Starting phenix.real_space_refine on Mon Sep 23 20:37:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qha_13968/09_2024/7qha_13968.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qha_13968/09_2024/7qha_13968.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qha_13968/09_2024/7qha_13968.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qha_13968/09_2024/7qha_13968.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qha_13968/09_2024/7qha_13968.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qha_13968/09_2024/7qha_13968.cif" } resolution = 2.97 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= 0.011 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 S 33 5.16 5 Na 2 4.78 5 C 3506 2.51 5 N 832 2.21 5 O 909 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 5282 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1257 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 4, 'TRANS': 148} Chain: "B" Number of atoms: 3208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3208 Classifications: {'peptide': 427} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 404} Chain: "C" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 815 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 4, 'TRANS': 99} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' NA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.63, per 1000 atoms: 0.69 Number of scatterers: 5282 At special positions: 0 Unit cell: (88.8769, 77.2481, 98.0138, 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 33 16.00 Na 2 11.00 O 909 8.00 N 832 7.00 C 3506 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 95 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.34 Conformation dependent library (CDL) restraints added in 649.0 milliseconds 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1248 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 3 sheets defined 71.3% alpha, 5.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 2 through 7 Processing helix chain 'A' and resid 8 through 34 Proline residue: A 16 - end of helix removed outlier: 3.510A pdb=" N ARG A 32 " --> pdb=" O GLN A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 64 removed outlier: 4.150A pdb=" N ALA A 59 " --> pdb=" O ILE A 55 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ILE A 60 " --> pdb=" O ILE A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 77 Processing helix chain 'A' and resid 78 through 111 Processing helix chain 'A' and resid 123 through 128 Processing helix chain 'A' and resid 128 through 152 removed outlier: 3.553A pdb=" N PHE A 136 " --> pdb=" O VAL A 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 15 Processing helix chain 'B' and resid 17 through 33 Processing helix chain 'B' and resid 37 through 47 removed outlier: 4.449A pdb=" N ALA B 42 " --> pdb=" O ILE B 38 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N GLN B 43 " --> pdb=" O ASN B 39 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE B 46 " --> pdb=" O ALA B 42 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLY B 47 " --> pdb=" O GLN B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 50 No H-bonds generated for 'chain 'B' and resid 48 through 50' Processing helix chain 'B' and resid 52 through 54 No H-bonds generated for 'chain 'B' and resid 52 through 54' Processing helix chain 'B' and resid 55 through 70 removed outlier: 4.097A pdb=" N PHE B 59 " --> pdb=" O LEU B 55 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL B 61 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ASN B 68 " --> pdb=" O GLY B 64 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER B 69 " --> pdb=" O HIS B 65 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA B 70 " --> pdb=" O LEU B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 85 Processing helix chain 'B' and resid 90 through 103 removed outlier: 4.129A pdb=" N VAL B 94 " --> pdb=" O SER B 90 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N SER B 99 " --> pdb=" O ASN B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 126 removed outlier: 3.517A pdb=" N ASP B 112 " --> pdb=" O SER B 108 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLN B 118 " --> pdb=" O GLY B 114 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N LEU B 119 " --> pdb=" O GLY B 115 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ASP B 126 " --> pdb=" O LYS B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 141 Processing helix chain 'B' and resid 142 through 145 Processing helix chain 'B' and resid 151 through 162 Processing helix chain 'B' and resid 164 through 172 removed outlier: 3.588A pdb=" N LEU B 168 " --> pdb=" O SER B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 195 removed outlier: 4.069A pdb=" N GLY B 176 " --> pdb=" O GLY B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 214 Processing helix chain 'B' and resid 218 through 230 removed outlier: 4.369A pdb=" N PHE B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER B 230 " --> pdb=" O GLY B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 250 Processing helix chain 'B' and resid 258 through 294 Processing helix chain 'B' and resid 295 through 307 removed outlier: 3.999A pdb=" N ILE B 306 " --> pdb=" O LEU B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 325 removed outlier: 3.580A pdb=" N LEU B 313 " --> pdb=" O ASN B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 337 Processing helix chain 'B' and resid 337 through 347 Proline residue: B 343 - end of helix Processing helix chain 'B' and resid 351 through 367 removed outlier: 3.503A pdb=" N PHE B 355 " --> pdb=" O ASP B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 384 Processing helix chain 'B' and resid 389 through 395 Processing helix chain 'B' and resid 398 through 411 Processing helix chain 'C' and resid 61 through 64 Processing helix chain 'C' and resid 103 through 107 Processing sheet with id=AA1, first strand: chain 'A' and resid 115 through 116 removed outlier: 3.814A pdb=" N ILE A 121 " --> pdb=" O LEU A 116 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 18 through 22 removed outlier: 3.675A pdb=" N LEU C 18 " --> pdb=" O MET C 82 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 57 through 59 removed outlier: 7.033A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N GLY C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N MET C 34 " --> pdb=" O GLY C 50 " (cutoff:3.500A) 349 hydrogen bonds defined for protein. 1014 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: 1.42 Time building geometry restraints manager: 1.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1596 1.35 - 1.46: 1294 1.46 - 1.58: 2458 1.58 - 1.70: 0 1.70 - 1.81: 57 Bond restraints: 5405 Sorted by residual: bond pdb=" CB ASN C 76 " pdb=" CG ASN C 76 " ideal model delta sigma weight residual 1.516 1.544 -0.028 2.50e-02 1.60e+03 1.27e+00 bond pdb=" CB ASP B 112 " pdb=" CG ASP B 112 " ideal model delta sigma weight residual 1.516 1.541 -0.025 2.50e-02 1.60e+03 9.63e-01 bond pdb=" C SER B 90 " pdb=" O SER B 90 " ideal model delta sigma weight residual 1.243 1.234 0.009 9.50e-03 1.11e+04 9.29e-01 bond pdb=" CB ASP C 30 " pdb=" CG ASP C 30 " ideal model delta sigma weight residual 1.516 1.539 -0.023 2.50e-02 1.60e+03 8.68e-01 bond pdb=" CB GLU B 301 " pdb=" CG GLU B 301 " ideal model delta sigma weight residual 1.520 1.545 -0.025 3.00e-02 1.11e+03 6.86e-01 ... (remaining 