Starting phenix.real_space_refine on Thu Dec 7 19:03:38 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sof_25269/12_2023/7sof_25269.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sof_25269/12_2023/7sof_25269.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sof_25269/12_2023/7sof_25269.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sof_25269/12_2023/7sof_25269.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sof_25269/12_2023/7sof_25269.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sof_25269/12_2023/7sof_25269.pdb" } resolution = 3.6 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= 0.045 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: 4 Type Number sf(0) Gaussians S 13 5.16 5 C 2426 2.51 5 N 611 2.21 5 O 685 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "L TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 110": "OD1" <-> "OD2" Residue "H PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 237": "NH1" <-> "NH2" Residue "A PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 3735 Number of models: 1 Model: "" Number of chains: 5 Chain: "L" Number of atoms: 730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 730 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 7, 'TRANS': 97} Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 30 Chain: "H" Number of atoms: 916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 916 Classifications: {'peptide': 125} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 7, 'TRANS': 117} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "A" Number of atoms: 1966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 1966 Classifications: {'peptide': 258} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 13, 'TRANS': 244} Chain breaks: 4 Unresolved non-hydrogen bonds: 135 Unresolved non-hydrogen angles: 171 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 4, 'ASP:plan': 7, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 77 Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 2.41, per 1000 atoms: 0.65 Number of scatterers: 3735 At special positions: 0 Unit cell: (73.341, 91.044, 77.556, 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 13 16.00 O 685 8.00 N 611 7.00 C 2426 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 87 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 97 " distance=2.03 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 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 BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 282 " " NAG A1303 " - " ASN A 165 " " NAG A1304 " - " ASN A 234 " " NAG A1305 " - " ASN A 149 " " NAG A1306 " - " ASN A 17 " " NAG B 1 " - " ASN A 122 " Time building additional restraints: 1.48 Conformation dependent library (CDL) restraints added in 823.3 milliseconds 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 912 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 6 sheets defined 4.7% alpha, 38.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'L' and resid 78 through 82 removed outlier: 3.797A pdb=" N GLU L 82 " --> pdb=" O THR L 79 " (cutoff:3.500A) Processing helix chain 'H' and resid 65 through 67 No H-bonds generated for 'chain 'H' and resid 65 through 67' Processing helix chain 'H' and resid 88 through 92 Processing helix chain 'A' and resid 294 through 303 Processing sheet with id=AA1, first strand: chain 'L' and resid 9 through 11 removed outlier: 6.529A pdb=" N VAL L 10 " --> pdb=" O THR L 104 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N TRP L 34 " --> pdb=" O VAL L 46 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 18 through 23 Processing sheet with id=AA3, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA4, first strand: chain 'H' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 11 through 12 current: chain 'H' and resid 48 through 54 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 59 through 61 current: chain 'H' and resid 108 through 115 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 108 through 115 current: chain 'A' and resid 116 through 121 removed outlier: 6.601A pdb=" N VAL A 126 " --> pdb=" O TYR A 170 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N TYR A 170 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ILE A 128 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N CYS A 136 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N TYR A 160 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ASP A 138 " --> pdb=" O ARG A 158 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N ARG A 158 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N PHE A 140 " --> pdb=" O GLU A 156 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N GLU A 156 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N ASP A 142 " --> pdb=" O LYS A 154 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N LYS A 154 " --> pdb=" O ASP A 142 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N TYR A 144 " --> pdb=" O TRP A 152 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N TRP A 152 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 27 through 31 removed outlier: 8.484A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ALA A 263 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.711A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) 116 hydrogen bonds defined for protein. 