Starting phenix.real_space_refine on Mon Aug 5 10:30:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xse_38617/08_2024/8xse_38617.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xse_38617/08_2024/8xse_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xse_38617/08_2024/8xse_38617.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xse_38617/08_2024/8xse_38617.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xse_38617/08_2024/8xse_38617.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xse_38617/08_2024/8xse_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 Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 5.56, per 1000 atoms: 0.68 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 - 3.50 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 Links applied NAG-ASN " NAG A 601 " - " ASN A 343 " Time building additional restraints: 2.88 Conformation dependent library (CDL) restraints added in 1.6 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: 1.09 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: 3.12 Time building geometry restraints manager: 3.15 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: 95.54 - 103.23: 82 103.23 - 110.93: 2949 110.93 - 118.62: 3534 118.62 - 126.31: 4621 126.31 - 134.00: 127 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: 10.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.860 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: 26.210 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.940 ------------------------------------------------------------------------------- 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 8317 Z= 0.233 Angle : 0.644 12.454 11313 Z= 0.346 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 *********************** 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 fitting. rotamer outliers: 49 poor density : 104 time to evaluate : 0.920 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: 0.8231 time to fit residues: 136.3262 Evaluate side-chains 148 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 100 time to evaluate : 0.930 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 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 8317 Z= 0.272 Angle : 0.616 8.624 11313 Z= 0.313 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 *********************** 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 fitting. rotamer outliers: 43 poor density : 109 time to evaluate : 0.871 Fit side-chains REVERT: H 34 MET cc_start: 0.8558 (mmp) cc_final: 0.8020 (mmp) REVERT: H 152 VAL cc_start: 0.7776 (t) cc_final: 0.7552 (m) outliers start: 43 outliers final: 24 residues processed: 142 average time/residue: 0.7704 time to fit residues: 119.5956 Evaluate side-chains 129 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 105 time to evaluate : 0.872 ------------------------------------------------------------------------------- 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 52 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 79 optimal weight: 0.0060 chunk 64 optimal weight: 0.9980 chunk 26 optimal weight: 0.0970 chunk 95 optimal weight: 0.9990 chunk 103 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 94 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 overall best weight: 0.4194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.0954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8317 Z= 0.180 Angle : 0.552 8.582 11313 Z= 0.279 Chirality : 0.042 0.145 1257 Planarity : 0.005 0.046 1458 Dihedral : 6.243 60.843 1194 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.40 % Favored : 94.41 % Rotamer: Outliers : 3.20 % Allowed : 26.74 % Favored : 70.06 % 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: -0.36 (0.26), residues: 1055 helix: -2.47 (0.68), residues: 46 sheet: 0.96 (0.25), residues: 456 loop : -1.11 (0.26), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP M 164 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 0.003 0.000 ARG L 108 *********************** 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 140 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 111 time to evaluate : 0.891 Fit side-chains REVERT: H 152 VAL cc_start: 0.7780 (t) cc_final: 0.7573 (m) REVERT: M 4 LEU cc_start: 0.7565 (OUTLIER) cc_final: 0.7329 (mt) outliers start: 29 outliers final: 18 residues processed: 135 average time/residue: 0.7943 time to fit residues: 117.4633 Evaluate side-chains 121 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 102 time to evaluate : 0.896 ------------------------------------------------------------------------------- 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 202 GLN Chi-restraints excluded: chain H residue 204 TYR Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 164 THR Chi-restraints excluded: chain M residue 4 LEU 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 109 