Starting phenix.real_space_refine on Thu Mar 6 08:09:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ymd_33927/03_2025/7ymd_33927.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ymd_33927/03_2025/7ymd_33927.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.176 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ymd_33927/03_2025/7ymd_33927.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ymd_33927/03_2025/7ymd_33927.map" model { file = "/net/cci-nas-00/data/ceres_data/7ymd_33927/03_2025/7ymd_33927.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ymd_33927/03_2025/7ymd_33927.cif" } resolution = 4.176 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= -0.000 sd= 0.007 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 25 5.16 5 C 3575 2.51 5 N 969 2.21 5 O 1084 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 5653 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 816 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 2573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2573 Classifications: {'peptide': 322} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 319} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 2264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2264 Classifications: {'peptide': 285} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 277} Chain breaks: 1 Time building chain proxies: 3.52, per 1000 atoms: 0.62 Number of scatterers: 5653 At special positions: 0 Unit cell: (77.256, 83.52, 99.18, 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 25 16.00 O 1084 8.00 N 969 7.00 C 3575 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 1.35 Conformation dependent library (CDL) restraints added in 653.6 milliseconds 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1344 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 5 sheets defined 50.9% alpha, 5.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'A' and resid 114 through 121 Processing helix chain 'A' and resid 131 through 140 Processing helix chain 'A' and resid 199 through 211 removed outlier: 3.523A pdb=" N ARG A 202 " --> pdb=" O THR A 199 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N HIS A 203 " --> pdb=" O SER A 200 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N TYR A 205 " --> pdb=" O ARG A 202 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLN A 207 " --> pdb=" O SER A 204 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N GLN A 208 " --> pdb=" O TYR A 205 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER A 210 " --> pdb=" O GLN A 207 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N HIS A 211 " --> pdb=" O GLN A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 227 removed outlier: 4.243A pdb=" N ILE A 223 " --> pdb=" O ASN A 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 27 removed outlier: 3.529A pdb=" N ALA B 18 " --> pdb=" O GLY B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 49 removed outlier: 5.015A pdb=" N ASP B 47 " --> pdb=" O ARG B 43 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA B 48 " --> pdb=" O LEU B 44 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER B 49 " --> pdb=" O GLU B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 77 removed outlier: 4.064A pdb=" N LEU B 77 " --> pdb=" O VAL B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 97 removed outlier: 4.346A pdb=" N LYS B 97 " --> pdb=" O ALA B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 168 Processing helix chain 'B' and resid 181 through 195 removed outlier: 3.881A pdb=" N GLU B 186 " --> pdb=" O ILE B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 219 Processing helix chain 'B' and resid 223 through 237 Processing helix chain 'B' and resid 251 through 258 removed outlier: 3.575A pdb=" N ILE B 255 " --> pdb=" O ASP B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 266 Processing helix chain 'B' and resid 306 through 316 Processing helix chain 'C' and resid 8 through 25 removed outlier: 4.549A pdb=" N LEU C 12 " --> pdb=" O SER C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 42 removed outlier: 4.054A pdb=" N ARG C 29 " --> pdb=" O ASN C 25 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LYS C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLU C 40 " --> pdb=" O LEU C 36 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLN C 42 " --> pdb=" O ARG