Starting phenix.real_space_refine on Thu Dec 7 20:40:47 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8el8_28224/12_2023/8el8_28224_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8el8_28224/12_2023/8el8_28224.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8el8_28224/12_2023/8el8_28224.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8el8_28224/12_2023/8el8_28224.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8el8_28224/12_2023/8el8_28224_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8el8_28224/12_2023/8el8_28224_updated.pdb" } resolution = 3.2 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= 0.108 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 27 5.16 5 C 2868 2.51 5 N 778 2.21 5 O 792 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 68": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 4467 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1046 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1046 Classifications: {'peptide': 140} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 4, 'TRANS': 135} Chain breaks: 5 Unresolved non-hydrogen bonds: 123 Unresolved non-hydrogen angles: 153 Unresolved non-hydrogen dihedrals: 97 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'HIS:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 82 Chain: "B" Number of atoms: 3421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 457, 3421 Classifications: {'peptide': 457} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PTRANS': 15, 'TRANS': 441} Chain breaks: 2 Unresolved non-hydrogen bonds: 221 Unresolved non-hydrogen angles: 269 Unresolved non-hydrogen dihedrals: 185 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'TPO:plan-1': 1, 'ASP:plan': 15, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'GLU:plan': 14, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 154 Time building chain proxies: 2.94, per 1000 atoms: 0.66 Number of scatterers: 4467 At special positions: 0 Unit cell: (53.6823, 80.9495, 110.773, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 27 16.00 P 2 15.00 O 792 8.00 N 778 7.00 C 2868 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.92 Conformation dependent library (CDL) restraints added in 761.2 milliseconds 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1148 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 31 helices and 1 sheets defined 58.8% alpha, 2.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'A' and resid 252 through 264 Processing helix chain 'A' and resid 281 through 290 Processing helix chain 'A' and resid 295 through 297 No H-bonds generated for 'chain 'A' and resid 295 through 297' Processing helix chain 'A' and resid 300 through 302 No H-bonds generated for 'chain 'A' and resid 300 through 302' Processing helix chain 'A' and resid 319 through 338 removed outlier: 4.069A pdb=" N ARG A 323 " --> pdb=" O PRO A 319 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ALA A 324 " --> pdb=" O LYS A 320 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE A 332 " --> pdb=" O ILE A 328 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ILE A 335 " --> pdb=" O LEU A 331 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER A 336 " --> pdb=" O PHE A 332 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA A 338 " --> pdb=" O ARG A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 376 Processing helix chain 'B' and resid 3 through 12 Processing helix chain 'B' and resid 15 through 28 removed outlier: 3.615A pdb=" N GLU B 19 " --> pdb=" O ALA B 15 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG B 20 " --> pdb=" O GLY B 16 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARG B 23 " --> pdb=" O GLU B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 53 removed outlier: 3.858A pdb=" N GLU B 40 " --> pdb=" O SER B 37 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N ASP B 41 " --> pdb=" O ALA B 38 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LYS B 42 " --> pdb=" O ASP B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 75 removed outlier: 3.881A pdb=" N ARG B 75 " --> pdb=" O ARG B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 83 removed outlier: 3.521A pdb=" N VAL B 81 " --> pdb=" O LYS B 78 " (cutoff:3.500A) Proline residue: B 82 - end of helix No H-bonds generated for 'chain 'B' and resid 78 through 83' Processing helix chain 'B' and resid 86 through 96 removed outlier: 3.577A pdb=" N ILE B 91 " --> pdb=" O GLU B 87 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU B 92 " --> pdb=" O ASN B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 127 Processing helix chain 'B' and resid 130 through 138 removed outlier: 3.821A pdb=" N