Starting phenix.real_space_refine on Mon Sep 23 13:49:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dwi_27755/09_2024/8dwi_27755.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dwi_27755/09_2024/8dwi_27755.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dwi_27755/09_2024/8dwi_27755.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dwi_27755/09_2024/8dwi_27755.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dwi_27755/09_2024/8dwi_27755.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dwi_27755/09_2024/8dwi_27755.cif" } resolution = 3.4 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= 0.002 sd= 0.018 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 14 5.16 5 C 2138 2.51 5 N 504 2.21 5 O 536 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 3192 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 3192 Classifications: {'peptide': 424} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 19, 'TRANS': 404} Chain breaks: 1 Unresolved non-hydrogen bonds: 118 Unresolved non-hydrogen angles: 150 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 2, 'ASN:plan1': 4, 'ASP:plan': 4, 'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 71 Time building chain proxies: 2.93, per 1000 atoms: 0.92 Number of scatterers: 3192 At special positions: 0 Unit cell: (71.38, 70.55, 72.21, 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 14 16.00 O 536 8.00 N 504 7.00 C 2138 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: 0.87 Conformation dependent library (CDL) restraints added in 359.0 milliseconds 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 772 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 0 sheets defined 76.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 38 through 67 removed outlier: 4.163A pdb=" N PHE A 47 " --> pdb=" O ILE A 44 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N PHE A 48 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N TYR A 54 " --> pdb=" O PHE A 51 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N ASN A 59 " --> pdb=" O LEU A 56 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LEU A 60 " --> pdb=" O ARG A 57 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER A 61 " --> pdb=" O VAL A 58 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N LEU A 64 " --> pdb=" O SER A 61 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N MET A 67 " --> pdb=" O LEU A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 133 removed outlier: 4.773A pdb=" N PHE A 115 " --> pdb=" O ILE A 111 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N PHE A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR A 117 " --> pdb=" O GLY A 113 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLY A 118 " --> pdb=" O SER A 114 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ILE A 121 " --> pdb=" O TYR A 117 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ILE A 124 " --> pdb=" O ILE A 120 " (cutoff:3.500A) Proline residue: A 125 - end of helix removed outlier: 4.502A pdb=" N TYR A 128 " --> pdb=" O ILE A 124 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS A 132 " --> pdb=" O TYR A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 151 Processing helix chain 'A' and resid 153 through 159 Processing helix chain 'A' and resid 161 through 168 Processing helix chain 'A' and resid 176 through 189 Proline residue: A 180 - end of helix removed outlier: 3.910A pdb=" N SER A 188 " --> pdb=" O ALA A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 223 removed outlier: 3.849A pdb=" N GLY A 205 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ALA A 206 " --> pdb=" O SER A 202 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLN A 207 " --> pdb=" O TYR A 203 " (cutoff:3.500A) Proline residue: A 215 - end of helix Processing helix chain 'A' and resid 226 through 247 removed outlier: 5.193A pdb=" N PHE A 233 " --> pdb=" O PHE A 230 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N TRP A 244 " --> pdb=" O PHE A 241 