C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 63 Processing helix chain 'C' and resid 68 through 83 Processing helix chain 'C' and resid 94 through 99 removed outlier: 4.030A pdb=" N ASN C 98 " --> pdb=" O LYS C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 134 through 146 removed outlier: 3.522A pdb=" N PHE C 138 " --> pdb=" O ASN C 134 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N THR C 146 " --> pdb=" O GLN C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 151 removed outlier: 3.744A pdb=" N ILE C 151 " --> pdb=" O TYR C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 155 Processing helix chain 'C' and resid 177 through 195 Processing helix chain 'C' and resid 201 through 209 Processing helix chain 'C' and resid 210 through 212 No H-bonds generated for 'chain 'C' and resid 210 through 212' Processing helix chain 'C' and resid 226 through 237 Processing helix chain 'C' and resid 259 through 266 Processing helix chain 'C' and resid 267 through 280 Processing helix chain 'C' and resid 282 through 287 removed outlier: 4.455A pdb=" N LYS C 287 " --> pdb=" O GLU C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 298 Processing sheet with id=AA1, first strand: chain 'B' and resid 31 through 33 removed outlier: 3.573A pdb=" N CYS B 32 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE B 133 " --> pdb=" O CYS B 32 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 206 through 208 removed outlier: 6.194A pdb=" N SER B 207 " --> pdb=" O ILE B 336 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY B 281 " --> pdb=" O VAL B 335 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 240 through 242 Processing sheet with id=AA4, first strand: chain 'C' and resid 46 through 47 removed outlier: 4.690A pdb=" N LYS C 122 " --> pdb=" O LEU C 91 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ILE C 124 " --> pdb=" O GLN C 89 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLN C 89 " --> pdb=" O ILE C 124 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 199 through 200 removed outlier: 3.954A pdb=" N ILE C 199 " --> pdb=" O TYR C 256 " (cutoff:3.500A) 233 hydrogen bonds defined for protein. 669 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: 1.32 Time building geometry restraints manager: 1.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1877 1.34 - 1.46: 874 1.46 - 1.58: 2954 1.58 - 1.69: 0 1.69 - 1.81: 39 Bond restraints: 5744 Sorted by residual: bond pdb=" N ALA A 114 " pdb=" CA ALA A 114 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.06e+00 bond pdb=" N ASP C 7 " pdb=" CA ASP C 7 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.95e+00 bond pdb=" N ASN B 286 " pdb=" CA ASN B 286 " ideal model delta sigma weight residual 1.457 1.468 -0.011 1.29e-02 6.01e+03 6.99e-01 bond pdb=" CB GLU B 45 " pdb=" CG GLU B 45 " ideal model delta sigma weight residual 1.520 1.543 -0.023 3.00e-02 1.11e+03 5.84e-01 bond pdb=" N THR C 168 " pdb=" CA THR C 168 " ideal model delta sigma weight residual 1.457 1.466 -0.009 1.29e-02 6.01e+03 4.69e-01 ... (remaining 5739 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.04: 7412 1.04 - 2.08: 278 2.08 - 3.12: 41 3.12 - 4.15: 16 4.15 - 5.19: 3 Bond angle restraints: 7750 Sorted by residual: angle pdb=" C ASN B 286 " pdb=" CA ASN B 286 " pdb=" CB ASN B 286 " ideal model delta sigma weight residual 110.42 115.61 -5.19 1.99e+00 2.53e-01 6.81e+00 angle pdb=" C TYR A 212 " pdb=" N ASN A 213 " pdb=" CA ASN A 213 " ideal model delta sigma weight residual 121.54 125.73 -4.19 1.91e+00 2.74e-01 4.81e+00 angle pdb=" C LYS C 196 " pdb=" N ASN C 197 " pdb=" CA ASN C 197 " ideal model delta sigma weight residual 121.54 125.46 -3.92 1.91e+00 2.74e-01 4.20e+00 angle pdb=" C THR C 168 " pdb=" CA THR C 168 " pdb=" CB THR C 168 " ideal model delta sigma weight residual 110.42 114.48 -4.06 1.99e+00 2.53e-01 4.15e+00 angle pdb=" C ARG A 127 " pdb=" CA ARG A 127 " pdb=" CB ARG A 127 " ideal model delta sigma weight residual 109.54 112.83 -3.29 1.84e+00 2.95e-01 3.19e+00 ... (remaining 7745 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 3220 17.94 - 35.88: 219 35.88 - 53.82: 40 53.82 - 71.76: 7 71.76 - 89.69: 3 Dihedral angle restraints: 3489 sinusoidal: 1422 harmonic: 2067 Sorted by residual: dihedral pdb=" CA ARG A 127 " pdb=" C ARG A 127 " pdb=" N SER A 128 " pdb=" CA SER A 128 " ideal model delta harmonic sigma weight residual -180.00 -155.48 -24.52 0 5.00e+00 4.00e-02 2.40e+01 dihedral pdb=" CA CYS B 32 " pdb=" C CYS B 32 " pdb=" N HIS B 33 " pdb=" CA HIS B 33 " ideal model delta harmonic sigma weight residual -180.00 -163.01 -16.99 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" CA MET B 265 " pdb=" C MET B 265 " pdb=" N TYR B 266 " pdb=" CA TYR B 266 " ideal model delta harmonic sigma weight residual 180.00 163.73 16.27 0 5.00e+00 4.00e-02 1.06e+01 ... (remaining 3486 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 562 0.025 - 0.050: 190 0.050 - 0.075: 73 0.075 - 0.100: 34 0.100 - 0.125: 25 Chirality restraints: 884 Sorted by residual: chirality pdb=" CA VAL C 129 " pdb=" N VAL C 129 " pdb=" C VAL C 129 " pdb=" CB VAL C 129 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.90e-01 chirality pdb=" CA ILE C 124 " pdb=" N ILE C 124 " pdb=" C ILE C 124 " pdb=" CB ILE C 124 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.52e-01 chirality pdb=" CA ILE C 254 " pdb=" N ILE C 254 " pdb=" C ILE C 254 " pdb=" CB ILE C 254 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.49e-01 ... (remaining 881 not shown) Planarity restraints: 993 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 160 " 0.009 2.00e-02 2.50e+03 7.84e-03 1.54e+00 pdb=" CG TRP B 160 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 TRP B 160 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TRP B 160 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 160 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 160 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 160 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 160 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 160 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 160 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 242 " 0.019 5.00e-02 4.00e+02 2.83e-02 1.28e+00 pdb=" N PRO A 243 " -0.049 5.00e-02 4.00e+02 pdb=" CA PRO A 243 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 243 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS C 196 " 0.005 2.00e-02 2.50e+03 1.11e-02 1.22e+00 pdb=" C LYS C 196 " -0.019 2.00e-02 2.50e+03 pdb=" O LYS C 196 " 0.007 2.00e-02 2.50e+03 pdb=" N ASN C 197 " 0.006 2.00e-02 2.50e+03 ... (remaining 990 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 79 2.60 - 3.18: 5545 3.18 - 3.75: 8420 3.75 - 4.33: 11466 4.33 - 4.90: 18681 Nonbonded interactions: 44191 Sorted by model distance: nonbonded pdb=" O SER B 213 " pdb=" OG1 THR B 214 " model vdw 2.026 3.040 nonbonded pdb=" OE2 GLU A 214 " pdb=" CG GLN A 217 " model vdw 2.216 3.440 nonbonded pdb=" O LEU C 80 " pdb=" N GLY C 85 " model vdw 2.219 3.120 nonbonded pdb=" OH TYR B 20 " pdb=" O PRO C 130 " model vdw 2.247 3.040 nonbonded pdb=" O LYS C 287 " pdb=" OG SER C 288 " model vdw 2.263 3.040 ... (remaining 44186 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: 0.170 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: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 16.430 Find NCS groups from input model: 0.070 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6938 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 : 0.002 0.033 5744 Z= 0.131 Angle : 0.481 5.193 7750 Z= 0.278 Chirality : 0.037 0.125 884 Planarity : 0.002 0.028 993 Dihedral : 12.735 89.694 2145 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % 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 (0.35), residues: 693 helix: 1.35 (0.31), residues: 330 sheet: -0.54 (1.16), residues: 22 loop : -1.13 (0.36), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 160 HIS 0.007 0.001 HIS C 56 PHE 0.015 0.001 PHE B 165 TYR 0.008 0.001 TYR B 261 ARG 0.005 0.000 ARG A 127 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 158 MET cc_start: 0.8043 (tpp) cc_final: 0.7781 (tpp) REVERT: B 222 LEU cc_start: 0.8632 (mm) cc_final: 0.7899 (tp) REVERT: C 197 ASN cc_start: 0.7333 (p0) cc_final: 0.7112 (p0) REVERT: C 224 ASN cc_start: 0.8580 (m-40) cc_final: 0.8119 (t0) REVERT: C 257 ARG cc_start: 0.7979 (mmm-85) cc_final: 0.7442 (tpt-90) REVERT: C 299 ASP cc_start: 0.7148 (p0) cc_final: 0.6436 (p0) outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.1430 time to fit residues: 34.0367 Evaluate side-chains 145 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 58 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 29 optimal weight: 10.0000 chunk 17 optimal weight: 10.0000 chunk 35 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 chunk 54 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 40 optimal weight: 20.0000 chunk 62 optimal weight: 8.