LEU B 136 " --> pdb=" O GLN B 132 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLU B 137 " --> pdb=" O GLN B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 151 removed outlier: 3.587A pdb=" N CYS B 151 " --> pdb=" O LEU B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 174 Processing helix chain 'B' and resid 176 through 184 Processing helix chain 'B' and resid 188 through 199 Processing helix chain 'B' and resid 221 through 237 Processing helix chain 'B' and resid 250 through 265 removed outlier: 3.675A pdb=" N VAL B 255 " --> pdb=" O HIS B 251 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N MET B 256 " --> pdb=" O GLN B 252 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU B 265 " --> pdb=" O ARG B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 286 removed outlier: 4.137A pdb=" N GLU B 275 " --> pdb=" O GLU B 271 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU B 276 " --> pdb=" O ASP B 272 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER B 286 " --> pdb=" O VAL B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 292 No H-bonds generated for 'chain 'B' and resid 290 through 292' Processing helix chain 'B' and resid 294 through 297 Processing helix chain 'B' and resid 340 through 354 removed outlier: 3.605A pdb=" N ASP B 354 " --> pdb=" O GLU B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 376 removed outlier: 3.729A pdb=" N ALA B 376 " --> pdb=" O GLU B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 388 Processing helix chain 'B' and resid 405 through 413 removed outlier: 3.750A pdb=" N MET B 413 " --> pdb=" O LEU B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 431 removed outlier: 3.984A pdb=" N ALA B 425 " --> pdb=" O LYS B 421 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU B 428 " --> pdb=" O ALA B 424 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU B 431 " --> pdb=" O PHE B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 442 removed outlier: 3.596A pdb=" N LYS B 441 " --> pdb=" O ASP B 437 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N TYR B 442 " --> pdb=" O SER B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 454 removed outlier: 5.193A pdb=" N GLY B 450 " --> pdb=" O GLY B 446 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N LEU B 451 " --> pdb=" O ASN B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 481 Processing sheet with id= A, first strand: chain 'A' and resid 208 through 210 removed outlier: 6.349A pdb=" N LEU A 45 " --> pdb=" O PHE A 209 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ALA A 230 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N SER A 273 " --> pdb=" O ILE A 231 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N TYR A 233 " --> pdb=" O SER A 273 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ILE A 275 " --> pdb=" O TYR A 233 " (cutoff:3.500A) 200 hydrogen bonds defined for protein. 564 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: 1.13 Time building geometry restraints manager: 2.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 853 1.33 - 1.45: 998 1.45 - 1.57: 2647 1.57 - 1.68: 2 1.68 - 1.80: 38 Bond restraints: 4538 Sorted by residual: bond pdb=" O3P SEP B 468 " pdb=" P SEP B 468 " ideal model delta sigma weight residual 1.610 1.476 0.134 2.00e-02 2.50e+03 4.48e+01 bond pdb=" O2P SEP B 468 " pdb=" P SEP B 468 " ideal model delta sigma weight residual 1.610 1.480 0.130 2.00e-02 2.50e+03 4.21e+01 bond pdb=" O1P SEP B 468 " pdb=" P SEP B 468 " ideal model delta sigma weight residual 1.610 1.481 0.129 2.00e-02 2.50e+03 4.17e+01 bond pdb=" OG1 TPO B 473 " pdb=" P TPO B 473 " ideal model delta sigma weight residual 1.717 1.598 0.119 2.00e-02 2.50e+03 3.55e+01 bond pdb=" CA LYS B 479 " pdb=" C LYS B 479 " ideal model delta sigma weight residual 1.523 1.468 0.055 1.35e-02 5.49e+03 1.67e+01 ... (remaining 4533 not shown) Histogram of bond angle deviations from ideal: 100.53 - 107.30: 132 107.30 - 114.06: 2677 114.06 - 120.82: 2104 120.82 - 127.59: 1219 127.59 - 134.35: 35 Bond angle restraints: 6167 Sorted by residual: angle pdb=" N ARG B 183 " pdb=" CA ARG B 183 " pdb=" C ARG B 183 " ideal model delta sigma weight residual 111.07 118.31 -7.24 1.07e+00 8.73e-01 4.58e+01 angle pdb=" N TYR B 442 " pdb=" CA TYR B 442 " pdb=" C TYR B 442 " ideal model delta sigma weight residual 111.36 117.49 -6.13 1.09e+00 8.42e-01 3.16e+01 angle pdb=" N THR B 443 " pdb=" CA THR B 443 " pdb=" C THR B 443 " ideal model delta sigma weight residual 112.68 119.02 -6.34 1.33e+00 5.65e-01 2.27e+01 angle pdb=" N GLY B 188 " pdb=" CA GLY B 188 " pdb=" C GLY B 188 " ideal model delta sigma weight residual 112.73 118.17 -5.44 1.20e+00 6.94e-01 2.06e+01 angle