THR Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 146 VAL Chi-restraints excluded: chain N residue 181 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 94 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 chunk 95 optimal weight: 0.2980 chunk 101 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 ASN M 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.1170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8317 Z= 0.266 Angle : 0.596 8.845 11313 Z= 0.301 Chirality : 0.044 0.152 1257 Planarity : 0.005 0.046 1458 Dihedral : 5.877 62.773 1184 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.16 % Favored : 93.65 % Rotamer: Outliers : 4.20 % Allowed : 25.64 % Favored : 70.17 % 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: -0.31 (0.26), residues: 1055 helix: -2.50 (0.68), residues: 46 sheet: 1.04 (0.25), residues: 454 loop : -1.12 (0.25), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 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 108 *********************** 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 156 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 118 time to evaluate : 0.860 Fit side-chains REVERT: A 408 ARG cc_start: 0.8392 (OUTLIER) cc_final: 0.8164 (ppt170) REVERT: M 4 LEU cc_start: 0.7613 (OUTLIER) cc_final: 0.7365 (mt) REVERT: N 91 SER cc_start: 0.8152 (p) cc_final: 0.7936 (t) outliers start: 38 outliers final: 22 residues processed: 151 average time/residue: 0.8139 time to fit residues: 133.7970 Evaluate side-chains 139 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 115 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 ARG 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 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 33 LEU Chi-restraints excluded: chain L residue 93 SER Chi-restraints excluded: chain L residue 164 THR Chi-restraints excluded: chain M residue 4 LEU 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 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 175 LEU Chi-restraints excluded: chain N residue 181 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 84 optimal weight: 0.6980 chunk 57 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 41 optimal weight: 0.0570 chunk 86 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 91 optimal weight: 0.3980 chunk 25 optimal weight: 0.6980 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 165 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8317 Z= 0.213 Angle : 0.575 8.663 11313 Z= 0.289 Chirality : 0.043 0.145 1257 Planarity : 0.005 0.045 1458 Dihedral : 5.220 58.167 1181 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.31 % Favored : 94.50 % Rotamer: Outliers : 4.97 % Allowed : 25.97 % 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: -0.25 (0.26), residues: 1055 helix: -2.39 (0.69), residues: 46 sheet: 1.02 (0.25), residues: 456 loop : -1.03 (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 0.002 0.000 ARG L 108 *********************** 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 156 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 111 time to evaluate : 0.887 Fit side-chains REVERT: A 408 ARG cc_start: 0.8345 (OUTLIER) cc_final: 0.8137 (ppt170) REVERT: N 11 LEU cc_start: 0.7930 (tp) cc_final: 0.7721 (tt) REVERT: N 91 SER cc_start: 0.8192 (p) cc_final: 0.7930 (t) outliers start: 45 outliers final: 27 residues processed: 148 average time/residue: 0.8573 time to fit residues: 138.4480 Evaluate side-chains 135 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 107 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 408 ARG 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 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 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 191 VAL Chi-restraints excluded: chain M residue 217 VAL Chi-restraints excluded: chain N residue 7 SER 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 34 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 chunk 25 optimal weight: 0.0970 chunk 101 optimal weight: 1.9990 chunk 84 optimal weight: 0.0060 chunk 47 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 165 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8317 Z= 0.216 Angle : 0.574 8.652 11313 Z= 0.290 Chirality : 0.043 0.147 1257 Planarity : 0.005 0.047 1458 Dihedral : 5.139 58.566 1179 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.78 % Favored : 94.03 % Rotamer: Outliers : 3.54 % Allowed : 26.85 % 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: -0.20 (0.26), residues: 1055 helix: -2.34 (0.70), residues: 46 sheet: 1.05 (0.25), residues: 456 loop : -0.99 (0.26), residues: 553 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 *********************** 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 142 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 110 time to evaluate : 0.916 Fit side-chains REVERT: A 408 ARG cc_start: 