5400 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 7235 1.95 - 3.90: 94 3.90 - 5.85: 15 5.85 - 7.79: 7 7.79 - 9.74: 1 Bond angle restraints: 7352 Sorted by residual: angle pdb=" C SER B 90 " pdb=" CA SER B 90 " pdb=" CB SER B 90 " ideal model delta sigma weight residual 117.23 110.33 6.90 1.36e+00 5.41e-01 2.58e+01 angle pdb=" C SER B 151 " pdb=" N ILE B 152 " pdb=" CA ILE B 152 " ideal model delta sigma weight residual 120.33 123.22 -2.89 8.00e-01 1.56e+00 1.31e+01 angle pdb=" CA SER B 90 " pdb=" C SER B 90 " pdb=" N LEU B 91 " ideal model delta sigma weight residual 119.98 116.95 3.03 8.50e-01 1.38e+00 1.27e+01 angle pdb=" C LYS A 64 " pdb=" N ASP A 65 " pdb=" CA ASP A 65 " ideal model delta sigma weight residual 121.54 127.42 -5.88 1.91e+00 2.74e-01 9.48e+00 angle pdb=" CA LEU B 421 " pdb=" CB LEU B 421 " pdb=" CG LEU B 421 " ideal model delta sigma weight residual 116.30 126.04 -9.74 3.50e+00 8.16e-02 7.75e+00 ... (remaining 7347 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.57: 2911 16.57 - 33.15: 192 33.15 - 49.72: 42 49.72 - 66.30: 7 66.30 - 82.87: 3 Dihedral angle restraints: 3155 sinusoidal: 1199 harmonic: 1956 Sorted by residual: dihedral pdb=" CA ASP C 103 " pdb=" CB ASP C 103 " pdb=" CG ASP C 103 " pdb=" OD1 ASP C 103 " ideal model delta sinusoidal sigma weight residual -30.00 -88.00 58.00 1 2.00e+01 2.50e-03 1.13e+01 dihedral pdb=" CA TYR C 94 " pdb=" C TYR C 94 " pdb=" N CYS C 95 " pdb=" CA CYS C 95 " ideal model delta harmonic sigma weight residual -180.00 -163.60 -16.40 0 5.00e+00 4.00e-02 1.08e+01 dihedral pdb=" CA ILE B 228 " pdb=" C ILE B 228 " pdb=" N PHE B 229 " pdb=" CA PHE B 229 " ideal model delta harmonic sigma weight residual -180.00 -164.65 -15.35 0 5.00e+00 4.00e-02 9.42e+00 ... (remaining 3152 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 623 0.039 - 0.078: 200 0.078 - 0.117: 47 0.117 - 0.155: 8 0.155 - 0.194: 2 Chirality restraints: 880 Sorted by residual: chirality pdb=" CA THR B 220 " pdb=" N THR B 220 " pdb=" C THR B 220 " pdb=" CB THR B 220 " both_signs ideal model delta sigma weight residual False 2.53 2.33 0.19 2.00e-01 2.50e+01 9.44e-01 chirality pdb=" CA VAL B 399 " pdb=" N VAL B 399 " pdb=" C VAL B 399 " pdb=" CB VAL B 399 " both_signs ideal model delta sigma weight residual False 2.44 2.29 0.16 2.00e-01 2.50e+01 6.09e-01 chirality pdb=" CB THR B 220 " pdb=" CA THR B 220 " pdb=" OG1 THR B 220 " pdb=" CG2 THR B 220 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 5.41e-01 ... (remaining 877 not shown) Planarity restraints: 897 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN C 76 " 0.009 2.00e-02 2.50e+03 1.88e-02 3.53e+00 pdb=" C ASN C 76 " -0.032 2.00e-02 2.50e+03 pdb=" O ASN C 76 " 0.013 2.00e-02 2.50e+03 pdb=" N THR C 77 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY B 145 " -0.020 5.00e-02 4.00e+02 3.10e-02 1.54e+00 pdb=" N PRO B 146 " 0.054 5.00e-02 4.00e+02 pdb=" CA PRO B 146 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 146 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 309 " -0.019 5.00e-02 4.00e+02 2.90e-02 1.34e+00 pdb=" N PRO B 310 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO B 310 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 310 " -0.016 5.00e-02 4.00e+02 ... (remaining 894 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 1295 2.79 - 3.32: 5415 3.32 - 3.85: 8530 3.85 - 4.37: 8948 4.37 - 4.90: 16317 Nonbonded interactions: 40505 Sorted by model distance: nonbonded pdb=" OG SER C 25 " pdb=" OD1 ASN C 76 " model vdw 2.268 3.040 nonbonded pdb=" O LEU B 302 " pdb=" OG SER B 305 " model vdw 2.293 3.040 nonbonded pdb=" OH TYR C 37 " pdb=" O TYR C 98 " model vdw 2.304 3.040 nonbonded pdb=" O SER B 103 " pdb="NA NA B 501 " model vdw 2.312 2.470 nonbonded pdb=" OG SER B 380 " pdb=" O ILE B 385 " model vdw 2.316 3.040 ... (remaining 40500 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.800 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: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.270 Find NCS groups from input model: 0.040 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:11.