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N ILE A 245 " --> pdb=" O LEU A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 272 Processing helix chain 'A' and resid 282 through 287 Processing helix chain 'A' and resid 289 through 310 Processing helix chain 'A' and resid 312 through 318 Processing helix chain 'A' and resid 324 through 354 removed outlier: 3.981A pdb=" N SER A 331 " --> pdb=" O ASN A 327 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER A 332 " --> pdb=" O GLY A 328 " (cutoff:3.500A) Proline residue: A 334 - end of helix removed outlier: 3.871A pdb=" N GLN A 347 " --> pdb=" O ILE A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 382 removed outlier: 4.217A pdb=" N GLY A 374 " --> pdb=" O ILE A 370 " (cutoff:3.500A) Proline residue: A 375 - end of helix Processing helix chain 'A' and resid 389 through 408 removed outlier: 3.960A pdb=" N PHE A 405 " --> pdb=" O THR A 401 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N CYS A 406 " --> pdb=" O LEU A 402 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N SER A 407 " --> pdb=" O GLY A 403 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N SER A 408 " --> pdb=" O GLY A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 417 removed outlier: 4.321A pdb=" N LEU A 415 " --> pdb=" O ILE A 412 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ILE A 417 " --> pdb=" O HIS A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 431 Processing helix chain 'A' and resid 435 through 445 Proline residue: A 441 - end of helix Processing helix chain 'A' and resid 453 through 477 Processing helix chain 'A' and resid 484 through 486 No H-bonds generated for 'chain 'A' and resid 484 through 486' 197 hydrogen bonds defined for protein. 480 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.72 Time building geometry restraints manager: 1.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 938 1.34 - 1.46: 817 1.46 - 1.58: 1515 1.58 - 1.69: 0 1.69 - 1.81: 22 Bond restraints: 3292 Sorted by residual: bond pdb=" N TYR A 117 " pdb=" CA TYR A 117 " ideal model delta sigma weight residual 1.457 1.483 -0.025 1.29e-02 6.01e+03 3.89e+00 bond pdb=" N PHE A 115 " pdb=" CA PHE A 115 " ideal model delta sigma weight residual 1.458 1.481 -0.024 1.30e-02 5.92e+03 3.31e+00 bond pdb=" C VAL A 58 " pdb=" O VAL A 58 " ideal model delta sigma weight residual 1.242 1.230 0.012 1.13e-02 7.83e+03 1.22e+00 bond pdb=" C LEU A 214 " pdb=" N PRO A 215 " ideal model delta sigma weight residual 1.335 1.350 -0.015 1.36e-02 5.41e+03 1.18e+00 bond pdb=" C PHE A 115 " pdb=" N PHE A 116 " ideal model delta sigma weight residual 1.334 1.320 0.014 1.43e-02 4.89e+03 9.67e-01 ... (remaining 3287 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.28: 4313 1.28 - 2.56: 148 2.56 - 3.84: 28 3.84 - 5.12: 13 5.12 - 6.40: 5 Bond angle restraints: 4507 Sorted by residual: angle pdb=" N ILE A 435 " pdb=" CA ILE A 435 " pdb=" C ILE A 435 " ideal model delta sigma weight residual 112.61 107.45 5.16 1.45e+00 4.76e-01 1.27e+01 angle pdb=" N PHE A 115 " pdb=" CA PHE A 115 " pdb=" C PHE A 115 " ideal model delta sigma weight residual 112.38 108.50 3.88 1.22e+00 6.72e-01 1.01e+01 angle pdb=" C LYS A 256 " pdb=" N ARG A 257 " pdb=" CA ARG A 257 " ideal model delta sigma weight residual 121.54 127.49 -5.95 1.91e+00 2.74e-01 9.71e+00 angle pdb=" N PHE A 116 " pdb=" CA PHE A 116 " pdb=" C PHE A 116 " ideal model delta sigma weight residual 111.69 107.87 3.82 1.23e+00 6.61e-01 9.63e+00 angle pdb=" N VAL A 177 " pdb=" CA VAL A 177 " pdb=" C VAL A 177 " ideal model delta sigma weight residual 113.07 109.28 3.79 1.36e+00 5.41e-01 7.75e+00 ... (remaining 4502 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.49: 1648 15.49 - 30.97: 142 30.97 - 46.46: 43 46.46 - 61.95: 3 61.95 - 77.44: 2 Dihedral angle restraints: 1838 sinusoidal: 627 harmonic: 1211 Sorted by residual: dihedral pdb=" CA LEU A 170 " pdb=" C LEU A 170 " pdb=" N GLU A 171 " pdb=" CA GLU A 171 " ideal model delta harmonic sigma weight residual 180.00 160.10 19.90 