 5.64e-02 5.09e+00 pdb=" N PRO L 120 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO L 120 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO L 120 " -0.032 5.00e-02 4.00e+02 ... (remaining 1456 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 395 2.72 - 3.26: 7017 3.26 - 3.81: 12438 3.81 - 4.35: 15502 4.35 - 4.90: 27723 Nonbonded interactions: 63075 Sorted by model distance: nonbonded pdb=" OG SER M 213 " pdb=" OG1 THR M 215 " model vdw 2.174 3.040 nonbonded pdb=" OD2 ASP L 105 " pdb=" OH TYR L 173 " model vdw 2.225 3.040 nonbonded pdb=" OD1 ASN N 137 " pdb=" OG SER N 174 " model vdw 2.251 3.040 nonbonded pdb=" O SER M 85 " pdb=" OG SER M 85 " model vdw 2.261 3.040 nonbonded pdb=" O THR A 333 " pdb=" OG1 THR A 333 " model vdw 2.262 3.040 ... (remaining 63070 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'H' and (resid 1 through 32 or resid 34 or resid 36 through 48 or resid 5 \ 1 through 52 or resid 55 or resid 59 through 97 or resid 99 or resid 106 or resi \ d 110 or resid 113 through 223)) selection = (chain 'M' and (resid 1 through 4 or (resid 5 and (name N or name CA or name C o \ r name O or name CB or name CG1)) or resid 6 through 32 or resid 34 or resid 36 \ through 48 or resid 51 through 52 or resid 55 or resid 59 through 97 or resid 99 \ or resid 106 or resid 110 or resid 113 through 223)) } ncs_group { reference = (chain 'L' and (resid 1 through 10 or resid 12 through 17 or resid 19 through 27 \ or resid 29 through 30 or resid 33 or resid 35 through 38 or resid 40 through 5 \ 1 or resid 54 or resid 57 through 76 or resid 78 through 79 or resid 81 through \ 90 or resid 93 or resid 95 or resid 97 through 99 or resid 101 through 212)) selection = (chain 'N' and (resid 1 through 10 or resid 12 through 17 or resid 19 through 27 \ or resid 29 through 30 or resid 33 or resid 35 through 38 or resid 40 through 5 \ 1 or resid 54 or resid 57 through 76 or resid 78 through 79 or resid 81 through \ 90 or resid 93 or resid 95 or resid 97 through 99 or resid 101 through 212)) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.060 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: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 22.320 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:11.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.171 8330 Z= 0.142 Angle : 0.646 12.454 11340 Z= 0.347 Chirality : 0.043 0.212 1257 Planarity : 0.006 0.094 1458 Dihedral : 17.935 89.664 2970 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.59 % Favored : 94.31 % Rotamer: Outliers : 5.41 % Allowed : 27.62 % Favored : 66.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.54 % 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: -0.52 (0.26), residues: 1055 helix: -3.51 (0.63), residues: 33 sheet: 0.79 (0.25), residues: 444 loop : -1.09 (0.26), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 436 HIS 0.003 0.001 HIS H 111 PHE 0.007 0.001 PHE N 139 TYR 0.012 0.001 TYR A 495 ARG 0.012 0.000 ARG L 211 Details of bonding type rmsd link_NAG-ASN : bond 0.00023 ( 1) link_NAG-ASN : angle 0.86284 ( 3) hydrogen bonds : bond 0.15175 ( 289) hydrogen bonds : angle 7.22823 ( 828) SS BOND : bond 0.00369 ( 12) SS BOND : angle 1.04073 ( 24) covalent geometry : bond 0.00372 ( 8317) covalent geometry : angle 0.64440 (11313) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 104 time to evaluate : 0.888 Fit side-chains REVERT: A 408 ARG cc_start: 0.8492 (OUTLIER) cc_final: 0.8276 (ppt170) REVERT: H 217 VAL cc_start: 0.7722 (p) cc_final: 0.7406 (t) REVERT: M 145 THR cc_start: 0.7641 (p) cc_final: 0.7416 (t) outliers start: 49 outliers final: 47 residues processed: 152 average time/residue: 0.8295 time to fit residues: 137.2238 Evaluate side-chains 148 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 100 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain H residue 1 GLN Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 100 HIS Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 125 SER Chi-restraints excluded: chain H residue 175 THR Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain H residue 188 LEU Chi-restraints excluded: chain H residue 202 GLN Chi-restraints excluded: chain H residue 204 TYR Chi-restraints excluded: chain H residue 205 