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 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 0.031 5405 Z= 0.175 Angle : 0.591 9.742 7352 Z= 0.311 Chirality : 0.041 0.194 880 Planarity : 0.004 0.031 897 Dihedral : 12.232 82.871 1904 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.85 (0.33), residues: 678 helix: 2.20 (0.25), residues: 428 sheet: -0.36 (0.97), residues: 35 loop : -0.50 (0.43), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 108 HIS 0.004 0.001 HIS B 388 PHE 0.019 0.001 PHE B 60 TYR 0.013 0.001 TYR B 129 ARG 0.001 0.000 ARG C 66 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.8801 (ttm) cc_final: 0.8601 (ttm) REVERT: A 71 THR cc_start: 0.8147 (t) cc_final: 0.7545 (t) REVERT: A 75 ASP cc_start: 0.9189 (m-30) cc_final: 0.8825 (m-30) REVERT: B 118 GLN cc_start: 0.8841 (tm-30) cc_final: 0.8548 (tm-30) REVERT: B 130 ASP cc_start: 0.8576 (t70) cc_final: 0.8205 (t0) REVERT: B 351 ASP cc_start: 0.8909 (p0) cc_final: 0.8662 (p0) REVERT: C 61 ASP cc_start: 0.8595 (t70) cc_final: 0.8350 (t0) REVERT: C 85 LEU cc_start: 0.8950 (mm) cc_final: 0.8664 (mm) outliers start: 0 outliers final: 1 residues processed: 137 average time/residue: 0.8979 time to fit residues: 129.5197 Evaluate side-chains 105 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 104 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 152 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 56 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 60 optimal weight: 0.0010 overall best weight: 0.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN B 95 ASN B 384 ASN C 81 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.1391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5405 Z= 0.195 Angle : 0.646 12.280 7352 Z= 0.320 Chirality : 0.041 0.190 880 Planarity : 0.005 0.035 897 Dihedral : 4.043 22.984 734 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.63 % Allowed : 14.04 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 2.04 (0.34), residues: 678 helix: 2.34 (0.25), residues: 440 sheet: -0.17 (0.96), residues: 35 loop : -0.60 (0.45), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 108 HIS 0.003 0.001 HIS B 354 PHE 0.014 0.001 PHE B 60 TYR 0.016 0.001 TYR B 425 ARG 0.007 0.001 ARG B 207 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 112 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 MET cc_start: 0.8958 (tpp) cc_final: 0.8571 (tpp) REVERT: A 53 MET cc_start: 0.8618 (ttm) cc_final: 0.8404 (ttm) REVERT: A 71 THR cc_start: 0.8268 (t) cc_final: 0.7718 (t) REVERT: A 75 ASP cc_start: 0.9230 (m-30) cc_final: 0.8915 (m-30) REVERT: B 118 GLN cc_start: 0.8850 (tm-30) cc_final: 0.8527 (tm-30) REVERT: B 130 ASP cc_start: 0.8211 (t70) cc_final: 0.7696 (t0) REVERT: B 351 ASP cc_start: 0.8925 (p0) cc_final: 0.8644 (p0) REVERT: B 372 MET cc_start: 0.7471 (tpp) cc_final: 0.6882 (tmm) REVERT: B 418 LEU cc_start: 0.9321 (OUTLIER) cc_final: 0.9005 (tm) REVERT: C 46 GLU cc_start: 0.7801 (tm-30) cc_final: 0.7104 (tm-30) REVERT: C 85 LEU cc_start: 0.9070 (mm) cc_final: 0.8780 (mm) REVERT: C 108 TRP cc_start: 0.7902 (m-10) cc_final: 0.7186 (m-10) outliers start: 15 outliers final: 4 residues processed: 121 average time/residue: 0.9887 time to fit residues: 125.5219 Evaluate side-chains 110 