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA LYS A 445 " pdb=" C LYS A 445 " pdb=" N SER A 446 " pdb=" CA SER A 446 " ideal model delta harmonic sigma weight residual 180.00 162.07 17.93 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA ALA A 382 " pdb=" C ALA A 382 " pdb=" N GLY A 383 " pdb=" CA GLY A 383 " ideal model delta harmonic sigma weight residual 180.00 162.09 17.91 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 1835 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 278 0.027 - 0.054: 148 0.054 - 0.082: 58 0.082 - 0.109: 32 0.109 - 0.136: 5 Chirality restraints: 521 Sorted by residual: chirality pdb=" CB VAL A 177 " pdb=" CA VAL A 177 " pdb=" CG1 VAL A 177 " pdb=" CG2 VAL A 177 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.62e-01 chirality pdb=" CA PHE A 115 " pdb=" N PHE A 115 " pdb=" C PHE A 115 " pdb=" CB PHE A 115 " both_signs ideal model delta sigma weight residual False 2.51 2.64 -0.13 2.00e-01 2.50e+01 4.24e-01 chirality pdb=" CA TRP A 186 " pdb=" N TRP A 186 " pdb=" C TRP A 186 " pdb=" CB TRP A 186 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.70e-01 ... (remaining 518 not shown) Planarity restraints: 547 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 435 " 0.050 5.00e-02 4.00e+02 7.51e-02 9.02e+00 pdb=" N PRO A 436 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO A 436 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 436 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 162 " -0.041 5.00e-02 4.00e+02 6.20e-02 6.15e+00 pdb=" N PRO A 163 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO A 163 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 163 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 374 " -0.037 5.00e-02 4.00e+02 5.66e-02 5.13e+00 pdb=" N PRO A 375 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO A 375 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 375 " -0.032 5.00e-02 4.00e+02 ... (remaining 544 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 816 2.79 - 3.32: 3337 3.32 - 3.84: 5401 3.84 - 4.37: 6043 4.37 - 4.90: 10257 Nonbonded interactions: 25854 Sorted by model distance: nonbonded pdb=" OG1 THR A 304 " pdb=" OD1 ASN A 467 " model vdw 2.258 3.040 nonbonded pdb=" N ASP A 104 " pdb=" OD1 ASP A 104 " model vdw 2.447 3.120 nonbonded pdb=" O ALA A 46 " pdb=" N PHE A 50 " model vdw 2.517 3.120 nonbonded pdb=" O PHE A 116 " pdb=" N GLY A 118 " model vdw 2.524 3.120 nonbonded pdb=" O ASN A 323 " pdb=" N ASN A 327 " model vdw 2.545 3.120 ... (remaining 25849 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: 2.070 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 12.980 Find NCS groups from input model: 0.030 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:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3203 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 : 0.003 0.032 3292 Z= 0.208 Angle : 0.629 6.398 4507 Z= 0.365 Chirality : 0.042 0.136 521 Planarity : 0.006 0.075 547 Dihedral : 13.015 77.435 1066 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % 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: 0.29 (0.43), residues: 420 helix: 0.78 (0.30), residues: 327 sheet: None (None), residues: 0 loop : -1.77 (0.61), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 246 HIS 0.007 0.001 HIS A 414 PHE 0.016 0.001 PHE A 299 TYR 0.010 0.001 TYR A 335 ARG 0.003 0.000 ARG A 168 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.317 Fit side-chains REVERT: A 230 PHE cc_start: 0.4985 (m-80) cc_final: 0.4557 (m-10) REVERT: A 244 TRP cc_start: 0.3185 (t60) cc_final: 0.2467 (t60) REVERT: A 247 LEU cc_start: 0.6669 (mt) cc_final: 0.6219 (pp) REVERT: A 342 MET cc_start: 0.5783 (ttm) cc_final: 0.5446 (mtm) REVERT: A 432 PHE cc_start: 0.3628 (m-80) cc_final: 0.2892 (m-10) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.1614 time to fit residues: 11.1231 Evaluate side-chains 34 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.7980 chunk 31 optimal weight: 0.0980 chunk 17 