ILE Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain L residue 202 SER Chi-restraints excluded: chain M residue 1 GLN Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 63 SER Chi-restraints excluded: chain M residue 65 LYS Chi-restraints excluded: chain M residue 71 SER Chi-restraints excluded: chain M residue 89 GLU Chi-restraints excluded: chain M residue 137 SER Chi-restraints excluded: chain M residue 138 SER Chi-restraints excluded: chain M residue 152 VAL Chi-restraints excluded: chain M residue 217 VAL Chi-restraints excluded: chain M residue 220 ARG Chi-restraints excluded: chain M residue 221 VAL Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 28 SER Chi-restraints excluded: chain N residue 53 SER Chi-restraints excluded: chain N residue 56 SER Chi-restraints excluded: chain N residue 106 ILE Chi-restraints excluded: chain N residue 109 THR Chi-restraints excluded: chain N residue 133 VAL Chi-restraints excluded: chain N residue 142 ARG Chi-restraints excluded: chain N residue 146 VAL Chi-restraints excluded: chain N residue 162 SER Chi-restraints excluded: chain N residue 181 LEU Chi-restraints excluded: chain N residue 188 LYS Chi-restraints excluded: chain N residue 191 VAL Chi-restraints excluded: chain N residue 197 THR Chi-restraints excluded: chain N residue 201 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 0.8980 chunk 79 optimal weight: 0.0980 chunk 44 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 chunk 95 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.135363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.119613 restraints weight = 11259.299| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 1.93 r_work: 0.3594 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3459 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.0853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 8330 Z= 0.174 Angle : 0.618 8.624 11340 Z= 0.314 Chirality : 0.044 0.155 1257 Planarity : 0.005 0.053 1458 Dihedral : 8.347 64.500 1253 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.78 % Favored : 94.03 % Rotamer: Outliers : 4.75 % Allowed : 26.63 % Favored : 68.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.54 % 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: -0.50 (0.26), residues: 1055 helix: -2.82 (0.63), residues: 46 sheet: 0.86 (0.25), residues: 456 loop : -1.19 (0.26), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP M 113 HIS 0.004 0.001 HIS H 111 PHE 0.012 0.001 PHE N 139 TYR 0.016 0.002 TYR N 49 ARG 0.005 0.000 ARG L 211 Details of bonding type rmsd link_NAG-ASN : bond 0.00227 ( 1) link_NAG-ASN : angle 1.11699 ( 3) hydrogen bonds : bond 0.03628 ( 289) hydrogen bonds : angle 5.77573 ( 828) SS BOND : bond 0.00516 ( 12) SS BOND : angle 1.30434 ( 24) covalent geometry : bond 0.00420 ( 8317) covalent geometry : angle 0.61597 (11313) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 109 time to evaluate : 0.860 Fit side-chains REVERT: H 34 MET cc_start: 0.8680 (mmp) cc_final: 0.8173 (mmp) outliers start: 43 outliers final: 24 residues processed: 142 average time/residue: 0.7589 time to fit residues: 117.9363 Evaluate side-chains 129 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 105 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 100 HIS Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 202 GLN Chi-restraints excluded: chain H residue 204 TYR Chi-restraints excluded: chain L residue 17 ASP Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 93 SER Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain L residue 164 THR Chi-restraints excluded: chain M residue 1 GLN Chi-restraints excluded: chain M residue 191 VAL Chi-restraints excluded: chain M residue 217 VAL Chi-restraints excluded: chain N residue 10 SER Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 109 THR Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 146 VAL Chi-restraints excluded: chain N residue 168 SER Chi-restraints excluded: chain N residue 175 LEU Chi-restraints excluded: chain N residue 181 LEU Chi-restraints excluded: chain N residue 191 VAL Chi-restraints excluded: chain N residue 201 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 37 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 81 optimal weight: 