0.8337 (OUTLIER) cc_final: 0.8127 (ppt170) REVERT: H 190 SER cc_start: 0.7630 (t) cc_final: 0.7322 (t) REVERT: N 91 SER cc_start: 0.8205 (p) cc_final: 0.7918 (t) outliers start: 32 outliers final: 24 residues processed: 136 average time/residue: 0.7801 time to fit residues: 116.0344 Evaluate side-chains 134 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 109 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 ARG 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 204 TYR 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 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 191 VAL Chi-restraints excluded: chain M residue 217 VAL Chi-restraints excluded: chain N residue 7 SER 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 97 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 57 optimal weight: 0.4980 chunk 74 optimal weight: 0.7980 chunk 85 optimal weight: 3.9990 chunk 56 optimal weight: 0.7980 chunk 101 optimal weight: 0.5980 chunk 63 optimal weight: 0.9990 chunk 61 optimal weight: 0.6980 chunk 46 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 77 ASN N 34 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 8317 Z= 0.237 Angle : 0.586 8.733 11313 Z= 0.296 Chirality : 0.043 0.148 1257 Planarity : 0.005 0.047 1458 Dihedral : 5.173 58.517 1179 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.69 % Favored : 94.12 % Rotamer: Outliers : 3.87 % Allowed : 26.19 % 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: -0.17 (0.26), residues: 1055 helix: -2.35 (0.70), residues: 46 sheet: 1.09 (0.25), residues: 454 loop : -0.98 (0.26), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP M 113 HIS 0.004 0.001 HIS H 111 PHE 0.012 0.001 PHE N 139 TYR 0.014 0.001 TYR L 49 ARG 0.006 0.000 ARG L 108 *********************** 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 145 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 110 time to evaluate : 0.960 Fit side-chains REVERT: A 408 ARG cc_start: 0.8343 (OUTLIER) cc_final: 0.8127 (ptt90) REVERT: H 152 VAL cc_start: 0.7818 (t) cc_final: 0.7589 (m) REVERT: H 190 SER cc_start: 0.7647 (t) cc_final: 0.7344 (t) REVERT: N 11 LEU cc_start: 0.7921 (tp) cc_final: 0.7713 (tt) outliers start: 35 outliers final: 26 residues processed: 137 average time/residue: 0.8147 time to fit residues: 121.6367 Evaluate side-chains 136 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 109 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 408 ARG 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 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 93 SER 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 40 optimal weight: 0.5980 chunk 60 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 68 optimal weight: 0.5980 chunk 50 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 79 optimal weight: 0.1980 chunk 92 optimal weight: 0.6980 chunk 96 optimal weight: 0.0870 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 77 ASN N 34 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8317 Z= 0.181 Angle : 0.553 8.571 11313 Z= 0.280 Chirality : 0.042 0.143 1257 Planarity : 0.005 0.048 1458 Dihedral : 5.004 59.815 1179 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.50 % Favored : 94.31 % Rotamer: Outliers : 3.20 % Allowed : 26.96 % Favored : 69.83 % 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: -0.10 (0.26), residues: 1055 helix: -2.25 (0.71), residues: 46 sheet: 1.12 (0.25), residues: 454 loop : -0.92 (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 0.009 0.001 PHE N 139 TYR 0.013 0.001 TYR L 49 ARG 0.005 0.000 ARG L 108 *********************** 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 144 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 115 time to evaluate : 0.860 Fit side-chains REVERT: H 152 VAL cc_start: 0.7799 (t) cc_final: 0.7574 (m) REVERT: H 190 SER cc_start: 0.7636 (t) cc_final: 0.7336 (t) REVERT: N 11 LEU cc_start: 0.7891 (tp) cc_final: 0.7691 (tt) REVERT: N 91 SER cc_start: 0.8246 (p) cc_final: 0.7988 (t) outliers start: 29 outliers final: 24 residues processed: 138 average time/residue: 0.7901 time to fit residues: 118.8784 Evaluate side-chains 137 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 113 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 409 GLN 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 204 TYR Chi-restraints excluded: chain L residue 3 GLN Chi-restraints excluded: chain L residue 14 SER 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 181 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 0.4980 chunk 94 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 chunk 41 optimal weight: 0.6980 chunk 74 optimal weight: 0.4980 chunk 28 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 89 optimal weight: 0.9980 chunk 93 optimal weight: 0.0980 chunk 61 optimal weight: 0.7980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 77 ASN ** N 