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 GLN A 207 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4445 moved from start: 0.4587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 3292 Z= 0.293 Angle : 0.764 6.870 4507 Z= 0.398 Chirality : 0.047 0.170 521 Planarity : 0.007 0.069 547 Dihedral : 5.253 18.884 448 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 3.18 % Allowed : 12.42 % Favored : 84.39 % 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 (0.40), residues: 420 helix: -0.10 (0.28), residues: 324 sheet: None (None), residues: 0 loop : -2.12 (0.60), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 103 HIS 0.007 0.003 HIS A 183 PHE 0.034 0.003 PHE A 116 TYR 0.013 0.002 TYR A 421 ARG 0.010 0.001 ARG A 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 51 time to evaluate : 0.297 Fit side-chains REVERT: A 227 THR cc_start: 0.5847 (p) cc_final: 0.5253 (p) REVERT: A 244 TRP cc_start: 0.3992 (t60) cc_final: 0.3342 (t60) REVERT: A 316 MET cc_start: 0.6632 (mpp) cc_final: 0.6146 (mmm) REVERT: A 438 MET cc_start: 0.6524 (tmm) cc_final: 0.5817 (ttm) outliers start: 10 outliers final: 4 residues processed: 56 average time/residue: 0.1278 time to fit residues: 9.1098 Evaluate side-chains 42 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 38 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 117 TYR Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 380 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 0.0670 chunk 25 optimal weight: 0.0060 chunk 10 optimal weight: 0.0970 chunk 38 optimal weight: 4.9990 chunk 41 optimal weight: 0.1980 chunk 34 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 30 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 overall best weight: 0.1932 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4487 moved from start: 0.5221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3292 Z= 0.177 Angle : 0.586 5.907 4507 Z= 0.299 Chirality : 0.040 0.112 521 Planarity : 0.006 0.062 547 Dihedral : 4.764 21.575 448 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 1.27 % Allowed : 18.15 % Favored : 80.57 % 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: -0.35 (0.41), residues: 420 helix: 0.35 (0.30), residues: 325 sheet: None (None), residues: 0 loop : -2.02 (0.58), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 240 HIS 0.007 0.002 HIS A 414 PHE 0.019 0.001 PHE A 299 TYR 0.010 0.001 TYR A 306 ARG 0.010 0.001 ARG A 365 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 39 time to evaluate : 0.324 Fit side-chains REVERT: A 117 TYR cc_start: 0.7038 (OUTLIER) cc_final: 0.6223 (t80) REVERT: A 244 TRP cc_start: 0.4019 (t60) cc_final: 0.3360 (t60) REVERT: A 438 MET cc_start: 0.6767 (tmm) cc_final: 0.6200 (ttp) outliers start: 4 outliers final: 2 residues processed: 42 average time/residue: 0.1153 time to fit residues: 6.4510 Evaluate side-chains 39 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 36 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 117 TYR Chi-restraints excluded: chain A residue 473 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 38 optimal weight: 7.9990 chunk 40 optimal weight: 0.6980 chunk 20 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 chunk 10 optimal weight: 0.2980 chunk 33 optimal weight: 0.0980 chunk 23 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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: 0.5288 moved from start: 0.7963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3292 Z= 0.246 Angle : 0.668 7.346 4507 Z= 0.345 Chirality : 0.044 0.150 521 Planarity : 0.007 0.065 547 Dihedral : 4.837 18.840 448 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 4.14 % Allowed : 20.70 % Favored : 75.16 % 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: -0.81 (0.39), residues: 420 helix: 0.12 (0.29), residues: 316 sheet: None (None), residues: 0 loop : -2.38 (0.51), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 103 HIS 0.004 0.001 HIS A 414 PHE 0.015 0.002 PHE A 299 TYR 0.019 0.002 TYR A 306 ARG 