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 303 GLN C 89 GLN C 145 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.198058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.153996 restraints weight = 9318.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.159313 restraints weight = 6084.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.162923 restraints weight = 4614.376| |-----------------------------------------------------------------------------| r_work (final): 0.3970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5744 Z= 0.178 Angle : 0.559 9.641 7750 Z= 0.294 Chirality : 0.042 0.143 884 Planarity : 0.003 0.044 993 Dihedral : 4.040 18.222 757 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % 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: -0.14 (0.34), residues: 693 helix: 0.91 (0.30), residues: 335 sheet: -1.63 (0.96), residues: 26 loop : -0.99 (0.37), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 160 HIS 0.006 0.001 HIS C 56 PHE 0.015 0.002 PHE C 207 TYR 0.013 0.002 TYR C 84 ARG 0.003 0.000 ARG B 242 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 PHE cc_start: 0.6328 (t80) cc_final: 0.6115 (t80) REVERT: A 226 LEU cc_start: 0.8332 (mp) cc_final: 0.8110 (mp) REVERT: B 163 GLU cc_start: 0.8559 (tt0) cc_final: 0.8099 (mm-30) REVERT: B 222 LEU cc_start: 0.8638 (mm) cc_final: 0.7987 (tp) REVERT: C 139 LYS cc_start: 0.8896 (mmtt) cc_final: 0.8663 (tttt) REVERT: C 148 GLU cc_start: 0.8467 (pt0) cc_final: 0.8200 (pt0) REVERT: C 189 LEU cc_start: 0.8769 (mt) cc_final: 0.8564 (mt) REVERT: C 197 ASN cc_start: 0.7595 (p0) cc_final: 0.7384 (p0) REVERT: C 299 ASP cc_start: 0.7158 (p0) cc_final: 0.6856 (p0) outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.1498 time to fit residues: 36.1481 Evaluate side-chains 147 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 56 optimal weight: 0.5980 chunk 10 optimal weight: 4.9990 chunk 18 optimal weight: 30.0000 chunk 64 optimal weight: 1.9990 chunk 50 optimal weight: 8.9990 chunk 49 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 46 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 22 optimal weight: 9.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 56 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.194526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.150071 restraints weight = 9508.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.155180 restraints weight = 6185.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.158719 restraints weight = 4683.690| |-----------------------------------------------------------------------------| r_work (final): 0.3920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5744 Z= 0.216 Angle : 0.589 8.387 7750 Z= 0.309 Chirality : 0.043 0.190 884 Planarity : 0.003 0.040 993 Dihedral : 4.195 21.375 757 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 0.16 % Allowed : 2.54 % Favored : 97.30 % 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: -0.45 (0.33), residues: 693 helix: 0.65 (0.29), residues: 334 sheet: -2.00 (0.90), residues: 26 loop : -1.12 (0.37), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 160 HIS 0.007 0.001 HIS C 56 PHE 0.018 0.002 PHE C 207 TYR 0.020 0.002 TYR B 313 ARG 0.003 0.000 ARG C 177 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 177 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 33 HIS cc_start: 0.8770 (t70) cc_final: 0.8500 (t-90) REVERT: B 89 ILE cc_start: 0.9078 (mp) cc_final: 0.8807 (pt) REVERT: B 158 MET cc_start: 0.8250 (tpp) cc_final: 0.7993 (tpp) REVERT: B 163 GLU cc_start: 0.8522 (tt0) cc_final: 0.8060 (mm-30) REVERT: C 31 MET cc_start: 0.8710 (tpp) cc_final: 0.8370 (tpp) REVERT: C 48 ARG cc_start: 0.8645 (tpt-90) cc_final: 0.8304 (mmm160) REVERT: C 237 ARG cc_start: 0.9022 (mtt180) cc_final: 0.8638 (ttm170) REVERT: C 257 ARG cc_start: 0.7124 (tpt170) cc_final: 0.6835 (tpt170) outliers start: 1 outliers final: 1 residues processed: 177 average time/residue: 0.1698 time to fit residues: 39.0311 Evaluate side-chains 152 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 151 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 26 optimal weight: 10.0000 chunk 22 optimal weight: 8.9990 chunk 18 optimal weight: 30.0000 chunk 27 optimal weight: 8.9990 chunk 28 optimal weight: 9.9990 chunk 19 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 67 optimal weight: 5.9990 chunk 11 optimal weight: 8.