288 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: 0.97 Time building geometry restraints manager: 1.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 730 1.33 - 1.45: 971 1.45 - 1.57: 2117 1.57 - 1.70: 0 1.70 - 1.82: 16 Bond restraints: 3834 Sorted by residual: bond pdb=" NE ARG A 246 " pdb=" CZ ARG A 246 " ideal model delta sigma weight residual 1.326 1.369 -0.043 1.10e-02 8.26e+03 1.50e+01 bond pdb=" NE ARG A 78 " pdb=" CZ ARG A 78 " ideal model delta sigma weight residual 1.326 1.367 -0.041 1.10e-02 8.26e+03 1.41e+01 bond pdb=" N ILE L 94 " pdb=" CA ILE L 94 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.19e-02 7.06e+03 8.85e+00 bond pdb=" C5 NAG A1303 " pdb=" O5 NAG A1303 " ideal model delta sigma weight residual 1.413 1.467 -0.054 2.00e-02 2.50e+03 7.31e+00 bond pdb=" C5 NAG A1305 " pdb=" O5 NAG A1305 " ideal model delta sigma weight residual 1.413 1.467 -0.054 2.00e-02 2.50e+03 7.17e+00 ... (remaining 3829 not shown) Histogram of bond angle deviations from ideal: 100.40 - 107.09: 141 107.09 - 113.78: 2111 113.78 - 120.47: 1414 120.47 - 127.16: 1546 127.16 - 133.85: 36 Bond angle restraints: 5248 Sorted by residual: angle pdb=" C GLN H 41 " pdb=" N PRO H 42 " pdb=" CA PRO H 42 " ideal model delta sigma weight residual 119.66 125.79 -6.13 7.30e-01 1.88e+00 7.05e+01 angle pdb=" C ASN A 81 " pdb=" N PRO A 82 " pdb=" CA PRO A 82 " ideal model delta sigma weight residual 120.03 127.20 -7.17 9.90e-01 1.02e+00 5.24e+01 angle pdb=" C GLY H 8 " pdb=" N PRO H 9 " pdb=" CA PRO H 9 " ideal model delta sigma weight residual 119.76 126.99 -7.23 1.03e+00 9.43e-01 4.93e+01 angle pdb=" C ASP A 138 " pdb=" N PRO A 139 " pdb=" CA PRO A 139 " ideal model delta sigma weight residual 119.76 126.70 -6.94 1.00e+00 1.00e+00 4.82e+01 angle pdb=" C ARG L 53 " pdb=" N PRO L 54 " pdb=" CA PRO L 54 " ideal model delta sigma weight residual 119.85 126.83 -6.98 1.01e+00 9.80e-01 4.78e+01 ... (remaining 5243 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.47: 2235 16.47 - 32.95: 62 32.95 - 49.42: 12 49.42 - 65.90: 4 65.90 - 82.37: 1 Dihedral angle restraints: 2314 sinusoidal: 897 harmonic: 1417 Sorted by residual: dihedral pdb=" C THR L 93 " pdb=" N THR L 93 " pdb=" CA THR L 93 " pdb=" CB THR L 93 " ideal model delta harmonic sigma weight residual -122.00 -132.33 10.33 0 2.50e+00 1.60e-01 1.71e+01 dihedral pdb=" CA GLY H 105 " pdb=" C GLY H 105 " pdb=" N GLU H 106 " pdb=" CA GLU H 106 " ideal model delta harmonic sigma weight residual 180.00 159.62 20.38 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" CA ARG L 53 " pdb=" C ARG L 53 " pdb=" N PRO L 54 " pdb=" CA PRO L 54 " ideal model delta harmonic sigma weight residual 180.00 162.64 17.36 0 5.00e+00 4.00e-02 1.21e+01 ... (remaining 2311 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 447 0.070 - 0.139: 136 0.139 - 0.209: 29 0.209 - 0.278: 4 0.278 - 0.348: 10 Chirality restraints: 626 Sorted by residual: chirality pdb=" C1 BMA B 3 " pdb=" O4 NAG B 2 " pdb=" C2 BMA B 3 " pdb=" O5 BMA B 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.52 0.12 2.00e-02 2.50e+03 3.71e+01 chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.47 0.07 2.00e-02 2.50e+03 1.13e+01 chirality pdb=" C5 BMA B 3 " pdb=" C4 BMA B 3 " pdb=" C6 BMA B 3 " pdb=" O5 BMA B 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.62 0.35 2.00e-01 2.50e+01 3.03e+00 ... (remaining 623 not shown) Planarity restraints: 659 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR H 96 " 0.034 2.00e-02 2.50e+03 1.80e-02 6.45e+00 pdb=" CG TYR H 96 " -0.016 2.00e-02 2.50e+03 pdb=" CD1 TYR H 96 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR H 96 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 TYR H 96 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR H 96 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR H 96 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR H 96 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY H 105 " 0.012 2.00e-02 2.50e+03 2.40e-02 5.75e+00 pdb=" C GLY H 105 " -0.041 2.00e-02 2.50e+03 pdb=" O GLY H 105 " 0.016 2.00e-02 2.50e+03 pdb=" N GLU H 106 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1303 " -0.026 2.00e-02 2.50e+03 2.12e-02 5.61e+00 pdb=" C7 NAG A1303 " -0.003 2.00e-02 2.50e+03 pdb=" C8 NAG A1303 " -0.016 2.00e-02 2.50e+03 pdb=" N2 NAG A1303 " 0.035 2.00e-02 2.50e+03 pdb=" O7 NAG A1303 " 0.010 2.00e-02 2.50e+03 ... (remaining 656 not shown) Histogram of nonbonded interaction distances: 2.56 - 3.03: 2165 3.03 - 3.50: 3156 3.50 - 3.97: 6049 3.97 - 4.43: 6775 4.43 - 4.90: 11258 