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 105 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 388 HIS Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain C residue 112 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 33 optimal weight: 0.5980 chunk 18 optimal weight: 6.9990 chunk 50 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 60 optimal weight: 5.9990 chunk 65 optimal weight: 10.0000 chunk 54 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 GLN B 384 ASN C 81 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5405 Z= 0.193 Angle : 0.634 11.384 7352 Z= 0.313 Chirality : 0.041 0.186 880 Planarity : 0.005 0.035 897 Dihedral : 3.919 21.161 732 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.68 % Allowed : 18.60 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 2.11 (0.33), residues: 678 helix: 2.42 (0.25), residues: 437 sheet: -0.38 (0.91), residues: 35 loop : -0.54 (0.45), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 108 HIS 0.005 0.001 HIS B 354 PHE 0.019 0.001 PHE B 340 TYR 0.009 0.001 TYR C 94 ARG 0.009 0.001 ARG B 207 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 109 time to evaluate : 0.632 Fit side-chains revert: symmetry clash REVERT: A 8 ASN cc_start: 0.8044 (m-40) cc_final: 0.7663 (m110) REVERT: A 11 GLU cc_start: 0.8418 (pm20) cc_final: 0.8205 (pm20) REVERT: A 71 THR cc_start: 0.8273 (t) cc_final: 0.7727 (t) REVERT: A 75 ASP cc_start: 0.9227 (m-30) cc_final: 0.8903 (m-30) REVERT: B 118 GLN cc_start: 0.8949 (tm-30) cc_final: 0.8690 (tm-30) REVERT: B 120 GLU cc_start: 0.9020 (mt-10) cc_final: 0.8736 (mt-10) REVERT: B 130 ASP cc_start: 0.8325 (t70) cc_final: 0.7574 (t0) REVERT: B 331 LEU cc_start: 0.9282 (tp) cc_final: 0.9027 (tm) REVERT: B 351 ASP cc_start: 0.8951 (p0) cc_final: 0.8672 (p0) REVERT: B 418 LEU cc_start: 0.9311 (OUTLIER) cc_final: 0.9061 (tm) REVERT: C 46 GLU cc_start: 0.7849 (tm-30) cc_final: 0.7146 (tm-30) REVERT: C 85 LEU cc_start: 0.9053 (mm) cc_final: 0.8705 (mm) REVERT: C 108 TRP cc_start: 0.8066 (m-10) cc_final: 0.7856 (m-10) outliers start: 21 outliers final: 7 residues processed: 120 average time/residue: 1.1153 time to fit residues: 140.9811 Evaluate side-chains 111 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 103 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 128 TYR Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 388 HIS Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 112 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 31 optimal weight: 0.9980 chunk 6 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 61 optimal weight: 8.9990 chunk 64 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 384 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 5405 Z= 0.364 Angle : 0.710 11.422 7352 Z= 0.350 Chirality : 0.043 0.166 880 Planarity : 0.005 0.034 897 Dihedral : 4.120 22.795 732 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.86 % Allowed : 20.35 % Favored : 75.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 2.03 (0.33), residues: 678 helix: 2.39 (0.25), residues: 435 sheet: -0.45 (0.92), residues: 35 loop : -0.61 (0.43), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 108 HIS 0.006 0.001 HIS B 354 PHE 0.010 0.001 PHE B 327 TYR 0.012 0.001 TYR C 94 ARG 0.007 0.001 ARG B 392 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 106 time to evaluate : 0.653 Fit side-chains revert: symmetry clash REVERT: A 11 GLU cc_start: 0.8454 (pm20) cc_final: 0.8090 (pm20) REVERT: A 44 GLU cc_start: 0.8969 (mm-30) cc_final: 0.8759 (mm-30) REVERT: A 66 ASP cc_start: 0.8995 (m-30) cc_final: 0.8655 (m-30) REVERT: A 71 THR cc_start: 0.8445 (t) cc_final: 0.7899 (t) REVERT: A 75 ASP cc_start: 0.9260 (m-30) cc_final: 