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN B 280 GLN C 52 GLN C 56 HIS C 89 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.182150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.136081 restraints weight = 9612.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.140548 restraints weight = 6404.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.143549 restraints weight = 4959.930| |-----------------------------------------------------------------------------| r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 5744 Z= 0.421 Angle : 0.777 10.173 7750 Z= 0.408 Chirality : 0.048 0.184 884 Planarity : 0.005 0.054 993 Dihedral : 5.105 22.233 757 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.82 % Favored : 89.18 % Rotamer: Outliers : 0.16 % Allowed : 4.29 % Favored : 95.55 % 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: -1.00 (0.33), residues: 693 helix: 0.14 (0.28), residues: 332 sheet: -2.36 (0.87), residues: 26 loop : -1.32 (0.37), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP B 160 HIS 0.009 0.002 HIS C 145 PHE 0.023 0.003 PHE A 148 TYR 0.025 0.003 TYR A 227 ARG 0.004 0.001 ARG B 242 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 163 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 129 MET cc_start: 0.8242 (mmm) cc_final: 0.7348 (tpp) REVERT: A 133 GLU cc_start: 0.8421 (tp30) cc_final: 0.7370 (tm-30) REVERT: A 140 LYS cc_start: 0.9142 (mtmm) cc_final: 0.8870 (mtmm) REVERT: B 33 HIS cc_start: 0.8841 (t70) cc_final: 0.7751 (t-90) REVERT: B 34 GLU cc_start: 0.7571 (pm20) cc_final: 0.7149 (pm20) REVERT: B 284 CYS cc_start: 0.8206 (t) cc_final: 0.8000 (t) REVERT: C 48 ARG cc_start: 0.8632 (tpt-90) cc_final: 0.8167 (mmm160) REVERT: C 124 ILE cc_start: 0.8141 (tp) cc_final: 0.7878 (tp) REVERT: C 139 LYS cc_start: 0.9097 (mtpp) cc_final: 0.8768 (ttmt) REVERT: C 146 THR cc_start: 0.8804 (p) cc_final: 0.8529 (t) REVERT: C 149 GLU cc_start: 0.8944 (pm20) cc_final: 0.8675 (pm20) REVERT: C 181 TYR cc_start: 0.9138 (t80) cc_final: 0.8477 (t80) REVERT: C 237 ARG cc_start: 0.9118 (mtt180) cc_final: 0.8719 (ttm170) outliers start: 1 outliers final: 1 residues processed: 164 average time/residue: 0.1545 time to fit residues: 33.6096 Evaluate side-chains 138 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 137 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 22 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 13 optimal weight: 0.1980 chunk 64 optimal weight: 7.9990 chunk 1 optimal weight: 7.9990 chunk 15 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 ASN B 280 GLN C 56 HIS C 89 GLN ** C 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.188540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.142034 restraints weight = 9502.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.146859 restraints weight = 6253.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.150170 restraints weight = 4807.132| |-----------------------------------------------------------------------------| r_work (final): 0.3822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5744 Z= 0.216 Angle : 0.641 10.874 7750 Z= 0.333 Chirality : 0.043 0.179 884 Planarity : 0.004 0.043 993 Dihedral : 4.880 24.221 757 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.51 % Favored : 91.49 % Rotamer: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % 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 (0.33), residues: 693 helix: 0.38 (0.29), residues: 335 sheet: -2.32 (0.88), residues: 26 loop : -1.37 (0.36), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 160 HIS 0.009 0.001 HIS C 56 PHE 0.026 0.002 PHE C 207 TYR 0.022 0.002 TYR B 313 ARG 0.005 0.000 ARG C 257 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 LYS cc_start: 0.9079 (mtmm) cc_final: 0.8854 (mtmm) REVERT: B 33 HIS cc_start: 0.8743 (t70) cc_final: 0.8276 (t70) REVERT: B 42 MET cc_start: 0.9121 (mtt) cc_final: 0.8694 (mtt) REVERT: B 89 ILE cc_start: 0.9039 (mp) cc_final: 0.8716 (pt) REVERT: B 216 LEU cc_start: 0.7785 (mp) cc_final: 0.7389 (mt) REVERT: B 284 CYS cc_start: 0.8074 (t) cc_final: 0.7871 (t) REVERT: C 31 MET cc_start: 0.8742 (tpp) cc_final: 0.8088 (tpp) REVERT: C 135 PHE cc_start: 0.8356 (t80) cc_final: 0.7893 (t80) REVERT: C 149 GLU cc_start: 0.8618 (pm20) cc_final: 0.8215 (pm20) REVERT: C 257 ARG cc_start: 0.7239 (tpt90) cc_final: 0.6826 (tpt170) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.1586 time to fit residues: 36.8860 Evaluate side-chains 145 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 19 optimal weight: 8.9990 chunk 4 optimal weight: 20.0000 chunk 39 optimal weight: 5.9990 chunk 50 optimal weight: 0.0870 chunk 21 optimal weight: 1.9990 chunk 25 optimal weight: 10.0000 chunk 34 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 overall best weight: 3.