Starting phenix.real_space_refine on Fri Dec 27 09:16:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sof_25269/12_2024/7sof_25269.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sof_25269/12_2024/7sof_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/cci-nas-00/data/ceres_data/7sof_25269/12_2024/7sof_25269.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sof_25269/12_2024/7sof_25269.map" model { file = "/net/cci-nas-00/data/ceres_data/7sof_25269/12_2024/7sof_25269.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sof_25269/12_2024/7sof_25269.cif" } 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. Time to flip 30 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 9 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: 4.65, per 1000 atoms: 1.24 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied 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: 1.07 Conformation dependent library (CDL) restraints added in 477.8 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: 0.45 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: 0.98 Time building geometry restraints manager: 1.20 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: 0.00 - 1.49: 4327 1.49 - 2.99: 734 2.99 - 4.48: 108 4.48 - 5.98: 52 5.98 - 7.47: 27 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 - 21.32: 2273 21.32 - 42.64: 44 42.64 - 63.96: 5 63.96 - 85.28: 7 85.28 - 106.60: 4 Dihedral angle restraints: 2333 sinusoidal: 916 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=" O4 BMA B 3 " pdb=" C4 BMA B 3 " pdb=" C5 BMA B 3 " pdb=" O5 BMA B 3 " ideal model delta sinusoidal sigma weight residual -71.29 -177.89 106.60 1 3.00e+01 1.11e-03 1.37e+01 ... (remaining 2330 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 3.040 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 3.120 ... (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 Time spend for trying shortcut: 0.00 ========== 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: 7.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.370 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.220 ------------------------------------------------------------------------------- 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 : 11.425 106.597 1406 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 to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.414 Fit side-chains REVERT: L 36 GLN cc_start: 0.8889 (tt0) cc_final: 0.8628 (tt0) REVERT: H 3 THR cc_start: 0.7351 (t) cc_final: 0.7149 (m) REVERT: H 62 SER cc_start: 0.8440 (t) cc_final: 0.8090 (p) REVERT: H 124 SER cc_start: 0.6718 (p) cc_final: 0.6437 (t) REVERT: A 154 LYS cc_start: 0.8401 (ttpt) cc_final: 0.8074 (ttpp) REVERT: A 258 TRP cc_start: 0.7458 (m-90) cc_final: 0.7186 (m-90) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.1843 time to fit residues: 19.7253 Evaluate side-chains 63 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.363 ------------------------------------------------------------------------------- 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: 0.0470 chunk 35 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 36 optimal weight: 0.5980 chunk 14 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 42 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 overall best weight: 0.5278 ------------------------------------------------------------------------------- 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: 0.7631 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3834 Z= 0.242 Angle : 0.605 6.341 5248 Z= 0.316 Chirality : 0.047 0.154 626 Planarity : 0.005 0.051 652 Dihedral : 8.101 60.530 704 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 1.96 Ramachandran Plot: Outliers : 0.21 % Allowed : 1.48 % Favored : 98.31 % Rotamer: Outliers : 1.47 % Allowed : 7.35 % Favored : 91.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.39), residues: 474 helix: 1.69 (1.55), residues: 11 sheet: 1.38 (0.38), residues: 191 loop : -0.07 (0.37), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 103 HIS 0.002 0.001 HIS A 245 PHE 0.015 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 72 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 67 time to evaluate : 0.398 Fit side-chains REVERT: A 108 THR cc_start: 0.8440 (p) cc_final: 0.8052 (t) REVERT: A 138 ASP cc_start: 0.7840 (t0) cc_final: 0.7616 (t0) REVERT: A 154 LYS cc_start: 0.8474 (ttpt) cc_final: 0.8200 (ttpp) REVERT: A 258 TRP cc_start: 0.7851 (m-90) cc_final: 0.7550 (m-90) outliers start: 5 outliers final: 2 residues processed: 69 average time/residue: 0.1760 time to fit residues: 14.9180 Evaluate side-chains 66 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 64 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain H residue 83 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 13 