0.6980 chunk 42 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 82 optimal weight: 0.6980 chunk 101 optimal weight: 0.8980 chunk 87 optimal weight: 0.5980 chunk 77 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.134943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.119001 restraints weight = 11484.376| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 1.95 r_work: 0.3586 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3450 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.1096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8330 Z= 0.168 Angle : 0.602 8.859 11340 Z= 0.304 Chirality : 0.044 0.151 1257 Planarity : 0.005 0.051 1458 Dihedral : 6.501 61.464 1194 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.69 % Favored : 94.12 % Rotamer: Outliers : 4.09 % Allowed : 25.97 % Favored : 69.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.26), residues: 1055 helix: -2.57 (0.67), residues: 46 sheet: 1.00 (0.24), residues: 464 loop : -1.20 (0.26), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP M 113 HIS 0.004 0.001 HIS H 111 PHE 0.012 0.001 PHE N 139 TYR 0.016 0.002 TYR N 49 ARG 0.004 0.000 ARG L 108 Details of bonding type rmsd link_NAG-ASN : bond 0.00125 ( 1) link_NAG-ASN : angle 1.27850 ( 3) hydrogen bonds : bond 0.03530 ( 289) hydrogen bonds : angle 5.64368 ( 828) SS BOND : bond 0.00508 ( 12) SS BOND : angle 1.23758 ( 24) covalent geometry : bond 0.00406 ( 8317) covalent geometry : angle 0.60008 (11313) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 113 time to evaluate : 0.943 Fit side-chains outliers start: 37 outliers final: 21 residues processed: 146 average time/residue: 0.8299 time to fit residues: 131.6463 Evaluate side-chains 130 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 109 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 98 LYS Chi-restraints excluded: chain H residue 100 HIS Chi-restraints excluded: chain H residue 166 SER Chi-restraints excluded: chain H residue 202 GLN Chi-restraints excluded: chain H residue 204 TYR Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 93 SER Chi-restraints excluded: chain L residue 164 THR Chi-restraints excluded: chain M residue 191 VAL Chi-restraints excluded: chain M residue 217 VAL Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 109 THR Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 146 VAL Chi-restraints excluded: chain N residue 168 SER Chi-restraints excluded: chain N residue 175 LEU Chi-restraints excluded: chain N residue 181 LEU Chi-restraints excluded: chain N residue 201 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 83 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 36 optimal weight: 0.0870 chunk 67 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 66 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.135453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.119552 restraints weight = 11359.700| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 1.95 r_work: 0.3596 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3461 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.1189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8330 Z= 0.135 Angle : 0.576 8.639 11340 Z= 0.290 Chirality : 0.043 0.146 1257 Planarity : 0.005 0.045 1458 Dihedral : 5.974 62.018 1186 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.78 % Favored : 94.03 % Rotamer: Outliers : 4.20 % Allowed : 26.63 % Favored : 69.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.54 % 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: -0.30 (0.26), residues: 1055 helix: -2.43 (0.69), residues: 46 sheet: 1.01 (0.25), residues: 456 loop : -1.08 (0.26), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP M 113 HIS 0.003 0.001 HIS H 111 PHE 0.011 0.001 PHE N 139 TYR 0.013 0.001 TYR L 49 ARG 0.003 0.000 ARG L 108 Details of bonding type rmsd link_NAG-ASN : bond 0.00058 ( 1) link_NAG-ASN : angle 1.26488 ( 3) hydrogen bonds : bond 0.03243 ( 289) hydrogen bonds : angle 5.48930 ( 828) SS BOND : bond 0.00435 ( 12) SS BOND : angle 1.12422 ( 24) covalent geometry : bond 0.00325 ( 8317) covalent geometry : angle 0.57438 (11313) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 115 time to evaluate : 0.871 Fit side-chains outliers start: 38 