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN B 280 GLN C 56 HIS C 89 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.183183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.137453 restraints weight = 9466.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.142168 restraints weight = 6176.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.145309 restraints weight = 4688.698| |-----------------------------------------------------------------------------| r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.3465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 5744 Z= 0.324 Angle : 0.689 9.784 7750 Z= 0.361 Chirality : 0.045 0.162 884 Planarity : 0.004 0.044 993 Dihedral : 5.111 25.074 757 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.96 % Favored : 90.04 % Rotamer: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % 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: -1.06 (0.33), residues: 693 helix: 0.16 (0.29), residues: 337 sheet: -2.15 (0.93), residues: 26 loop : -1.49 (0.36), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 160 HIS 0.009 0.002 HIS A 147 PHE 0.022 0.002 PHE A 215 TYR 0.020 0.002 TYR A 227 ARG 0.005 0.001 ARG C 237 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 LYS cc_start: 0.9129 (mtmm) cc_final: 0.8907 (mtmm) REVERT: B 29 ARG cc_start: 0.8420 (tpp-160) cc_final: 0.8176 (tpp-160) REVERT: B 33 HIS cc_start: 0.8618 (t70) cc_final: 0.8092 (t-90) REVERT: B 42 MET cc_start: 0.9194 (mtt) cc_final: 0.8727 (mtt) REVERT: B 89 ILE cc_start: 0.9028 (mp) cc_final: 0.8677 (pt) REVERT: B 265 MET cc_start: 0.8960 (tmm) cc_final: 0.8566 (tmm) REVERT: C 31 MET cc_start: 0.8746 (tpp) cc_final: 0.8061 (tpp) outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.1568 time to fit residues: 33.7006 Evaluate side-chains 135 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 64 optimal weight: 8.9990 chunk 61 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 chunk 19 optimal weight: 0.5980 chunk 35 optimal weight: 7.9990 chunk 58 optimal weight: 0.8980 chunk 26 optimal weight: 6.9990 chunk 45 optimal weight: 4.9990 chunk 3 optimal weight: 7.9990 chunk 39 optimal weight: 0.1980 chunk 65 optimal weight: 0.8980 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 280 GLN C 56 HIS C 89 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.188364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.139818 restraints weight = 9659.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.144973 restraints weight = 6369.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.148423 restraints weight = 4882.929| |-----------------------------------------------------------------------------| r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.3481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5744 Z= 0.206 Angle : 0.636 9.631 7750 Z= 0.330 Chirality : 0.043 0.154 884 Planarity : 0.003 0.046 993 Dihedral : 4.956 24.474 757 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.80 % Favored : 91.20 % Rotamer: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % 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: -0.94 (0.33), residues: 693 helix: 0.23 (0.29), residues: 342 sheet: -1.99 (0.97), residues: 26 loop : -1.42 (0.37), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 160 HIS 0.008 0.001 HIS C 56 PHE 0.020 0.002 PHE A 215 TYR 0.022 0.002 TYR B 313 ARG 0.002 0.000 ARG C 257 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 LYS cc_start: 0.9114 (mtmm) cc_final: 0.8893 (mtmm) REVERT: A 226 LEU cc_start: 0.8279 (mp) cc_final: 0.7897 (mp) REVERT: B 42 MET cc_start: 0.9099 (mtt) cc_final: 0.8609 (mtt) REVERT: B 89 ILE cc_start: 0.9027 (mp) cc_final: 0.8728 (pt) REVERT: B 265 MET cc_start: 0.8949 (tmm) cc_final: 0.8486 (tmm) REVERT: B 305 TRP cc_start: 0.5780 (m-90) cc_final: 0.5061 (m-90) REVERT: C 31 MET cc_start: 0.8826 (tpp) cc_final: 0.8348 (tpp) REVERT: C 72 MET cc_start: 0.8311 (tpt) cc_final: 0.7961 (tpp) outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.1517 time to fit residues: 32.9319 Evaluate side-chains 138 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 61 optimal weight: 7.9990 chunk 34 optimal weight: 3.9990 chunk 16 optimal weight: 6.9990 chunk 56 optimal weight: 10.0000 chunk 14 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 58 optimal weight: 0.5980 chunk 59 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 42 optimal weight: 7.