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 chunk 46 optimal weight: 0.3980 chunk 38 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 34 optimal weight: 0.0470 chunk 32 optimal weight: 0.0000 chunk 22 optimal weight: 0.9990 overall best weight: 0.4082 ------------------------------------------------------------------------------- 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: 0.7654 moved from start: 0.2586 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= 0.185 Angle : 0.541 5.776 5248 Z= 0.279 Chirality : 0.045 0.171 626 Planarity : 0.004 0.051 652 Dihedral : 5.607 34.610 704 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.65 % Allowed : 8.82 % 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: 0.86 (0.39), residues: 474 helix: 2.79 (1.63), residues: 11 sheet: 1.31 (0.35), residues: 214 loop : -0.18 (0.39), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 103 HIS 0.002 0.001 HIS A 146 PHE 0.009 0.001 PHE A 55 TYR 0.017 0.001 TYR L 48 ARG 0.002 0.000 ARG A 78 *********************** 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 75 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 0.410 Fit side-chains revert: symmetry clash REVERT: A 138 ASP cc_start: 0.7922 (t0) cc_final: 0.7673 (t0) REVERT: A 154 LYS cc_start: 0.8522 (ttpt) cc_final: 0.8263 (ttpp) REVERT: A 258 TRP cc_start: 0.7956 (m-90) cc_final: 0.7644 (m-90) outliers start: 9 outliers final: 6 residues processed: 71 average time/residue: 0.1764 time to fit residues: 15.3263 Evaluate side-chains 68 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 62 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 15 THR Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 210 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 4 optimal weight: 1.9990 chunk 20 optimal weight: 0.0050 chunk 28 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 45 optimal weight: 7.9990 chunk 22 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 25 optimal weight: 4.9990 chunk 0 optimal weight: 1.9990 overall best weight: 1.0598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 88 GLN A 121 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.3289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 3834 Z= 0.383 Angle : 0.637 8.388 5248 Z= 0.328 Chirality : 0.047 0.168 626 Planarity : 0.005 0.056 652 Dihedral : 5.571 38.822 704 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 4.71 % Allowed : 7.06 % 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: 0.31 (0.38), residues: 474 helix: 3.12 (1.63), residues: 11 sheet: 0.85 (0.37), residues: 187 loop : -0.34 (0.37), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP H 115 HIS 0.003 0.001 HIS A 245 PHE 0.016 0.002 PHE A 238 TYR 0.018 0.002 TYR H 96 ARG 0.009 0.001 ARG A 158 *********************** 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 71 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 55 time to evaluate : 0.401 Fit side-chains revert: symmetry clash REVERT: L 2 TYR cc_start: 0.8750 (t80) cc_final: 0.8357 (t80) REVERT: A 154 LYS cc_start: 0.8581 (ttpt) cc_final: 0.8299 (ttpp) REVERT: A 258 TRP cc_start: 0.8050 (m-90) cc_final: 0.7509 (m-90) outliers start: 16 outliers final: 11 residues processed: 64 average time/residue: 0.2027 time to fit residues: 15.5865 Evaluate side-chains 64 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 53 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain H residue 15 THR Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 286 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 33 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 11 optimal weight: 0.2980 chunk 15 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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: 0.7763 moved from start: 0.3479 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= 0.255 Angle : 0.562 7.488 5248 Z= 0.289 Chirality : 0.045 0.161 626 Planarity : 0.004 0.047 652 Dihedral : 5.325 37.486 704 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 4.41 % Allowed : 10.00 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.39), residues: 474 helix: 3.26 (1.65), residues: 11 sheet: 0.82 (0.36), residues: 191 loop : -0.31 (0.39), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 103 HIS 0.003 0.001 HIS A 207 PHE 0.011 0.002 PHE A 238 TYR 0.016 0.002 TYR L 48 ARG 0.004 0.000 ARG A 158 *********************** 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 67 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 52 time to evaluate : 0.401 Fit side-chains revert: symmetry clash REVERT: A 154 LYS cc_start: 0.8556 (ttpt) cc_final: 0.8268 (ttpp) REVERT: A 258 TRP cc_start: 0.7849 (m-90) cc_final: 0.7534 (m-90) outliers start: 15 outliers final: 13 residues processed: 61 average time/residue: 0.2007 time to fit residues: 