0.013 0.001 ARG A 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 43 time to evaluate : 0.318 Fit side-chains REVERT: A 432 PHE cc_start: 0.7291 (OUTLIER) cc_final: 0.6545 (t80) outliers start: 13 outliers final: 6 residues processed: 53 average time/residue: 0.1239 time to fit residues: 8.4568 Evaluate side-chains 42 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 35 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 117 TYR Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 432 PHE Chi-restraints excluded: chain A residue 473 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 28 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 20 optimal weight: 0.9990 chunk 36 optimal weight: 0.0670 chunk 10 optimal weight: 0.9980 chunk 13 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5540 moved from start: 0.9243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 3292 Z= 0.220 Angle : 0.611 5.311 4507 Z= 0.310 Chirality : 0.041 0.193 521 Planarity : 0.006 0.061 547 Dihedral : 4.791 20.666 448 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 2.87 % Allowed : 21.66 % Favored : 75.48 % 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: -0.35 (0.41), residues: 420 helix: 0.43 (0.30), residues: 322 sheet: None (None), residues: 0 loop : -2.28 (0.54), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 226 HIS 0.007 0.002 HIS A 414 PHE 0.014 0.001 PHE A 299 TYR 0.009 0.001 TYR A 306 ARG 0.004 0.001 ARG A 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 44 time to evaluate : 0.333 Fit side-chains REVERT: A 165 ILE cc_start: 0.8431 (OUTLIER) cc_final: 0.8127 (tp) REVERT: A 203 TYR cc_start: 0.7394 (OUTLIER) cc_final: 0.6755 (t80) REVERT: A 432 PHE cc_start: 0.7238 (OUTLIER) cc_final: 0.6422 (t80) outliers start: 9 outliers final: 4 residues processed: 51 average time/residue: 0.1297 time to fit residues: 8.4764 Evaluate side-chains 46 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 39 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 432 PHE Chi-restraints excluded: chain A residue 473 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 33 optimal weight: 0.3980 chunk 18 optimal weight: 0.0970 chunk 3 optimal weight: 0.9990 chunk 13 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 chunk 39 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5782 moved from start: 1.0333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 3292 Z= 0.248 Angle : 0.662 8.095 4507 Z= 0.325 Chirality : 0.041 0.133 521 Planarity : 0.006 0.063 547 Dihedral : 4.716 18.923 448 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 3.82 % Allowed : 22.29 % Favored : 73.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.40), residues: 420 helix: 0.30 (0.29), residues: 322 sheet: None (None), residues: 0 loop : -2.24 (0.54), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 189 HIS 0.008 0.002 HIS A 414 PHE 0.012 0.001 PHE A 299 TYR 0.011 0.001 TYR A 203 ARG 0.019 0.001 ARG A 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 52 time to evaluate : 0.297 Fit side-chains REVERT: A 165 ILE cc_start: 0.8636 (tp) cc_final: 0.8390 (tp) REVERT: A 203 TYR cc_start: 0.7564 (OUTLIER) cc_final: 0.6755 (t80) REVERT: A 432 PHE cc_start: 0.7420 (OUTLIER) cc_final: 0.6640 (t80) outliers start: 12 outliers final: 5 residues processed: 60 average time/residue: 0.1174 time to fit residues: 9.1006 Evaluate side-chains 46 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 39 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 189 TRP Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain A residue 233 PHE Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 432 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 25 optimal weight: 0.2980 chunk 24 optimal weight: 0.9980 chunk 18 optimal weight: 0.0570 chunk 16 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 20 optimal weight: 5.9990 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5894 moved from start: 1.1004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3292 Z= 0.230 Angle : 0.658 12.245 4507 Z= 0.320 Chirality : 0.042 0.207 521 Planarity : 0.005 0.054 547 Dihedral : 4.772 18.529 448 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 3.82 % Allowed : 23.89 % Favored : 72.