outliers final: 24 residues processed: 150 average time/residue: 0.7545 time to fit residues: 123.7974 Evaluate side-chains 136 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 112 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 100 HIS Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 166 SER Chi-restraints excluded: chain H residue 179 VAL Chi-restraints excluded: chain H residue 204 TYR Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 93 SER Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 164 THR Chi-restraints excluded: chain M residue 117 THR Chi-restraints excluded: chain M residue 152 VAL Chi-restraints excluded: chain M residue 191 VAL Chi-restraints excluded: chain M residue 217 VAL Chi-restraints excluded: chain N residue 109 THR Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 146 VAL Chi-restraints excluded: chain N residue 162 SER Chi-restraints excluded: chain N residue 168 SER Chi-restraints excluded: chain N residue 181 LEU Chi-restraints excluded: chain N residue 201 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 23 optimal weight: 1.9990 chunk 13 optimal weight: 0.1980 chunk 65 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 66 optimal weight: 0.0030 chunk 93 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 overall best weight: 0.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.134591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.118617 restraints weight = 11247.532| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 1.96 r_work: 0.3585 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3450 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8330 Z= 0.175 Angle : 0.616 8.880 11340 Z= 0.308 Chirality : 0.044 0.150 1257 Planarity : 0.005 0.047 1458 Dihedral : 5.429 56.957 1182 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.16 % Favored : 93.65 % Rotamer: Outliers : 4.20 % Allowed : 26.19 % Favored : 69.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.54 % 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: -0.24 (0.26), residues: 1055 helix: -2.45 (0.69), residues: 46 sheet: 1.09 (0.25), residues: 464 loop : -1.12 (0.26), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP M 113 HIS 0.004 0.001 HIS H 111 PHE 0.013 0.001 PHE N 139 TYR 0.016 0.002 TYR N 49 ARG 0.002 0.000 ARG L 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00142 ( 1) link_NAG-ASN : angle 1.38776 ( 3) hydrogen bonds : bond 0.03540 ( 289) hydrogen bonds : angle 5.58432 ( 828) SS BOND : bond 0.00514 ( 12) SS BOND : angle 1.23012 ( 24) covalent geometry : bond 0.00424 ( 8317) covalent geometry : angle 0.61321 (11313) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 115 time to evaluate : 0.811 Fit side-chains outliers start: 38 outliers final: 26 residues processed: 147 average time/residue: 0.7061 time to fit residues: 113.8394 Evaluate side-chains 136 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 110 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 100 HIS Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 166 SER Chi-restraints excluded: chain H residue 179 VAL Chi-restraints excluded: chain H residue 202 GLN Chi-restraints excluded: chain H residue 204 TYR Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 164 THR Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain M residue 117 THR Chi-restraints excluded: chain M residue 191 VAL Chi-restraints excluded: chain M residue 217 VAL Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 146 VAL Chi-restraints excluded: chain N residue 162 SER Chi-restraints excluded: chain N residue 168 SER Chi-restraints excluded: chain N residue 175 LEU Chi-restraints excluded: chain N residue 181 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 63 optimal weight: 0.3980 chunk 62 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 104 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 99 optimal weight: 0.0970 chunk 28 optimal weight: 0.0980 chunk 39 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 GLN M 209 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.136133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.120222 restraints weight = 11293.125| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 1.95 r_work: 0.3607 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3473 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.1342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8330 Z= 0.114 Angle : 0.557 8.582 11340 Z= 0.281 Chirality : 0.042 0.143 1257 Planarity : 0.005 0.044 1458 Dihedral : 5.031 59.001 1179 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.31 % Favored : 94.50 % Rotamer: Outliers : 2.87 % Allowed : 27.62 % Favored : 69.