14.7494 Evaluate side-chains 63 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 50 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain H residue 15 THR Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 286 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 11 optimal weight: 0.0970 chunk 45 optimal weight: 7.9990 chunk 37 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 overall best weight: 0.9980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 88 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.3841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 3834 Z= 0.359 Angle : 0.615 8.587 5248 Z= 0.316 Chirality : 0.046 0.164 626 Planarity : 0.004 0.048 652 Dihedral : 5.599 39.351 704 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 5.00 % Allowed : 8.82 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.39), residues: 474 helix: 3.23 (1.62), residues: 11 sheet: 0.56 (0.36), residues: 191 loop : -0.44 (0.39), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 115 HIS 0.004 0.001 HIS A 245 PHE 0.015 0.002 PHE A 238 TYR 0.016 0.002 TYR H 96 ARG 0.004 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 67 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 50 time to evaluate : 0.382 Fit side-chains revert: symmetry clash REVERT: A 154 LYS cc_start: 0.8560 (ttpt) cc_final: 0.8271 (ttpp) REVERT: A 258 TRP cc_start: 0.7843 (m-90) cc_final: 0.7576 (m-90) outliers start: 17 outliers final: 14 residues processed: 61 average time/residue: 0.2116 time to fit residues: 15.3798 Evaluate side-chains 63 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 49 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain H residue 15 THR Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 286 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 25 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 13 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 30 optimal weight: 0.4980 chunk 22 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 88 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.3902 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= 0.257 Angle : 0.567 7.886 5248 Z= 0.292 Chirality : 0.045 0.158 626 Planarity : 0.004 0.045 652 Dihedral : 5.398 38.271 704 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 4.41 % Allowed : 9.41 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.39), residues: 474 helix: 3.16 (1.64), residues: 11 sheet: 0.54 (0.36), residues: 191 loop : -0.46 (0.39), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 103 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 0.006 0.001 ARG A 246 *********************** 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 66 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 51 time to evaluate : 0.457 Fit side-chains revert: symmetry clash REVERT: A 154 LYS cc_start: 0.8525 (ttpt) cc_final: 0.8239 (ttpp) REVERT: A 258 TRP cc_start: 0.7820 (m-90) cc_final: 0.7552 (m-90) outliers start: 15 outliers final: 14 residues processed: 61 average time/residue: 0.2147 time to fit residues: 15.7839 Evaluate side-chains 65 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 51 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain H residue 15 THR Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 286 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 4 optimal weight: 0.5980 chunk 35 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 42 optimal weight: 0.9980 chunk 25 optimal weight: 0.2980 chunk 18 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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: 0.7785 moved from start: 0.4057 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= 0.258 Angle : 0.577 7.975 5248 Z= 0.291 Chirality : 0.045 0.160 626 Planarity : 0.004 0.047 652 Dihedral : 5.309 38.079 704 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 4.41 % Allowed : 9.71 % 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: -0.01 (0.39), residues: 474 helix: 3.53 (1.70), residues: 11 sheet: 0.56 (0.34), residues: 217 loop : -0.68 (0.41), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 103 HIS 0.003 0.001 HIS A 207 PHE 0.017 0.002 PHE A 55 TYR 0.015 0.001 TYR L 48 ARG 0.005 0.001 ARG A 246 *********************** 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 65 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 50 time to evaluate : 0.412 Fit side-chains revert: symmetry clash REVERT: A 154 LYS cc_start: 0.8485 (ttpt) cc_final: 0.8219 (ttpp) outliers start: 15 outliers final: 13 residues processed: 59 average time/residue: 0.2373 time to fit residues: 17.0854 Evaluate side-chains 62 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 49 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain H residue 15 THR Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 286 