Nonbonded interactions: 29403 Sorted by model distance: nonbonded pdb=" ND1 HIS A 146 " pdb=" N LYS A 147 " model vdw 2.563 3.200 nonbonded pdb=" O PRO H 14 " pdb=" OG1 THR H 15 " model vdw 2.593 2.440 nonbonded pdb=" N ASN A 148 " pdb=" O ASN A 148 " model vdw 2.603 2.496 nonbonded pdb=" N THR H 10 " pdb=" N LEU H 11 " model vdw 2.608 2.560 nonbonded pdb=" OD1 ASP H 113 " pdb=" N VAL H 114 " model vdw 2.625 2.520 ... (remaining 29398 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 27.060 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 14.240 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 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 : 0.010 0.054 3834 Z= 0.681 Angle : 1.308 7.472 5248 Z= 0.869 Chirality : 0.080 0.348 626 Planarity : 0.005 0.024 652 Dihedral : 8.425 82.371 1387 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 1.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.38), residues: 474 helix: 0.56 (1.75), residues: 11 sheet: 1.23 (0.35), residues: 207 loop : -0.24 (0.37), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.004 TRP L 90 HIS 0.002 0.001 HIS A 207 PHE 0.014 0.003 PHE A 220 TYR 0.034 0.005 TYR H 96 ARG 0.001 0.000 ARG H 40 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 0.342 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.1767 time to fit residues: 19.0103 Evaluate side-chains 60 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 0.428 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 39 optimal weight: 4.9990 chunk 35 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 14 optimal weight: 0.0670 chunk 22 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 49 GLN H 79 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3834 Z= 0.268 Angle : 0.603 5.701 5248 Z= 0.318 Chirality : 0.047 0.169 626 Planarity : 0.005 0.052 652 Dihedral : 5.232 34.783 685 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.21 % Allowed : 1.48 % Favored : 98.31 % Rotamer: Outliers : 1.76 % Allowed : 7.94 % Favored : 90.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.39), residues: 474 helix: 1.76 (1.53), residues: 11 sheet: 1.32 (0.38), residues: 191 loop : -0.10 (0.37), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 258 HIS 0.002 0.001 HIS A 245 PHE 0.016 0.002 PHE A 55 TYR 0.026 0.002 TYR L 48 ARG 0.004 0.000 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 69 time to evaluate : 0.410 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 70 average time/residue: 0.1880 time to fit residues: 16.0309 Evaluate side-chains 60 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 57 time to evaluate : 0.409 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0386 time to fit residues: 0.7670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 13 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 chunk 42 optimal weight: 0.9980 chunk 46 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 3834 Z= 0.321 Angle : 0.599 5.882 5248 Z= 0.312 Chirality : 0.046 0.172 626 Planarity : 0.005 0.053 652 Dihedral : 5.187 37.030 685 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.53 % Allowed : 8.82 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.38), residues: 474 helix: 2.79 (1.62), residues: 11 sheet: 1.12 (0.37), residues: 191 loop : -0.39 (0.37), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 258 HIS 0.003 0.001 HIS A 245 PHE 0.013 0.002 PHE A 238 TYR 0.020 0.002 TYR L 48 ARG 0.003 0.000 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 55 time to evaluate : 0.447 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 8 residues processed: 64 average time/residue: 0.1882 time to fit residues: 14.4771 Evaluate side-chains 61 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 53 time to evaluate : 0.355 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0351 time to fit residues: 0.9930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 4 optimal weight: 0.0050 chunk 20 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 45 optimal weight: 5.9990 chunk 22 optimal weight: 0.2980 chunk 40 optimal weight: 0.0050 chunk 12 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 25 optimal weight: 3.9990 chunk 0 optimal weight: 1.9990 overall best weight: 0.3608 ------------------------------------------------------------------------------- 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: 0.7687 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3834 Z= 0.171 Angle : 0.532 6.947 5248 Z= 0.273 Chirality : 0.044 0.166 626 Planarity : 0.004 0.051 652 Dihedral : 4.925 35.995 685 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.47 % Allowed : 10.00 % Favored : 88.