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.40), residues: 420 helix: 0.32 (0.30), residues: 316 sheet: None (None), residues: 0 loop : -2.44 (0.51), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 244 HIS 0.007 0.002 HIS A 414 PHE 0.033 0.002 PHE A 241 TYR 0.007 0.001 TYR A 203 ARG 0.003 0.001 ARG A 57 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 44 time to evaluate : 0.333 Fit side-chains REVERT: A 203 TYR cc_start: 0.7598 (OUTLIER) cc_final: 0.6873 (t80) REVERT: A 432 PHE cc_start: 0.7459 (OUTLIER) cc_final: 0.6664 (t80) outliers start: 12 outliers final: 5 residues processed: 51 average time/residue: 0.0895 time to fit residues: 6.4384 Evaluate side-chains 48 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 41 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 372 MET Chi-restraints excluded: chain A residue 432 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 36 optimal weight: 0.0980 chunk 38 optimal weight: 0.6980 chunk 35 optimal weight: 4.9990 chunk 37 optimal weight: 0.5980 chunk 22 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 34 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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: 0.6185 moved from start: 1.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3292 Z= 0.228 Angle : 0.682 7.892 4507 Z= 0.339 Chirality : 0.044 0.186 521 Planarity : 0.006 0.062 547 Dihedral : 4.808 17.694 448 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 2.87 % Allowed : 26.11 % Favored : 71.02 % 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: -0.81 (0.40), residues: 420 helix: 0.07 (0.29), residues: 313 sheet: None (None), residues: 0 loop : -2.14 (0.54), residues: 107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 244 HIS 0.007 0.001 HIS A 414 PHE 0.019 0.002 PHE A 179 TYR 0.012 0.001 TYR A 203 ARG 0.006 0.001 ARG A 321 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 58 time to evaluate : 0.356 Fit side-chains REVERT: A 104 ASP cc_start: 0.4539 (p0) cc_final: 0.3781 (m-30) REVERT: A 110 TRP cc_start: 0.7690 (m100) cc_final: 0.7315 (m100) REVERT: A 137 MET cc_start: 0.6850 (mpp) cc_final: 0.6559 (mmt) REVERT: A 182 MET cc_start: 0.6291 (tmm) cc_final: 0.5885 (tmm) REVERT: A 203 TYR cc_start: 0.7543 (OUTLIER) cc_final: 0.6754 (t80) REVERT: A 226 TRP cc_start: 0.6659 (p-90) cc_final: 0.6407 (p-90) outliers start: 9 outliers final: 4 residues processed: 63 average time/residue: 0.1274 time to fit residues: 10.4294 Evaluate side-chains 58 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 53 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 473 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.0570 chunk 37 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 41 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- 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: 0.6303 moved from start: 1.3281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3292 Z= 0.233 Angle : 0.686 9.014 4507 Z= 0.338 Chirality : 0.043 0.177 521 Planarity : 0.006 0.062 547 Dihedral : 4.946 18.232 448 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 1.91 % Allowed : 28.34 % Favored : 69.75 % 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: -0.83 (0.40), residues: 420 helix: 0.08 (0.29), residues: 313 sheet: None (None), residues: 0 loop : -2.23 (0.53), residues: 107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 292 HIS 0.008 0.001 HIS A 414 PHE 0.023 0.002 PHE A 115 TYR 0.016 0.001 TYR A 203 ARG 0.018 0.002 ARG A 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 53 time to evaluate : 0.329 Fit side-chains revert: symmetry clash REVERT: A 104 ASP cc_start: 0.4815 (p0) cc_final: 0.4071 (m-30) REVERT: A 110 TRP cc_start: 0.7647 (m100) cc_final: 0.7351 (m100) REVERT: A 137 MET cc_start: 0.6816 (mpp) cc_final: 0.6568 (mmt) REVERT: A 182 MET cc_start: 0.6474 (tmm) cc_final: 0.6184 (tmm) REVERT: A 203 TYR cc_start: 0.6608 (OUTLIER) cc_final: 0.6127 (t80) REVERT: A 284 PRO cc_start: 0.6503 (Cg_exo) cc_final: 0.6211 (Cg_endo) outliers start: 6 outliers final: 3 residues processed: 57 average time/residue: 0.1273 time to fit residues: 9.2251 Evaluate side-chains 54 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 50 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain A residue 248 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 35 optimal weight: 0.2980 chunk 10 optimal weight: 0.0870 chunk 30 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 34 optimal weight: 0.0980 chunk 6 optimal weight: 3.9990 overall best weight: 0.3758 ------------------------------------------------------------------------------- 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: 0.6326 moved from start: 1.3649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3292 Z= 0.193 Angle : 0.640 8.171 4507 Z= 0.313 Chirality : 0.042 0.165 521 Planarity : 0.005 0.056 547 Dihedral : 4.759 17.984 448 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 1.59 % Allowed : 29.94 % Favored : 68.47 % 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: -0.64 (0.41), residues: 420 helix: 0.20 (0.30), residues: 314 sheet: None (None), residues: 0 loop : -2.10 (0.54), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 226 HIS 0.008 0.001 HIS A 414 PHE 0.014 0.001 PHE A 299 TYR 0.011 0.001 TYR A 40 ARG 0.007 0.001 ARG A 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 57 time to evaluate : 0.268 Fit side-chains revert: symmetry clash REVERT: A 104 ASP cc_start: 0.4882 (p0) cc_final: 0.4075 (m-30) REVERT: A 110 TRP cc_start: 0.7674 (m100) cc_final: 0.7310 (m100) REVERT: A 128 TYR cc_start: 0.7801 (t80) cc_final: 0.6814 (m-10) REVERT: A 137 MET cc_start: 0.6904 (mpp) cc_final: 0.6667 (mmt) REVERT: A 203 TYR cc_start: 0.6256 (OUTLIER) cc_final: 0.5914 (t80) REVERT: A 283 VAL cc_start: 0.6448 (t) cc_final: 0.6245 (t) REVERT: A 284 PRO cc_start: 0.6392 (Cg_exo) cc_final: 0.6034 (Cg_endo) outliers start: 5 outliers final: 4 residues processed: 61 average time/residue: 0.1241 time to fit residues: 9.3799 Evaluate side-chains 59 residues out of total 349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 54 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain A residue 248 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 0.0040 chunk 1 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 38 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 16 optimal weight: 0.3980 chunk 15 optimal weight: 0.5980 chunk 41 optimal weight: 0.8980 overall best weight: 0.5192 ------------------------------------------------------------------------------- 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 = 0.4609 r_free = 0.4609 target = 0.210705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.174414 restraints weight = 4592.051| |-----------------------------------------------------------------------------| r_work (start): 0.4400 rms_B_bonded: 3.57 r_work: 0.4281 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.4281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6800 moved from start: 1.4343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3292 Z= 0.222 Angle : 0.675 8.913 4507 Z= 0.334 Chirality : 0.043 0.175 521 Planarity : 0.006 0.057 547 Dihedral : 4.719 17.945 448 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 1.91 % Allowed : 29.62 % Favored : 68.47 % 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: -0.62 (0.40), residues: 420 helix: 0.20 (0.30), residues: 313 sheet: None (None), residues: 0 loop : -2.04 (0.52), residues: 107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 292 HIS 0.008 0.001 HIS A 414 PHE 0.015 0.001 PHE A 299 TYR 0.008 0.001 TYR A 117 ARG 0.016 0.001 ARG A 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1180.94 seconds wall clock time: 21 minutes 32.61 seconds (1292.61 seconds total)