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 39 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 46 optimal weight: 10.0000 chunk 43 optimal weight: 0.9990 chunk 37 optimal weight: 0.5980 chunk 3 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.4142 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= 0.277 Angle : 0.599 9.317 5248 Z= 0.301 Chirality : 0.046 0.163 626 Planarity : 0.004 0.050 652 Dihedral : 5.330 38.415 704 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 4.12 % Allowed : 12.06 % Favored : 83.82 % 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: -0.12 (0.39), residues: 474 helix: 3.47 (1.71), residues: 11 sheet: 0.48 (0.34), residues: 217 loop : -0.75 (0.41), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 115 HIS 0.003 0.001 HIS A 245 PHE 0.018 0.002 PHE A 55 TYR 0.015 0.001 TYR L 48 ARG 0.007 0.001 ARG A 246 *********************** 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 64 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 50 time to evaluate : 0.391 Fit side-chains revert: symmetry clash REVERT: A 154 LYS cc_start: 0.8498 (ttpt) cc_final: 0.8227 (ttpp) outliers start: 14 outliers final: 13 residues processed: 59 average time/residue: 0.2128 time to fit residues: 15.0127 Evaluate side-chains 63 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 50 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain H residue 15 THR Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 286 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 22 optimal weight: 9.9990 chunk 29 optimal weight: 0.5980 chunk 39 optimal weight: 4.9990 chunk 11 optimal weight: 0.0170 chunk 34 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 overall best weight: 0.5618 ------------------------------------------------------------------------------- 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: 0.4213 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= 0.229 Angle : 0.577 7.917 5248 Z= 0.288 Chirality : 0.045 0.167 626 Planarity : 0.004 0.055 652 Dihedral : 5.198 37.675 704 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.82 % Allowed : 12.06 % Favored : 84.12 % 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: -0.10 (0.39), residues: 474 helix: 3.39 (1.69), residues: 11 sheet: 0.68 (0.35), residues: 212 loop : -0.90 (0.39), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 103 HIS 0.003 0.001 HIS A 207 PHE 0.019 0.002 PHE A 55 TYR 0.015 0.001 TYR L 48 ARG 0.004 0.001 ARG A 158 ********************** 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 64 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 51 time to evaluate : 0.319 Fit side-chains revert: symmetry clash REVERT: L 60 ARG cc_start: 0.7846 (mtm180) cc_final: 0.7483 (mtm180) REVERT: A 154 LYS cc_start: 0.8485 (ttpt) cc_final: 0.8213 (ttpp) outliers start: 13 outliers final: 13 residues processed: 60 average time/residue: 0.2028 time to fit residues: 14.5485 Evaluate side-chains 64 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 51 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain H residue 15 THR Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 286 THR 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: 1.9990 chunk 2 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 25 optimal weight: 5.9990 chunk 31 optimal weight: 0.1980 chunk 1 optimal weight: 5.9990 chunk 29 optimal weight: 0.4980 chunk 28 optimal weight: 0.7980 chunk 27 optimal weight: 0.0870 overall best weight: 0.4558 ------------------------------------------------------------------------------- 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 = 0.3730 r_free = 0.3730 target = 0.158869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.126862 restraints weight = 4313.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.128890 restraints weight = 3781.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.129897 restraints weight = 3663.936| |-----------------------------------------------------------------------------| r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.4248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3834 Z= 0.202 Angle : 0.570 7.552 5248 Z= 0.285 Chirality : 0.045 0.169 626 Planarity : 0.004 0.057 652 Dihedral : 5.063 37.065 704 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 4.12 % Allowed : 12.06 % Favored : 83.82 % 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: -0.10 (0.39), residues: 474 helix: 3.22 (1.67), residues: 11 sheet: 0.68 (0.37), residues: 186 loop : -0.73 (0.38), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 90 HIS 0.004 0.001 HIS A 207 PHE 0.019 0.001 PHE A 55 TYR 0.015 0.001 TYR L 48 ARG 0.004 0.000 ARG A 158 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1534.14 seconds wall clock time: 29 minutes 14.11 seconds (1754.11 seconds total)