pdb=" C LYS B 482 " pdb=" N PRO B 483 " pdb=" CA PRO B 483 " ideal model delta sigma weight residual 119.05 114.40 4.65 1.11e+00 8.12e-01 1.75e+01 ... (remaining 6162 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.84: 2477 16.84 - 33.67: 216 33.67 - 50.51: 38 50.51 - 67.34: 5 67.34 - 84.18: 3 Dihedral angle restraints: 2739 sinusoidal: 986 harmonic: 1753 Sorted by residual: dihedral pdb=" C TPO B 473 " pdb=" N TPO B 473 " pdb=" CA TPO B 473 " pdb=" CB TPO B 473 " ideal model delta harmonic sigma weight residual -122.60 -113.34 -9.26 0 2.50e+00 1.60e-01 1.37e+01 dihedral pdb=" CB GLU B 223 " pdb=" CG GLU B 223 " pdb=" CD GLU B 223 " pdb=" OE1 GLU B 223 " ideal model delta sinusoidal sigma weight residual 0.00 84.18 -84.18 1 3.00e+01 1.11e-03 9.59e+00 dihedral pdb=" CB LYS B 273 " pdb=" CG LYS B 273 " pdb=" CD LYS B 273 " pdb=" CE LYS B 273 " ideal model delta sinusoidal sigma weight residual -60.00 -114.69 54.69 3 1.50e+01 4.44e-03 9.30e+00 ... (remaining 2736 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 511 0.040 - 0.079: 197 0.079 - 0.119: 33 0.119 - 0.158: 11 0.158 - 0.198: 4 Chirality restraints: 756 Sorted by residual: chirality pdb=" CA TYR B 442 " pdb=" N TYR B 442 " pdb=" C TYR B 442 " pdb=" CB TYR B 442 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.76e-01 chirality pdb=" CB VAL B 83 " pdb=" CA VAL B 83 " pdb=" CG1 VAL B 83 " pdb=" CG2 VAL B 83 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 9.27e-01 chirality pdb=" CA TPO B 473 " pdb=" N TPO B 473 " pdb=" C TPO B 473 " pdb=" CB TPO B 473 " both_signs ideal model delta sigma weight residual False 2.53 2.70 -0.18 2.00e-01 2.50e+01 7.75e-01 ... (remaining 753 not shown) Planarity restraints: 771 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR B 478 " 0.010 2.00e-02 2.50e+03 2.04e-02 4.15e+00 pdb=" C TYR B 478 " -0.035 2.00e-02 2.50e+03 pdb=" O TYR B 478 " 0.013 2.00e-02 2.50e+03 pdb=" N LYS B 479 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 81 " -0.031 5.00e-02 4.00e+02 4.61e-02 3.39e+00 pdb=" N PRO B 82 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO B 82 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 82 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 347 " -0.024 5.00e-02 4.00e+02 3.70e-02 2.19e+00 pdb=" N PRO A 348 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO A 348 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 348 " -0.020 5.00e-02 4.00e+02 ... (remaining 768 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 1688 2.90 - 3.40: 4154 3.40 - 3.90: 6539 3.90 - 4.40: 6992 4.40 - 4.90: 12591 Nonbonded interactions: 31964 Sorted by model distance: nonbonded pdb=" OD1 ASP B 206 " pdb=" N GLU B 207 " model vdw 2.403 2.520 nonbonded pdb=" O LEU A 259 " pdb=" OG SER A 262 " model vdw 2.431 2.440 nonbonded pdb=" OE1 GLN A 281 " pdb=" NZ LYS A 325 " model vdw 2.449 2.520 nonbonded pdb=" O LEU B 300 " pdb=" OG1 THR B 301 " model vdw 2.459 2.440 nonbonded pdb=" N GLU B 185 " pdb=" O GLU B 185 " model vdw 2.473 2.496 ... (remaining 31959 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.990 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: 3.520 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 16.610 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.134 4538 Z= 0.474 Angle : 0.704 9.354 6167 Z= 0.416 Chirality : 0.044 0.198 756 Planarity : 0.004 0.046 771 Dihedral : 13.199 84.180 1591 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % 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: 0.75 (0.35), residues: 573 helix: 1.29 (0.28), residues: 348 sheet: 1.88 (0.99), residues: 28 loop : -1.14 (0.42), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 268 HIS 0.007 0.001 HIS A 344 PHE 0.017 0.002 PHE B 163 TYR 0.008 0.001 TYR B 208 ARG 0.003 0.001 ARG B 435 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 535 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 0.482 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.1685 time to fit residues: 12.8555 Evaluate side-chains 46 residues out of total 535 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.543 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 49 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 15 optimal weight: 9.9990 chunk 30 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 46 optimal weight: 0.2980 chunk 17 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 34 optimal weight: 0.4980 chunk 53 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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: 0.8071 moved from start: 0.0692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 4538 Z= 0.140 Angle : 0.425 6.686 6167 Z= 0.219 Chirality : 0.036 0.127 756 Planarity : 0.003 0.036 771 Dihedral : 3.725 24.632 639 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 1.