Starting phenix.real_space_refine on Sun Dec 10 07:22:11 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sk8_25176/12_2023/7sk8_25176_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sk8_25176/12_2023/7sk8_25176.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sk8_25176/12_2023/7sk8_25176.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sk8_25176/12_2023/7sk8_25176.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sk8_25176/12_2023/7sk8_25176_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sk8_25176/12_2023/7sk8_25176_trim_updated.pdb" } resolution = 3.3 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= 0.083 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 39 5.16 5 C 4515 2.51 5 N 1093 2.21 5 O 1229 1.98 5 H 6513 0.53 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-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 13389 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 5020 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 306, 5006 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 11, 'TRANS': 294} Conformer: "B" Number of residues, atoms: 306, 5006 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 11, 'TRANS': 294} bond proxies already assigned to first conformer: 5062 Chain: "B" Number of atoms: 1040 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 1040 Classifications: {'peptide': 62} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 58} Chain: "C" Number of atoms: 1653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 1653 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 101} Chain: "D" Number of atoms: 1934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1934 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "E" Number of atoms: 1618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 1618 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "F" Number of atoms: 1871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1871 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "A" Number of atoms: 253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 253 Unusual residues: {'CLR': 6, 'GJ9': 1, 'LMN': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 10 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N HIS A 121 " occ=0.50 ... (29 atoms not shown) pdb=" HE1BHIS A 121 " occ=0.50 Time building chain proxies: 9.05, per 1000 atoms: 0.68 Number of scatterers: 13389 At special positions: 0 Unit cell: (71.28, 76.68, 153.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 39 16.00 O 1229 8.00 N 1093 7.00 C 4515 6.00 H 6513 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 117 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS B 9 " - pdb=" SG CYS B 34 " distance=2.03 Simple disulfide: pdb=" SG CYS B 11 " - pdb=" SG CYS B 50 " distance=2.02 Simple disulfide: pdb=" SG CYS C 24 " - pdb=" SG CYS C 89 " distance=2.04 Simple disulfide: pdb=" SG CYS D 25 " - pdb=" SG CYS D 99 " distance=2.03 Simple disulfide: pdb=" SG CYS E 24 " - pdb=" SG CYS E 89 " distance=2.04 Simple disulfide: pdb=" SG CYS F 25 " - pdb=" SG CYS F 99 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.83 Conformation dependent library (CDL) restraints added in 1.8 seconds 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1578 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 17 helices and 11 sheets defined 30.5% alpha, 20.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.86 Creating SS restraints... Processing helix chain 'A' and resid 41 through 71 removed outlier: 3.849A pdb=" N PHE A 53 " --> pdb=" O PHE A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 105 removed outlier: 3.552A pdb=" N ALA A 87 " --> pdb=" O ILE A 83 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR A 96 " --> pdb=" O TRP A 92 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE A 97 " --> pdb=" O VAL A 93 " (cutoff:3.500A) Proline residue: A 98 - end of helix Processing helix chain 'A' and resid 114 through 147 removed outlier: 3.773A pdb=" N TYR A 143 " --> pdb=" O SER A 139 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE A 146 " --> pdb=" O ARG A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 182 Proline residue: A 178 - end of helix removed outlier: 3.783A pdb=" N TYR A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 218 removed outlier: 3.628A pdb=" N GLY A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 241 Processing helix chain 'A' and resid 244 through 248 Processing helix chain 'A' and resid 252 through 279 Proline residue: A 267 - end of helix Processing helix chain 'A' and resid 287 through 315 removed outlier: 3.635A pdb=" N ALA A 296 " --> pdb=" O ALA A 292 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU A 305 " --> pdb=" O GLN A 301 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N