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.39), residues: 474 helix: 3.04 (1.65), residues: 11 sheet: 1.16 (0.37), residues: 190 loop : -0.40 (0.38), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 258 HIS 0.003 0.001 HIS A 207 PHE 0.010 0.001 PHE A 65 TYR 0.018 0.001 TYR L 48 ARG 0.003 0.000 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 54 time to evaluate : 0.422 Fit side-chains outliers start: 5 outliers final: 5 residues processed: 57 average time/residue: 0.2105 time to fit residues: 14.3770 Evaluate side-chains 56 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 51 time to evaluate : 0.382 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0451 time to fit residues: 0.9370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 33 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 40 optimal weight: 0.4980 chunk 11 optimal weight: 0.1980 chunk 15 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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: 0.7777 moved from start: 0.3474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 3834 Z= 0.345 Angle : 0.597 7.975 5248 Z= 0.308 Chirality : 0.046 0.173 626 Planarity : 0.004 0.057 652 Dihedral : 5.379 38.978 685 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.06 % Allowed : 9.71 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.38), residues: 474 helix: 3.26 (1.65), residues: 11 sheet: 0.86 (0.36), residues: 191 loop : -0.41 (0.38), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 152 HIS 0.003 0.001 HIS A 245 PHE 0.014 0.002 PHE A 238 TYR 0.016 0.002 TYR A 265 ARG 0.002 0.000 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 55 time to evaluate : 0.411 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 59 average time/residue: 0.1980 time to fit residues: 14.1599 Evaluate side-chains 55 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 51 time to evaluate : 0.427 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0406 time to fit residues: 0.8808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 11 optimal weight: 0.3980 chunk 45 optimal weight: 0.8980 chunk 37 optimal weight: 0.5980 chunk 21 optimal weight: 0.4980 chunk 3 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 5 optimal weight: 0.4980 chunk 25 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.3623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3834 Z= 0.228 Angle : 0.545 7.265 5248 Z= 0.280 Chirality : 0.045 0.165 626 Planarity : 0.004 0.053 652 Dihedral : 5.180 38.187 685 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.35 % Allowed : 10.29 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.39), residues: 474 helix: 3.36 (1.66), residues: 11 sheet: 0.89 (0.36), residues: 191 loop : -0.44 (0.39), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 115 HIS 0.003 0.001 HIS A 207 PHE 0.010 0.002 PHE A 238 TYR 0.016 0.001 TYR L 48 ARG 0.006 0.001 ARG A 246 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 50 time to evaluate : 0.424 Fit side-chains outliers start: 8 outliers final: 7 residues processed: 55 average time/residue: 0.2197 time to fit residues: 14.5100 Evaluate side-chains 56 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 49 time to evaluate : 0.437 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0403 time to fit residues: 1.1066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 25 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 13 optimal weight: 0.0970 chunk 8 optimal weight: 0.5980 chunk 30 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- 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: 0.7762 moved from start: 0.3780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3834 Z= 0.253 Angle : 0.551 7.355 5248 Z= 0.283 Chirality : 0.045 0.163 626 Planarity : 0.004 0.053 652 Dihedral : 5.169 37.870 685 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 0.29 % Allowed : 12.06 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.39), residues: 474 helix: 3.42 (1.67), residues: 11 sheet: 0.77 (0.36), residues: 191 loop : -0.45 (0.39), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 115 HIS 0.003 0.001 HIS A 245 PHE 0.012 0.002 PHE A 55 TYR 0.015 0.001 TYR A 265 ARG 0.003 0.000 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 52 time to evaluate : 0.454 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 52 average time/residue: 0.2277 time to fit residues: 14.3503 Evaluate side-chains 49 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 48 time to evaluate : 0.382 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0391 time to fit residues: 0.5941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 4 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 41 optimal weight: 0.1980 chunk 43 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 42 optimal weight: 0.2980 chunk 25 optimal weight: 0.5980 chunk 18 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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: 0.7756 moved from start: 0.3906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3834 Z= 0.230 Angle : 0.561 9.480 5248 Z= 0.283 Chirality : 0.045 0.159 626 Planarity : 0.004 0.051 652 Dihedral : 5.110 38.216 685 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.18 % Allowed : 12.94 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.39), residues: 474 helix: 3.75 (1.73), residues: 11 sheet: 0.73 (0.36), residues: 191 loop : -0.45 (0.39), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 258 HIS 0.003 0.001 HIS A 207 PHE 0.016 0.002 PHE A 55 TYR 0.015 0.001 TYR L 48 ARG 0.002 0.000 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 50 time to evaluate : 0.441 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 51 average time/residue: 0.2311 time to fit residues: 14.3160 Evaluate side-chains 50 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 47 time to evaluate : 0.438 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0402 time to fit residues: 0.7398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 39 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 chunk 27 optimal weight: 0.4980 chunk 44 optimal weight: 0.5980 chunk 21 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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: 0.7775 moved from start: 0.4003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3834 Z= 0.267 Angle : 0.558 7.261 5248 Z= 0.287 Chirality : 0.045 0.164 626 Planarity : 0.004 0.052 652 Dihedral : 5.204 38.945 685 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.29 % Allowed : 12.65 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.39), residues: 474 helix: 3.33 (1.68), residues: 11 sheet: 0.59 (0.36), residues: 191 loop : -0.51 (0.39), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 258 HIS 0.002 0.001 HIS A 245 PHE 0.019 0.002 PHE A 55 TYR 0.015 0.001 TYR L 48 ARG 0.002 0.000 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 46 time to evaluate : 0.400 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 47 average time/residue: 0.2287 time to fit residues: 12.9027 Evaluate side-chains 47 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 46 time to evaluate : 0.417 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0371 time to fit residues: 0.6031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 22 optimal weight: 7.9990 chunk 29 optimal weight: 0.5980 chunk 39 optimal weight: 4.9990 chunk 11 optimal weight: 0.4980 chunk 34 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 chunk 37 optimal weight: 0.5980 chunk 15 optimal weight: 0.8980 chunk 38 optimal weight: 0.5980 chunk 4 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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: 0.7761 moved from start: 0.4119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3834 Z= 0.233 Angle : 0.557 8.052 5248 Z= 0.280 Chirality : 0.045 0.158 626 Planarity : 0.004 0.050 652 Dihedral : 5.131 38.949 685 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.18 % Allowed : 12.06 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.39), residues: 474 helix: 3.80 (1.75), residues: 11 sheet: 0.53 (0.37), residues: 191 loop : -0.56 (0.39), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 258 HIS 0.003 0.001 HIS A 207 PHE 0.021 0.002 PHE A 55 TYR 0.014 0.001 TYR L 48 ARG 0.002 0.000 ARG A 102 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 45 time to evaluate : 0.431 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 47 average time/residue: 0.2339 time to fit residues: 13.1606 Evaluate side-chains 47 residues out of total 432 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 44 time to evaluate : 0.438 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0399 time to fit residues: 0.8140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 6 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 25 optimal weight: 5.9990 chunk 31 optimal weight: 0.5980 chunk 1 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 28 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4029 r_free = 0.4029 target = 0.181651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.151198 restraints weight = 4225.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.154134 restraints weight = 3238.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.154912 restraints weight = 3154.130| |-----------------------------------------------------------------------------| r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.4166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3834 Z= 0.272 Angle : 0.579 9.250 5248 Z= 0.293 Chirality : 0.045 0.160 626 Planarity : 0.004 0.050 652 Dihedral : 5.228 38.891 685 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 0.29 % Allowed : 12.65 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.39), residues: 474 helix: 3.68 (1.76), residues: 11 sheet: 0.50 (0.34), residues: 218 loop : -0.84 (0.40), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 258 HIS 0.002 0.001 HIS A 245 PHE 0.020 0.002 PHE A 55 TYR 0.015 0.001 TYR L 48 ARG 0.002 0.000 ARG A 102 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1532.74 seconds wall clock time: 28 minutes 27.48 seconds (1707.48 seconds total)