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % 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: 1.11 (0.36), residues: 573 helix: 1.69 (0.29), residues: 351 sheet: 0.82 (0.95), residues: 33 loop : -1.12 (0.44), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 466 HIS 0.004 0.001 HIS B 491 PHE 0.010 0.001 PHE B 163 TYR 0.004 0.001 TYR A 233 ARG 0.002 0.000 ARG B 154 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 535 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 0.545 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.1744 time to fit residues: 11.0616 Evaluate side-chains 42 residues out of total 535 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.545 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 29 optimal weight: 4.9990 chunk 16 optimal weight: 7.9990 chunk 44 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 14 optimal weight: 7.9990 chunk 53 optimal weight: 0.7980 chunk 57 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 40 optimal weight: 0.0000 overall best weight: 1.0986 ------------------------------------------------------------------------------- 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: 0.8098 moved from start: 0.0752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 4538 Z= 0.171 Angle : 0.421 5.552 6167 Z= 0.218 Chirality : 0.037 0.135 756 Planarity : 0.004 0.044 771 Dihedral : 3.551 14.609 639 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 1.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.45 % Allowed : 9.26 % Favored : 90.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.36), residues: 573 helix: 1.73 (0.29), residues: 352 sheet: 0.93 (0.94), residues: 33 loop : -1.21 (0.43), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 264 HIS 0.004 0.001 HIS B 491 PHE 0.012 0.001 PHE B 163 TYR 0.004 0.001 TYR B 184 ARG 0.002 0.000 ARG B 154 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 535 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 44 time to evaluate : 0.543 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 46 average time/residue: 0.1551 time to fit residues: 9.7000 Evaluate side-chains 43 residues out of total 535 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 42 time to evaluate : 0.538 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0429 time to fit residues: 0.8180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 27 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 57 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 15 optimal weight: 10.0000 chunk 47 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 486 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.0795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 4538 Z= 0.193 Angle : 0.422 5.403 6167 Z= 0.220 Chirality : 0.037 0.127 756 Planarity : 0.003 0.038 771 Dihedral : 3.540 15.008 639 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 1.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.23 % Allowed : 11.74 % Favored : 88.04 % 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: 1.04 (0.36), residues: 573 helix: 1.66 (0.28), residues: 352 sheet: 1.05 (0.95), residues: 33 loop : -1.28 (0.43), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 264 HIS 0.004 0.001 HIS A 344 PHE 0.012 0.001 PHE B 163 TYR 0.006 0.001 TYR B 442 ARG 0.002 0.000 ARG B 154 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 535 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 42 time to evaluate : 0.531 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 43 average time/residue: 0.1653 time to fit residues: 9.5665 Evaluate side-chains 39 residues out of total 535 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.544 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 0 optimal weight: 10.0000 chunk 42 optimal weight: 0.5980 chunk 23 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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: 0.8116 moved from start: 0.0891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 4538 Z= 0.186 Angle : 0.416 5.368 6167 Z= 0.217 Chirality : 0.037 0.127 756 Planarity : 0.003 0.041 771 Dihedral : 3.497 14.873 639 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.13 % Allowed : 12.19 % Favored : 86.68 % 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: 1.04 (0.36), residues: 573 helix: 1.67 (0.29), residues: 352 sheet: 1.08 (0.94), residues: 33 loop : -1.30 (0.43), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 466 HIS 0.004 0.001 HIS A 344 PHE 0.012 0.001 PHE B 163 TYR 0.006 0.001 TYR B 442 ARG 0.001 0.000 ARG B 375 