VAL A 306 " --> pdb=" O CYS A 302 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N HIS A 307 " --> pdb=" O LEU A 303 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N CYS A 308 " --> pdb=" O SER A 304 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N CYS A 309 " --> pdb=" O LEU A 305 " (cutoff:3.500A) Proline residue: A 312 - end of helix Processing helix chain 'A' and resid 320 through 330 Processing helix chain 'B' and resid 20 through 22 No H-bonds generated for 'chain 'B' and resid 20 through 22' Processing helix chain 'B' and resid 56 through 67 removed outlier: 3.694A pdb=" N GLU B 60 " --> pdb=" O LYS B 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 34 No H-bonds generated for 'chain 'D' and resid 32 through 34' Processing helix chain 'D' and resid 91 through 93 No H-bonds generated for 'chain 'D' and resid 91 through 93' Processing helix chain 'E' and resid 81 through 83 No H-bonds generated for 'chain 'E' and resid 81 through 83' Processing helix chain 'F' and resid 32 through 34 No H-bonds generated for 'chain 'F' and resid 32 through 34' Processing helix chain 'F' and resid 91 through 93 No H-bonds generated for 'chain 'F' and resid 91 through 93' Processing sheet with id= A, first strand: chain 'A' and resid 183 through 187 Processing sheet with id= B, first strand: chain 'B' and resid 26 through 29 Processing sheet with id= C, first strand: chain 'C' and resid 11 through 14 removed outlier: 6.511A pdb=" N LYS C 104 " --> pdb=" O LEU C 12 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N ALA C 14 " --> pdb=" O LYS C 104 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N GLU C 106 " --> pdb=" O ALA C 14 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'C' and resid 21 through 25 Processing sheet with id= E, first strand: chain 'C' and resid 86 through 91 removed outlier: 6.294A pdb=" N GLN C 38 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N LEU C 47 " --> pdb=" O GLN C 38 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 6 through 10 Processing sheet with id= G, first strand: chain 'D' and resid 122 through 124 removed outlier: 5.949A pdb=" N ARG D 41 " --> pdb=" O TRP D 50 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N TRP D 50 " --> pdb=" O ARG D 41 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'E' and resid 5 through 8 removed outlier: 3.718A pdb=" N THR E 73 " --> pdb=" O SER E 66 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 86 through 91 removed outlier: 6.045A pdb=" N GLN E 38 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N LEU E 47 " --> pdb=" O GLN E 38 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'F' and resid 6 through 10 Processing sheet with id= K, first strand: chain 'F' and resid 124 through 126 removed outlier: 3.760A pdb=" N SER F 36 " --> pdb=" O VAL F 102 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N ARG F 41 " --> pdb=" O TRP F 50 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N TRP F 50 " --> pdb=" O ARG F 41 " (cutoff:3.500A) 282 hydrogen bonds defined for protein. 800 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: 4.77 Time building geometry restraints manager: 11.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 6502 1.03 - 1.23: 52 1.23 - 1.42: 2993 1.42 - 1.62: 3994 1.62 - 1.82: 54 Bond restraints: 13595 Sorted by residual: bond pdb=" C1 LMN A 406 " pdb=" O5 LMN A 406 " ideal model delta sigma weight residual 1.403 1.528 -0.125 2.00e-02 2.50e+03 3.92e+01 bond pdb=" CBT LMN A 406 " pdb=" CCM LMN A 406 " ideal model delta sigma weight residual 1.533 1.650 -0.117 2.00e-02 2.50e+03 3.43e+01 bond pdb=" C4 LMN A 406 " pdb=" O4 LMN A 406 " ideal model delta sigma weight residual 1.409 1.509 -0.100 2.00e-02 2.50e+03 2.52e+01 bond pdb=" CBL LMN A 406 " pdb=" CBR LMN A 406 " ideal model delta sigma weight residual 1.525 1.606 -0.081 2.00e-02 2.50e+03 1.65e+01 bond pdb=" C3 LMN A 406 " pdb=" C4 LMN A 406 " ideal model delta sigma weight residual 1.525 1.446 0.079 2.00e-02 2.50e+03 1.56e+01 ... (remaining 13590 not shown) Histogram of bond angle deviations from ideal: 89.78 - 98.63: 1 98.63 - 107.48: 586 107.48 - 116.33: 16529 116.33 - 125.18: 6917 125.18 - 134.02: 313 Bond angle restraints: 24346 Sorted by residual: angle pdb=" C06 GJ9 A 408 " pdb=" N05 GJ9 A 408 " pdb=" C37 GJ9 A 408 " ideal model delta sigma weight residual 121.17 112.37 8.80 3.00e+00 1.11e-01 8.60e+00 angle pdb=" C08 GJ9 A 408 " pdb=" C09 GJ9 A 408 " pdb=" N10 GJ9 A 408 " ideal model delta sigma weight residual 108.48 116.68 -8.20 3.00e+00 1.11e-01 7.47e+00 angle pdb=" C22 CLR A 407 " pdb=" C23 CLR A 407 " pdb=" C24 CLR A 407 " ideal model delta sigma weight residual 111.95 103.85 8.10 3.00e+00 1.11e-01 7.29e+00 angle pdb=" C22 CLR A 401 " pdb=" C23 CLR A 