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.54 % 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: -0.19 (0.26), residues: 1055 helix: -2.31 (0.70), residues: 46 sheet: 1.06 (0.25), residues: 454 loop : -0.98 (0.26), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 436 HIS 0.003 0.001 HIS H 111 PHE 0.010 0.001 PHE L 139 TYR 0.013 0.001 TYR L 49 ARG 0.006 0.000 ARG L 108 Details of bonding type rmsd link_NAG-ASN : bond 0.00034 ( 1) link_NAG-ASN : angle 1.30762 ( 3) hydrogen bonds : bond 0.03012 ( 289) hydrogen bonds : angle 5.35991 ( 828) SS BOND : bond 0.00390 ( 12) SS BOND : angle 1.02270 ( 24) covalent geometry : bond 0.00273 ( 8317) covalent geometry : angle 0.55521 (11313) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 110 time to evaluate : 0.775 Fit side-chains REVERT: H 34 MET cc_start: 0.8576 (mmp) cc_final: 0.8235 (mmp) REVERT: N 11 LEU cc_start: 0.8121 (tp) cc_final: 0.7920 (tt) outliers start: 26 outliers final: 23 residues processed: 131 average time/residue: 0.7400 time to fit residues: 106.2306 Evaluate side-chains 133 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 110 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain H residue 100 HIS Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 166 SER Chi-restraints excluded: chain H residue 204 TYR Chi-restraints excluded: chain L residue 3 GLN Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 164 THR Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain M residue 89 GLU Chi-restraints excluded: chain M residue 117 THR Chi-restraints excluded: chain M residue 191 VAL Chi-restraints excluded: chain M residue 217 VAL Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 146 VAL Chi-restraints excluded: chain N residue 162 SER Chi-restraints excluded: chain N residue 181 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 84 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 88 optimal weight: 0.5980 chunk 19 optimal weight: 3.9990 chunk 92 optimal weight: 0.2980 chunk 91 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 45 optimal weight: 0.2980 chunk 73 optimal weight: 0.7980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.135444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.119506 restraints weight = 11305.376| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 1.95 r_work: 0.3608 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3475 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8330 Z= 0.135 Angle : 0.571 8.671 11340 Z= 0.288 Chirality : 0.043 0.147 1257 Planarity : 0.005 0.046 1458 Dihedral : 5.048 59.168 1179 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.69 % Favored : 94.12 % Rotamer: Outliers : 3.98 % Allowed : 26.63 % Favored : 69.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.54 % 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: -0.16 (0.26), residues: 1055 helix: -2.29 (0.70), residues: 46 sheet: 1.11 (0.25), residues: 450 loop : -0.99 (0.26), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 113 HIS 0.003 0.001 HIS H 111 PHE 0.011 0.001 PHE N 139 TYR 0.014 0.001 TYR L 49 ARG 0.007 0.000 ARG L 108 Details of bonding type rmsd link_NAG-ASN : bond 0.00053 ( 1) link_NAG-ASN : angle 1.35416 ( 3) hydrogen bonds : bond 0.03192 ( 289) hydrogen bonds : angle 5.38914 ( 828) SS BOND : bond 0.00437 ( 12) SS BOND : angle 1.13172 ( 24) covalent geometry : bond 0.00324 ( 8317) covalent geometry : angle 0.56920 (11313) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 110 time to evaluate : 0.805 Fit side-chains REVERT: M 215 THR cc_start: 0.7726 (m) cc_final: 0.7448 (m) outliers start: 36 outliers final: 30 residues processed: 138 average time/residue: 0.8324 time to fit residues: 125.3788 Evaluate side-chains 137 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 107 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 