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 535 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 43 time to evaluate : 0.578 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 48 average time/residue: 0.1552 time to fit residues: 10.2360 Evaluate side-chains 43 residues out of total 535 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 41 time to evaluate : 0.543 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0462 time to fit residues: 0.9002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 14 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 4 optimal weight: 0.0570 chunk 18 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 6 optimal weight: 0.0770 chunk 32 optimal weight: 0.5980 chunk 41 optimal weight: 3.9990 overall best weight: 0.7058 ------------------------------------------------------------------------------- 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: 0.8081 moved from start: 0.1049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 4538 Z= 0.128 Angle : 0.392 5.346 6167 Z= 0.206 Chirality : 0.036 0.127 756 Planarity : 0.003 0.041 771 Dihedral : 3.338 14.057 639 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.13 % Allowed : 12.87 % Favored : 86.00 % 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: 1.17 (0.36), residues: 573 helix: 1.83 (0.29), residues: 351 sheet: 0.50 (1.01), residues: 29 loop : -1.19 (0.43), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP B 466 HIS 0.003 0.001 HIS A 344 PHE 0.010 0.001 PHE B 163 TYR 0.004 0.001 TYR B 442 ARG 0.003 0.000 ARG B 154 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 535 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 43 time to evaluate : 0.570 Fit side-chains outliers start: 5 outliers final: 1 residues processed: 47 average time/residue: 0.1608 time to fit residues: 10.3233 Evaluate side-chains 44 residues out of total 535 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 43 time to evaluate : 0.548 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0640 time to fit residues: 0.8340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 32 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 56 optimal weight: 6.9990 chunk 35 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 22 optimal weight: 0.0040 chunk 33 optimal weight: 0.8980 chunk 17 optimal weight: 10.0000 chunk 11 optimal weight: 0.0040 overall best weight: 0.5604 ------------------------------------------------------------------------------- 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: 0.8057 moved from start: 0.1209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 4538 Z= 0.113 Angle : 0.380 6.024 6167 Z= 0.197 Chirality : 0.035 0.126 756 Planarity : 0.003 0.040 771 Dihedral : 3.172 13.923 639 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 1.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.23 % Allowed : 14.22 % Favored : 85.55 % 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: 1.35 (0.36), residues: 573 helix: 1.98 (0.29), residues: 352 sheet: 0.57 (1.02), residues: 29 loop : -1.15 (0.43), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 264 HIS 0.002 0.001 HIS B 491 PHE 0.010 0.001 PHE B 163 TYR 0.003 0.000 TYR A 233 ARG 0.002 0.000 ARG B 154 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 535 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 45 time to evaluate : 0.563 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 46 average time/residue: 0.1627 time to fit residues: 10.0505 Evaluate side-chains 43 residues out of total 535 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 0.513 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 11 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- 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: 0.8117 moved from start: 0.1029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4538 Z= 0.232 Angle : 0.446 6.021 6167 Z= 0.234 Chirality : 0.038 0.126 756 Planarity : 0.004 0.042 771 Dihedral : 3.435 14.726 639 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.45 % Allowed : 14.22 % Favored : 85.33 % 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: 1.07 (0.36), residues: 573 helix: 1.71 (0.28), residues: 354 sheet: 0.70 (1.05), residues: 29 loop : -1.25 (0.43), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 264 HIS 0.004 0.001 HIS A 349 PHE 0.014 0.001 PHE B 163 TYR 0.006 0.001 TYR B 208 ARG 0.002 0.000 ARG B 154 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 535 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 42 time to evaluate : 0.597 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 43 average time/residue: 0.1673 time to fit residues: 9.6850 Evaluate side-chains 