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 GLN C 56 HIS C 118 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.189196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.145441 restraints weight = 9158.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.150615 restraints weight = 5804.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.154147 restraints weight = 4329.836| |-----------------------------------------------------------------------------| r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5744 Z= 0.202 Angle : 0.633 10.054 7750 Z= 0.328 Chirality : 0.043 0.150 884 Planarity : 0.003 0.047 993 Dihedral : 4.850 24.183 757 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.67 % Favored : 90.33 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % 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: -0.93 (0.33), residues: 693 helix: 0.18 (0.29), residues: 345 sheet: -1.90 (0.98), residues: 26 loop : -1.36 (0.37), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 160 HIS 0.008 0.001 HIS C 56 PHE 0.013 0.002 PHE C 135 TYR 0.013 0.002 TYR A 212 ARG 0.003 0.000 ARG B 43 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 LYS cc_start: 0.9115 (mtmm) cc_final: 0.8890 (mtmm) REVERT: A 226 LEU cc_start: 0.8277 (mp) cc_final: 0.7873 (mp) REVERT: B 42 MET cc_start: 0.9063 (mtt) cc_final: 0.8620 (mtt) REVERT: B 89 ILE cc_start: 0.9066 (mp) cc_final: 0.8744 (pt) REVERT: B 265 MET cc_start: 0.8967 (tmm) cc_final: 0.8454 (tmm) REVERT: B 305 TRP cc_start: 0.5747 (m-90) cc_final: 0.5141 (m-90) REVERT: C 31 MET cc_start: 0.8831 (tpp) cc_final: 0.8335 (tpp) REVERT: C 72 MET cc_start: 0.8234 (tpt) cc_final: 0.7935 (tpp) REVERT: C 237 ARG cc_start: 0.9118 (mtt180) cc_final: 0.8866 (ttm170) outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.1562 time to fit residues: 33.2863 Evaluate side-chains 135 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 19 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 56 optimal weight: 9.9990 chunk 66 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 chunk 9 optimal weight: 9.9990 chunk 17 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 GLN C 56 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.186525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.141452 restraints weight = 9314.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.146417 restraints weight = 5949.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.149579 restraints weight = 4472.100| |-----------------------------------------------------------------------------| r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.3709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5744 Z= 0.265 Angle : 0.677 9.768 7750 Z= 0.350 Chirality : 0.044 0.146 884 Planarity : 0.004 0.047 993 Dihedral : 4.916 23.732 757 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % 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: -1.10 (0.33), residues: 693 helix: 0.10 (0.29), residues: 341 sheet: -2.00 (0.94), residues: 26 loop : -1.50 (0.37), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 160 HIS 0.007 0.001 HIS C 56 PHE 0.017 0.002 PHE C 135 TYR 0.025 0.002 TYR B 313 ARG 0.003 0.000 ARG C 48 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 LYS cc_start: 0.9127 (mtmm) cc_final: 0.8841 (mtmm) REVERT: A 226 LEU cc_start: 0.8305 (mp) cc_final: 0.7918 (mp) REVERT: B 29 ARG cc_start: 0.8371 (tpp-160) cc_final: 0.8045 (tpp-160) REVERT: B 34 GLU cc_start: 0.7668 (pm20) cc_final: 0.7281 (pm20) REVERT: B 89 ILE cc_start: 0.9023 (mp) cc_final: 0.8696 (pt) REVERT: B 129 SER cc_start: 0.7473 (p) cc_final: 0.6602 (m) REVERT: B 265 MET cc_start: 0.8961 (tmm) cc_final: 0.8509 (tmm) REVERT: B 305 TRP cc_start: 0.5826 (m-90) cc_final: 0.5174 (m-90) REVERT: C 31 MET cc_start: 0.8882 (tpp) cc_final: 0.8378 (tpp) REVERT: C 72 MET cc_start: 0.8304 (tpt) cc_final: 0.7973 (tpp) REVERT: C 149 GLU cc_start: 0.8420 (mp0) cc_final: 0.8186 (mp0) outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.1511 time to fit residues: 32.6759 Evaluate side-chains 138 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 22 optimal weight: 7.9990 chunk 21 optimal weight: 0.6980 chunk 34 optimal weight: 7.9990 chunk 65 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 12 optimal weight: 0.0040 chunk 30 optimal weight: 7.9990 chunk 39 optimal weight: 0.0170 chunk 52 optimal weight: 5.9990 chunk 10 optimal weight: 0.8980 overall best weight: 0.5230 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 GLN C 56 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.193148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.149269 restraints weight = 9280.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.154694 restraints weight = 5866.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.158372 restraints weight = 4325.524| |-----------------------------------------------------------------------------| r_work (final): 0.3899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.3698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5744 Z= 0.167 Angle : 0.637 11.021 7750 Z= 0.327 Chirality : 0.043 0.146 884 Planarity : 0.003 0.048 993 Dihedral : 4.727 24.291 757 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.51 % Favored : 91.49 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % 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: -0.95 (0.33), residues: 693 helix: 0.21 (0.29), residues: 342 sheet: -1.79 (0.99), residues: 26 loop : -1.43 (0.37), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 160 HIS 0.008 0.001 HIS C 56 PHE 0.016 0.002 PHE C 135 TYR 0.022 0.002 TYR B 313 ARG 0.004 0.000 ARG C 177 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 PHE cc_start: 0.6844 (t80) cc_final: 0.6533 (t80) REVERT: A 226 LEU cc_start: 0.8134 (mp) cc_final: 0.7705 (mp) REVERT: B 42 MET cc_start: 0.9044 (mtt) cc_final: 0.8577 (mtt) REVERT: B 89 ILE cc_start: 0.8985 (mp) cc_final: 0.8665 (pt) REVERT: B 305 TRP cc_start: 0.5769 (m-90) cc_final: 0.5224 (m-90) REVERT: C 31 MET cc_start: 0.8744 (tpp) cc_final: 0.8305 (tpp) REVERT: C 72 MET cc_start: 0.8151 (tpt) cc_final: 0.7919 (tpp) REVERT: C 149 GLU cc_start: 0.8208 (mp0) cc_final: 0.7907 (mp0) REVERT: C 181 TYR cc_start: 0.8790 (t80) cc_final: 0.8337 (t80) REVERT: C 237 ARG cc_start: 0.9009 (mtt180) cc_final: 0.8716 (ttm170) outliers start: 0 outliers final: 0 residues processed: 170 average time/residue: 0.1533 time to fit residues: 34.9960 Evaluate side-chains 148 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 39 optimal weight: 0.3980 chunk 3 optimal weight: 8.9990 chunk 22 optimal weight: 5.9990 chunk 44 optimal weight: 0.9990 chunk 45 optimal weight: 5.9990 chunk 50 optimal weight: 7.9990 chunk 42 optimal weight: 3.9990 chunk 25 optimal weight: 40.0000 chunk 55 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 overall best weight: 2.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN ** B 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.187849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.139418 restraints weight = 9663.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.144407 restraints weight = 6380.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.147981 restraints weight = 4900.103| |-----------------------------------------------------------------------------| r_work (final): 0.3793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.3724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5744 Z= 0.234 Angle : 0.657 9.891 7750 Z= 0.341 Chirality : 0.043 0.152 884 Planarity : 0.003 0.049 993 Dihedral : 4.764 23.821 757 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % 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: -1.01 (0.33), residues: 693 helix: 0.18 (0.29), residues: 341 sheet: -1.79 (0.97), residues: 26 loop : -1.48 (0.37), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 160 HIS 0.004 0.001 HIS A 147 PHE 0.018 0.002 PHE C 135 TYR 0.018 0.002 TYR A 227 ARG 0.003 0.000 ARG A 127 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1978.66 seconds wall clock time: 35 minutes 6.82 seconds (2106.82 seconds total)