98 LYS Chi-restraints excluded: chain H residue 100 HIS Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 166 SER Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 202 GLN Chi-restraints excluded: chain H residue 204 TYR Chi-restraints excluded: chain L residue 3 GLN Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 164 THR Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain M residue 89 GLU Chi-restraints excluded: chain M residue 117 THR Chi-restraints excluded: chain M residue 191 VAL Chi-restraints excluded: chain M residue 217 VAL Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 146 VAL Chi-restraints excluded: chain N residue 162 SER Chi-restraints excluded: chain N residue 168 SER Chi-restraints excluded: chain N residue 175 LEU Chi-restraints excluded: chain N residue 181 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 75 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 chunk 26 optimal weight: 0.0040 chunk 103 optimal weight: 0.7980 chunk 51 optimal weight: 0.4980 chunk 57 optimal weight: 3.9990 chunk 66 optimal weight: 0.3980 chunk 58 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.135929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.119871 restraints weight = 11468.986| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 1.99 r_work: 0.3610 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3476 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8330 Z= 0.127 Angle : 0.561 8.633 11340 Z= 0.284 Chirality : 0.042 0.145 1257 Planarity : 0.005 0.048 1458 Dihedral : 5.003 59.923 1179 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.50 % Favored : 94.31 % Rotamer: Outliers : 3.54 % Allowed : 27.18 % Favored : 69.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.54 % 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: -0.12 (0.26), residues: 1055 helix: -2.27 (0.71), residues: 46 sheet: 1.12 (0.25), residues: 452 loop : -0.93 (0.26), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP M 113 HIS 0.003 0.001 HIS H 111 PHE 0.010 0.001 PHE N 139 TYR 0.013 0.001 TYR L 49 ARG 0.007 0.000 ARG L 108 Details of bonding type rmsd link_NAG-ASN : bond 0.00054 ( 1) link_NAG-ASN : angle 1.35124 ( 3) hydrogen bonds : bond 0.03092 ( 289) hydrogen bonds : angle 5.33922 ( 828) SS BOND : bond 0.00408 ( 12) SS BOND : angle 1.03493 ( 24) covalent geometry : bond 0.00305 ( 8317) covalent geometry : angle 0.55960 (11313) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 108 time to evaluate : 0.827 Fit side-chains REVERT: M 215 THR cc_start: 0.7704 (m) cc_final: 0.7419 (m) outliers start: 32 outliers final: 28 residues processed: 133 average time/residue: 0.7821 time to fit residues: 113.5630 Evaluate side-chains 134 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 106 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 100 HIS Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 166 SER Chi-restraints excluded: chain H residue 202 GLN Chi-restraints excluded: chain H residue 204 TYR Chi-restraints excluded: chain L residue 3 GLN Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 164 THR Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain M residue 1 GLN Chi-restraints excluded: chain M residue 89 GLU Chi-restraints excluded: chain M residue 117 THR Chi-restraints excluded: chain M residue 191 VAL Chi-restraints excluded: chain M residue 217 VAL Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 146 VAL Chi-restraints excluded: chain N residue 162 SER Chi-restraints excluded: chain N residue 168 SER Chi-restraints excluded: chain N residue 181 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 58 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 chunk 67 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 69 optimal weight: 0.1980 chunk 95 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.136217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.120125 restraints weight = 11446.061| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 1.99 r_work: 0.3606 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3471 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8330 Z= 0.134 Angle : 0.570 8.640 11340 Z= 0.287 Chirality : 0.043 0.146 1257 Planarity : 0.005 0.048 1458 Dihedral : 5.016 59.854 1179 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.69 % Favored : 94.12 % Rotamer: Outliers : 3.54 % Allowed : 27.40 % Favored : 69.