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 8317 Z= 0.208 Angle : 0.584 12.487 11313 Z= 0.296 Chirality : 0.043 0.270 1257 Planarity : 0.005 0.049 1458 Dihedral : 5.046 59.834 1179 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.50 % Favored : 94.31 % Rotamer: Outliers : 3.54 % Allowed : 26.63 % Favored : 69.83 % 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: -0.08 (0.26), residues: 1055 helix: -2.25 (0.71), residues: 46 sheet: 1.15 (0.25), residues: 448 loop : -0.90 (0.26), residues: 561 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 0.010 0.001 PHE N 139 TYR 0.013 0.001 TYR L 49 ARG 0.005 0.000 ARG L 108 *********************** 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 142 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 110 time to evaluate : 0.929 Fit side-chains REVERT: H 152 VAL cc_start: 0.7808 (t) cc_final: 0.7587 (m) REVERT: H 190 SER cc_start: 0.7630 (t) cc_final: 0.7334 (t) REVERT: N 11 LEU cc_start: 0.7902 (tp) cc_final: 0.7695 (tt) REVERT: N 91 SER cc_start: 0.8235 (p) cc_final: 0.7975 (t) outliers start: 32 outliers final: 28 residues processed: 135 average time/residue: 0.7907 time to fit residues: 116.8259 Evaluate side-chains 135 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 107 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 409 GLN 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 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 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 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 181 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 99 optimal weight: 0.0050 chunk 60 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 104 optimal weight: 0.7980 chunk 96 optimal weight: 0.6980 chunk 83 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 64 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 66 optimal weight: 0.4980 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 77 ASN ** N 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 8317 Z= 0.219 Angle : 0.594 14.210 11313 Z= 0.300 Chirality : 0.043 0.255 1257 Planarity : 0.005 0.049 1458 Dihedral : 5.090 59.726 1179 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.69 % Favored : 94.12 % Rotamer: Outliers : 3.20 % Allowed : 27.07 % Favored : 69.72 % 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: -0.08 (0.26), residues: 1055 helix: -2.24 (0.71), residues: 46 sheet: 1.14 (0.25), residues: 453 loop : -0.91 (0.26), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 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 0.005 0.000 ARG L 108 ********************** REFINEMENT MACRO_CYCLE 10 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 137 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 108 time to evaluate : 0.875 Fit side-chains REVERT: H 152 VAL cc_start: 0.7814 (t) cc_final: 0.7593 (m) REVERT: H 190 SER cc_start: 0.7643 (t) cc_final: 0.7343 (t) outliers start: 29 outliers final: 28 residues processed: 131 average time/residue: 0.7912 time to fit residues: 113.0932 Evaluate side-chains 136 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 108 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 409 GLN 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 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 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 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 181 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 0.7980 chunk 25 optimal weight: 0.0040 chunk 76 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 34 optimal weight: 0.5980 chunk 85 optimal weight: 4.9990 chunk 10 optimal weight: 0.6980 chunk 15 optimal weight: 0.0980 chunk 73 optimal weight: 0.0570 overall best weight: 0.2910 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 77 ASN N 34 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.137455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.121439 restraints weight = 11259.028| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 1.99 r_work: 0.3633 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3502 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.077 8317 Z= 0.152 Angle : 0.553 13.674 11313 Z= 0.280 Chirality : 0.042 0.228 1257 Planarity : 0.004 0.050 1458 Dihedral : 4.784 57.097 1179 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.02 % Favored : 94.88 % Rotamer: Outliers : 2.43 % Allowed : 27.62 % 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: -0.00 (0.26), residues: 1055 helix: -2.15 (0.72), residues: 46 sheet: 1.19 (0.25), residues: 447 loop : -0.83 (0.26), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 436 HIS 0.002 0.001 HIS H 111 PHE 0.009 0.001 PHE L 139 TYR 0.012 0.001 TYR L 49 ARG 0.004 0.000 ARG L 108 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3119.60 seconds wall clock time: 55 minutes 49.43 seconds (3349.43 seconds total)