401 " pdb=" C24 CLR A 401 " ideal model delta sigma weight residual 111.95 103.98 7.97 3.00e+00 1.11e-01 7.06e+00 angle pdb=" C22 CLR A 403 " pdb=" C23 CLR A 403 " pdb=" C24 CLR A 403 " ideal model delta sigma weight residual 111.95 104.24 7.71 3.00e+00 1.11e-01 6.60e+00 ... (remaining 24341 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.51: 6436 23.51 - 47.02: 285 47.02 - 70.53: 35 70.53 - 94.04: 6 94.04 - 117.55: 9 Dihedral angle restraints: 6771 sinusoidal: 3706 harmonic: 3065 Sorted by residual: dihedral pdb=" CB CYS E 24 " pdb=" SG CYS E 24 " pdb=" SG CYS E 89 " pdb=" CB CYS E 89 " ideal model delta sinusoidal sigma weight residual 93.00 49.44 43.56 1 1.00e+01 1.00e-02 2.64e+01 dihedral pdb=" O2 LMN A 406 " pdb=" C2 LMN A 406 " pdb=" C3 LMN A 406 " pdb=" O3 LMN A 406 " ideal model delta sinusoidal sigma weight residual 295.11 177.56 117.55 1 3.00e+01 1.11e-03 1.56e+01 dihedral pdb=" C1 LMN A 406 " pdb=" C2 LMN A 406 " pdb=" C3 LMN A 406 " pdb=" O3 LMN A 406 " ideal model delta sinusoidal sigma weight residual 174.26 57.17 117.09 1 3.00e+01 1.11e-03 1.55e+01 ... (remaining 6768 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 985 0.079 - 0.159: 86 0.159 - 0.238: 3 0.238 - 0.318: 15 0.318 - 0.397: 9 Chirality restraints: 1098 Sorted by residual: chirality pdb=" C17 CLR A 405 " pdb=" C13 CLR A 405 " pdb=" C16 CLR A 405 " pdb=" C20 CLR A 405 " both_signs ideal model delta sigma weight residual False 2.55 2.95 -0.40 2.00e-01 2.50e+01 3.94e+00 chirality pdb=" C17 CLR A 402 " pdb=" C13 CLR A 402 " pdb=" C16 CLR A 402 " pdb=" C20 CLR A 402 " both_signs ideal model delta sigma weight residual False 2.55 2.95 -0.39 2.00e-01 2.50e+01 3.84e+00 chirality pdb=" C17 CLR A 407 " pdb=" C13 CLR A 407 " pdb=" C16 CLR A 407 " pdb=" C20 CLR A 407 " both_signs ideal model delta sigma weight residual False 2.55 2.93 -0.38 2.00e-01 2.50e+01 3.53e+00 ... (remaining 1095 not shown) Planarity restraints: 1939 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER E 8 " 0.020 5.00e-02 4.00e+02 2.93e-02 1.37e+00 pdb=" N PRO E 9 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO E 9 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO E 9 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 223 " 0.017 5.00e-02 4.00e+02 2.52e-02 1.01e+00 pdb=" N PRO A 224 " -0.044 5.00e-02 4.00e+02 pdb=" CA PRO A 224 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 224 " 0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER F 55 " -0.016 5.00e-02 4.00e+02 2.44e-02 9.56e-01 pdb=" N PRO F 56 " 0.042 5.00e-02 4.00e+02 pdb=" CA PRO F 56 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO F 56 " -0.014 5.00e-02 4.00e+02 ... (remaining 1936 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 402 2.17 - 2.78: 25249 2.78 - 3.38: 35283 3.38 - 3.99: 47844 3.99 - 4.60: 74589 Nonbonded interactions: 183367 Sorted by model distance: nonbonded pdb="HE22 GLN E 39 " pdb=" OE1 GLN F 42 " model vdw 1.560 1.850 nonbonded pdb=" H ASP A 78 " pdb=" O SER F 112 " model vdw 1.625 1.850 nonbonded pdb=" HH TYR C 37 " pdb=" OE1 GLN C 90 " model vdw 1.632 1.850 nonbonded pdb="HH12 ARG D 70 " pdb=" OD2 ASP D 93 " model vdw 1.636 1.850 nonbonded pdb=" O ILE A 123 " pdb="HD22 ASN A 127 " model vdw 1.658 1.850 ... (remaining 183362 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'C' and (resid 3 through 91 or resid 93 through 94 or resid 98 through 10 \ 8)) selection = (chain 'E' and ((resid 3 and (name N or name CA or name C or name O or name CB o \ r name CG1 or name CG2 or name CD1 or name HA or name HB or name HG12 or name HG \ 13 or name HG21 or name HG22 or name HG23 or name HD11 or name HD12 or name HD13 \ )) or resid 4 through 91 or resid 93 through 94 or resid 98 through 108)) } ncs_group { reference = (chain 'D' and ((resid 5 and (name N or name CA or name C or name O or name CB o \ r name CG1 or name CG2 or name HA or name HB or name HG11 or name HG12 or name H \ G13 or name HG21 or name HG22 or name HG23)) or resid 6 through 31 or resid 33 o \ r resid 35 through 52 or resid 54 or resid 57 through 102 or resid 105 through 1 \ 06 or resid 111 or resid 113 or resid 116 through 127)) selection = (chain 'F' and (resid 5 through 31 or resid 33 or resid 35 through 52 or resid 5 \ 4 or resid 57 through 102 or resid 105 or resid 109 or resid 114 or resid 116 or \ resid 118 through 129)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.290 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: 0.200 Extract box with map and model: 6.530 Check model and map are aligned: 0.210 Set scattering table: 0.120 Process input model: 48.770 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 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 : 0.007 0.125 7082 Z= 0.470 Angle : 0.726 8.799 9678 Z= 0.305 Chirality : 