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.54 % 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: -0.11 (0.26), residues: 1055 helix: -2.28 (0.71), residues: 46 sheet: 1.14 (0.25), residues: 452 loop : -0.94 (0.26), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 113 HIS 0.003 0.001 HIS H 111 PHE 0.011 0.001 PHE N 139 TYR 0.013 0.001 TYR L 49 ARG 0.008 0.000 ARG L 108 Details of bonding type rmsd link_NAG-ASN : bond 0.00055 ( 1) link_NAG-ASN : angle 1.37245 ( 3) hydrogen bonds : bond 0.03155 ( 289) hydrogen bonds : angle 5.39576 ( 828) SS BOND : bond 0.00432 ( 12) SS BOND : angle 1.09069 ( 24) covalent geometry : bond 0.00322 ( 8317) covalent geometry : angle 0.56798 (11313) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2110 Ramachandran restraints generated. 1055 Oldfield, 0 Emsley, 1055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 107 time to evaluate : 0.931 Fit side-chains REVERT: M 215 THR cc_start: 0.7662 (m) cc_final: 0.7380 (m) outliers start: 32 outliers final: 29 residues processed: 132 average time/residue: 0.7771 time to fit residues: 112.2855 Evaluate side-chains 134 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 105 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 100 HIS Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain H residue 166 SER Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain H residue 202 GLN Chi-restraints excluded: chain H residue 204 TYR Chi-restraints excluded: chain L residue 3 GLN Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 164 THR Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain M residue 117 THR Chi-restraints excluded: chain M residue 191 VAL Chi-restraints excluded: chain M residue 217 VAL Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 146 VAL Chi-restraints excluded: chain N residue 162 SER Chi-restraints excluded: chain N residue 168 SER Chi-restraints excluded: chain N residue 181 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 60.5189 > 50: distance: 129 - 136: 12.024 distance: 136 - 137: 4.780 distance: 137 - 138: 15.362 distance: 137 - 140: 3.545 distance: 138 - 139: 11.190 distance: 138 - 145: 24.818 distance: 140 - 141: 13.345 distance: 141 - 142: 8.615 distance: 142 - 143: 8.513 distance: 142 - 144: 11.843 distance: 145 - 146: 17.946 distance: 146 - 147: 18.942 distance: 146 - 149: 29.021 distance: 147 - 148: 10.543 distance: 147 - 150: 4.689 distance: 150 - 151: 10.407 distance: 151 - 152: 20.418 distance: 151 - 154: 33.287 distance: 152 - 153: 14.488 distance: 152 - 158: 26.911 distance: 154 - 155: 15.991 distance: 155 - 156: 9.838 distance: 155 - 157: 25.775 distance: 158 - 159: 11.148 distance: 159 - 160: 30.772 distance: 160 - 161: 24.991 distance: 160 - 164: 27.591 distance: 162 - 163: 16.101 distance: 164 - 165: 13.928 distance: 165 - 166: 8.325 distance: 165 - 168: 21.744 distance: 166 - 167: 11.356 distance: 166 - 175: 20.731 distance: 168 - 169: 8.521 distance: 169 - 170: 28.927 distance: 169 - 171: 17.564 distance: 170 - 172: 13.919 distance: 171 - 173: 7.011 distance: 172 - 174: 16.265 distance: 173 - 174: 31.127 distance: 175 - 176: 20.001 distance: 175 - 181: 19.126 distance: 176 - 177: 15.904 distance: 176 - 179: 18.789 distance: 177 - 178: 23.402 distance: 177 - 182: 9.451 distance: 179 - 180: 18.394 distance: 180 - 181: 23.984 distance: 182 - 183: 10.019 distance: 183 - 184: 10.270 distance: 183 - 186: 11.830 distance: 184 - 185: 19.259 distance: 184 - 190: 13.686 distance: 186 - 187: 3.264 distance: 187 - 189: 13.171 distance: 190 - 191: 6.056 distance: 191 - 194: 3.770 distance: 192 - 193: 16.741 distance: 192 - 197: 25.505 distance: 194 - 195: 4.110 distance: 194 - 196: 7.153 distance: 197 - 198: 8.728 distance: 198 - 199: 7.868 distance: 199 - 200: 9.008 distance: 199 - 208: 9.168 distance: 201 - 202: 6.741 distance: 202 - 203: 6.782 distance: 202 - 204: 4.525 distance: 203 - 205: 4.531 distance: 204 - 206: 4.106 distance: 205 - 207: 3.411 distance: 206 - 207: 4.938 distance: 208 - 209: 4.069 distance: 209 - 210: 5.985 distance: 210 - 211: 8.611 distance: 210 - 212: 12.263