44 residues out of total 535 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 43 time to evaluate : 0.544 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0684 time to fit residues: 0.8653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 23 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 16 optimal weight: 6.9990 chunk 47 optimal weight: 0.7980 chunk 50 optimal weight: 0.0270 chunk 52 optimal weight: 0.9990 chunk 34 optimal weight: 0.0010 chunk 56 optimal weight: 7.9990 chunk 26 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 overall best weight: 1.1648 ------------------------------------------------------------------------------- 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: 0.8104 moved from start: 0.1082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4538 Z= 0.177 Angle : 0.414 6.030 6167 Z= 0.216 Chirality : 0.037 0.127 756 Planarity : 0.004 0.044 771 Dihedral : 3.433 14.672 639 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.00 % Allowed : 14.90 % Favored : 85.10 % 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: 1.05 (0.36), residues: 573 helix: 1.69 (0.28), residues: 352 sheet: 0.75 (1.06), residues: 29 loop : -1.20 (0.44), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 466 HIS 0.004 0.001 HIS A 344 PHE 0.012 0.001 PHE B 163 TYR 0.005 0.001 TYR B 442 ARG 0.002 0.000 ARG B 154 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 535 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 0.574 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 0.1685 time to fit residues: 9.7882 Evaluate side-chains 41 residues out of total 535 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.561 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 54 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 4 optimal weight: 0.0470 chunk 36 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 43 optimal weight: 0.0070 chunk 6 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 overall best weight: 1.4102 ------------------------------------------------------------------------------- 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: 0.8119 moved from start: 0.1058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4538 Z= 0.210 Angle : 0.445 5.999 6167 Z= 0.233 Chirality : 0.037 0.127 756 Planarity : 0.004 0.045 771 Dihedral : 3.494 14.924 639 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.45 % Allowed : 14.67 % Favored : 84.88 % 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: 0.97 (0.36), residues: 573 helix: 1.63 (0.28), residues: 353 sheet: 0.79 (1.07), residues: 29 loop : -1.28 (0.43), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 264 HIS 0.004 0.001 HIS A 344 PHE 0.013 0.001 PHE B 163 TYR 0.005 0.001 TYR B 442 ARG 0.002 0.000 ARG B 154 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1146 Ramachandran restraints generated. 573 Oldfield, 0 Emsley, 573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 535 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 37 time to evaluate : 0.591 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 37 average time/residue: 0.1760 time to fit residues: 8.7870 Evaluate side-chains 39 residues out of total 535 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 37 time to evaluate : 0.570 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0463 time to fit residues: 0.9267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 46 optimal weight: 0.9980 chunk 19 optimal weight: 0.0970 chunk 48 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 40 optimal weight: 3.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- 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 = 0.3501 r_free = 0.3501 target = 0.129872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.095434 restraints weight = 5608.758| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 2.43 r_work: 0.2905 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.1156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 4538 Z= 0.156 Angle : 0.414 5.935 6167 Z= 0.217 Chirality : 0.036 0.127 756 Planarity : 0.004 0.050 771 Dihedral : 3.384 14.593 639 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.00 % Allowed : 14.90 % Favored : 85.10 % 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: 1.11 (0.36), residues: 573 helix: 1.74 (0.28), residues: 351 sheet: 0.83 (1.08), residues: 29 loop : -1.20 (0.44), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP B 466 HIS 0.003 0.001 HIS A 344 PHE 0.011 0.001 PHE B 163 TYR 0.004 0.001 TYR B 442 ARG 0.002 0.000 ARG B 154 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1166.12 seconds wall clock time: 21 minutes 45.60 seconds (1305.60 seconds total)