0.064 0.397 1098 Planarity : 0.003 0.029 1143 Dihedral : 15.202 117.550 2882 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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 (0.30), residues: 824 helix: 1.89 (0.34), residues: 240 sheet: -0.80 (0.31), residues: 256 loop : -0.81 (0.35), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 50 HIS 0.003 0.001 HIS A 307 PHE 0.009 0.001 PHE A 55 TYR 0.012 0.001 TYR C 50 ARG 0.005 0.000 ARG F 22 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 1.080 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.4990 time to fit residues: 60.2073 Evaluate side-chains 84 residues out of total 731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 0.978 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 0.5980 chunk 60 optimal weight: 0.2980 chunk 33 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 40 optimal weight: 0.0770 chunk 32 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 72 optimal weight: 0.5980 overall best weight: 0.4338 ------------------------------------------------------------------------------- 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: 0.8141 moved from start: 0.0736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 7082 Z= 0.153 Angle : 0.483 7.920 9678 Z= 0.247 Chirality : 0.041 0.149 1098 Planarity : 0.003 0.037 1143 Dihedral : 8.715 87.156 1429 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.41 % Allowed : 4.64 % Favored : 94.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: 0.14 (0.30), residues: 824 helix: 2.15 (0.33), residues: 245 sheet: -0.76 (0.31), residues: 256 loop : -0.70 (0.36), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 50 HIS 0.002 0.001 HIS A 307 PHE 0.015 0.001 PHE A 173 TYR 0.013 0.001 TYR D 53 ARG 0.003 0.000 ARG F 22 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 86 time to evaluate : 1.099 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 87 average time/residue: 0.4640 time to fit residues: 52.6520 Evaluate side-chains 82 residues out of total 731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 79 time to evaluate : 1.041 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1479 time to fit residues: 2.1072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 40 optimal weight: 0.9990 chunk 22 optimal weight: 0.4980 chunk 60 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 64 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 58 optimal weight: 0.5980 chunk 71 optimal weight: 0.3980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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: 0.8152 moved from start: 0.0832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7082 Z= 0.194 Angle : 0.464 4.209 9678 Z= 0.242 Chirality : 0.040 0.140 1098 Planarity : 0.003 0.026 1143 Dihedral : 7.596 86.101 1429 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 0.14 % Allowed : 6.00 % Favored : 93.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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 (0.30), residues: 824 helix: 2.22 (0.33), residues: 245 sheet: -0.76 (0.31), residues: 256 loop : -0.73 (0.36), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 50 HIS 0.003 0.001 HIS A 307 PHE 0.013 0.001 PHE A 173 TYR 0.013 0.001 TYR D 53 ARG 0.003 0.000 ARG F 22 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 88 time to evaluate : 1.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 89 average time/residue: 0.4781 time to fit residues: 55.6434 Evaluate side-chains 83 residues out of total 731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 82 time to evaluate : 1.132 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1481 time to fit residues: 1.6967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 54 optimal weight: 2.9990 chunk 37 optimal weight: 0.3980 chunk 8 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 69 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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: 0.8167 moved from start: 0.0907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7082 Z= 0.242 Angle : 0.484 4.274 9678 Z= 0.252 Chirality : 0.041 0.141 1098 Planarity : 0.003 0.026 1143 Dihedral : 7.650 81.048 1429 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 0.14 % Allowed : 7.09 % Favored : 92.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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 (0.30), residues: 824 helix: 2.13 (0.32), residues: 245 sheet: -0.77 (0.31), residues: 256 loop : -0.79 (0.35), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 50 HIS 0.004 0.001 HIS A 307 PHE 0.012 0.001 PHE A 173 TYR 0.015 0.001 TYR D 53 ARG 0.003 0.000 ARG F 22 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 83 time to evaluate : 1.090 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 83 average time/residue: 0.4428 time to fit residues: 48.4153 Evaluate side-chains 81 residues out of total 731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 80 time to evaluate : 1.042 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1417 time to fit residues: 1.5072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 43 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 0 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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: 0.8179 moved from start: 0.0965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 7082 Z= 0.263 Angle : 0.495 4.284 9678 Z= 0.259 Chirality : 0.041 0.143 1098 Planarity : 0.003 0.028 1143 Dihedral : 7.706 71.041 1429 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 0.14 % Allowed : 9.14 % Favored : 90.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: 0.03 (0.30), residues: 824 helix: 2.09 (0.32), residues: 245 sheet: -0.79 (0.32), residues: 256 loop : -0.82 (0.35), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 50 HIS 0.004 0.001 HIS A 307 PHE 0.012 0.001 PHE A 173 TYR 0.017 0.001 TYR D 53 ARG 0.003 0.000 ARG F 22 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 88 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 88 average time/residue: 0.4831 time to fit residues: 54.8404 Evaluate side-chains 84 residues out of total 731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 83 time to evaluate : 1.063 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1501 time to fit residues: 1.5856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 69 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 64 optimal weight: 0.5980 chunk 35 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 40 optimal weight: 0.3980 chunk 74 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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: 0.8165 moved from start: 0.1026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7082 Z= 0.206 Angle : 0.471 4.206 9678 Z= 0.247 Chirality : 0.041 0.143 1098 Planarity : 0.003 0.028 1143 Dihedral : 7.267 72.003 1429 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 0.27 % Allowed : 9.96 % Favored : 89.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: 0.13 (0.30), residues: 824 helix: 2.20 (0.32), residues: 245 sheet: -0.77 (0.32), residues: 256 loop : -0.75 (0.36), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 50 HIS 0.003 0.001 HIS A 307 PHE 0.011 0.001 PHE A 173 TYR 0.014 0.001 TYR D 53 ARG 0.003 0.000 ARG F 22 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 83 time to evaluate : 1.355 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 84 average time/residue: 0.4893 time to fit residues: 54.1406 Evaluate side-chains 81 residues out of total 731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 79 time to evaluate : 1.155 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1394 time to fit residues: 1.7399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 8 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 43 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 46 optimal weight: 0.5980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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: 0.8169 moved from start: 0.1066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7082 Z= 0.220 Angle : 0.477 4.351 9678 Z= 0.249 Chirality : 0.041 0.142 1098 Planarity : 0.003 0.030 1143 Dihedral : 7.137 74.670 1429 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 0.14 % Allowed : 10.91 % Favored : 88.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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 (0.30), residues: 824 helix: 2.19 (0.32), residues: 245 sheet: -0.77 (0.32), residues: 256 loop : -0.78 (0.36), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 50 HIS 0.004 0.001 HIS A 307 PHE 0.011 0.001 PHE A 173 TYR 0.014 0.001 TYR D 53 ARG 0.003 0.000 ARG F 22 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 83 time to evaluate : 1.085 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 84 average time/residue: 0.4639 time to fit residues: 51.6301 Evaluate side-chains 80 residues out of total 731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 79 time to evaluate : 1.096 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1616 time to fit residues: 1.6590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 23 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 38 optimal weight: 0.0270 chunk 7 optimal weight: 0.0870 chunk 60 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 chunk 67 optimal weight: 0.5980 overall best weight: 0.4816 ------------------------------------------------------------------------------- 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: 0.8143 moved from start: 0.1153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7082 Z= 0.158 Angle : 0.448 4.862 9678 Z= 0.234 Chirality : 0.040 0.141 1098 Planarity : 0.003 0.027 1143 Dihedral : 6.837 75.884 1429 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.14 % Allowed : 10.78 % Favored : 89.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: 0.33 (0.30), residues: 824 helix: 2.41 (0.33), residues: 245 sheet: -0.67 (0.32), residues: 257 loop : -0.66 (0.36), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 107 HIS 0.003 0.001 HIS A 307 PHE 0.010 0.001 PHE A 173 TYR 0.011 0.001 TYR D 53 ARG 0.003 0.000 ARG E 25 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 80 time to evaluate : 1.110 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 80 average time/residue: 0.4621 time to fit residues: 48.6533 Evaluate side-chains 77 residues out of total 731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 0.972 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 71 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 67 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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: 0.8174 moved from start: 0.1148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7082 Z= 0.252 Angle : 0.487 4.295 9678 Z= 0.254 Chirality : 0.041 0.139 1098 Planarity : 0.003 0.029 1143 Dihedral : 7.130 70.872 1429 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 0.00 % Allowed : 11.60 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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 (0.30), residues: 824 helix: 2.25 (0.32), residues: 245 sheet: -0.74 (0.32), residues: 256 loop : -0.79 (0.36), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 50 HIS 0.004 0.001 HIS A 307 PHE 0.011 0.001 PHE A 55 TYR 0.016 0.001 TYR D 53 ARG 0.003 0.000 ARG D 101 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 1.171 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.4579 time to fit residues: 48.7967 Evaluate side-chains 81 residues out of total 731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 1.069 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 36 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 63 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 50 optimal weight: 0.5980 chunk 67 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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: 0.8169 moved from start: 0.1153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7082 Z= 0.221 Angle : 0.477 4.270 9678 Z= 0.250 Chirality : 0.041 0.142 1098 Planarity : 0.003 0.028 1143 Dihedral : 7.074 72.074 1429 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 0.00 % Allowed : 11.73 % Favored : 88.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: 0.18 (0.30), residues: 824 helix: 2.28 (0.33), residues: 245 sheet: -0.73 (0.32), residues: 256 loop : -0.78 (0.36), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 50 HIS 0.004 0.001 HIS A 307 PHE 0.010 0.001 PHE A 55 TYR 0.015 0.001 TYR D 53 ARG 0.003 0.000 ARG F 22 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 1.064 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.4555 time to fit residues: 48.0948 Evaluate side-chains 77 residues out of total 731 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 1.158 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 58 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 = 0.3268 r_free = 0.3268 target = 0.117797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.100885 restraints weight = 30268.783| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 1.58 r_work: 0.2951 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2826 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2826 r_free = 0.2826 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2825 r_free = 0.2825 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2825 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.1164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 7082 Z= 0.251 Angle : 0.492 4.283 9678 Z= 0.258 Chirality : 0.041 0.142 1098 Planarity : 0.003 0.032 1143 Dihedral : 7.146 70.580 1429 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 0.14 % Allowed : 11.60 % Favored : 88.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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 (0.30), residues: 824 helix: 2.18 (0.32), residues: 245 sheet: -0.77 (0.32), residues: 256 loop : -0.85 (0.35), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 50 HIS 0.004 0.001 HIS A 307 PHE 0.012 0.001 PHE A 55 TYR 0.017 0.001 TYR D 53 ARG 0.004 0.000 ARG E 25 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3646.29 seconds wall clock time: 65 minutes 5.32 seconds (3905.32 seconds total)