0.8953 (m-30) REVERT: B 118 GLN cc_start: 0.9013 (tm-30) cc_final: 0.8809 (tm-30) REVERT: B 130 ASP cc_start: 0.8333 (t70) cc_final: 0.7489 (t0) REVERT: B 197 MET cc_start: 0.8095 (ppp) cc_final: 0.7881 (ppp) REVERT: B 259 MET cc_start: 0.8298 (pmm) cc_final: 0.7996 (pmm) REVERT: B 268 GLU cc_start: 0.8898 (mm-30) cc_final: 0.8570 (mm-30) REVERT: B 294 GLN cc_start: 0.8289 (tp-100) cc_final: 0.7930 (tp40) REVERT: B 331 LEU cc_start: 0.9359 (tp) cc_final: 0.9109 (tm) REVERT: B 351 ASP cc_start: 0.8931 (p0) cc_final: 0.8664 (p0) REVERT: B 384 ASN cc_start: 0.9063 (t0) cc_final: 0.8746 (t0) REVERT: B 418 LEU cc_start: 0.9319 (OUTLIER) cc_final: 0.9059 (tm) REVERT: C 46 GLU cc_start: 0.7820 (tm-30) cc_final: 0.6972 (tm-30) REVERT: C 82 MET cc_start: 0.8997 (mpt) cc_final: 0.8744 (mpp) REVERT: C 85 LEU cc_start: 0.9153 (mm) cc_final: 0.8848 (mm) REVERT: C 102 ASP cc_start: 0.8664 (t0) cc_final: 0.8226 (t0) REVERT: C 108 TRP cc_start: 0.8223 (m-10) cc_final: 0.8005 (m-10) outliers start: 22 outliers final: 12 residues processed: 120 average time/residue: 0.9901 time to fit residues: 125.0442 Evaluate side-chains 115 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 102 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 128 TYR Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 388 HIS Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 112 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 48 optimal weight: 0.8980 chunk 26 optimal weight: 0.2980 chunk 55 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 58 optimal weight: 0.2980 chunk 16 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5405 Z= 0.190 Angle : 0.673 11.109 7352 Z= 0.325 Chirality : 0.040 0.141 880 Planarity : 0.004 0.032 897 Dihedral : 4.009 21.577 732 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.81 % Allowed : 21.75 % Favored : 75.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 2.05 (0.33), residues: 678 helix: 2.41 (0.25), residues: 436 sheet: -0.49 (0.94), residues: 35 loop : -0.65 (0.43), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 108 HIS 0.004 0.001 HIS B 354 PHE 0.008 0.001 PHE B 60 TYR 0.010 0.001 TYR A 103 ARG 0.008 0.001 ARG A 47 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 107 time to evaluate : 0.668 Fit side-chains revert: symmetry clash REVERT: A 11 GLU cc_start: 0.8432 (pm20) cc_final: 0.8092 (pm20) REVERT: A 71 THR cc_start: 0.8352 (t) cc_final: 0.7804 (t) REVERT: A 75 ASP cc_start: 0.9234 (m-30) cc_final: 0.8924 (m-30) REVERT: B 118 GLN cc_start: 0.8993 (tm-30) cc_final: 0.8778 (tm-30) REVERT: B 130 ASP cc_start: 0.8297 (t70) cc_final: 0.7375 (t0) REVERT: B 268 GLU cc_start: 0.8868 (mm-30) cc_final: 0.8525 (mm-30) REVERT: B 331 LEU cc_start: 0.9313 (tp) cc_final: 0.9101 (tm) REVERT: B 351 ASP cc_start: 0.8999 (p0) cc_final: 0.8733 (p0) REVERT: B 384 ASN cc_start: 0.9020 (t0) cc_final: 0.8647 (t0) REVERT: B 418 LEU cc_start: 0.9314 (OUTLIER) cc_final: 0.9024 (tm) REVERT: C 46 GLU cc_start: 0.7796 (tm-30) cc_final: 0.7032 (tm-30) REVERT: C 82 MET cc_start: 0.8956 (mpt) cc_final: 0.8706 (mpp) REVERT: C 85 LEU cc_start: 0.9094 (mm) cc_final: 0.8786 (mm) REVERT: C 108 TRP cc_start: 0.8155 (m-10) cc_final: 0.7168 (m-10) outliers start: 16 outliers final: 7 residues processed: 117 average time/residue: 0.9322 time to fit residues: 115.0840 Evaluate side-chains 112 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 104 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 128 TYR Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 388 HIS Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain C residue 112 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 15 optimal weight: 2.9990 chunk 64 optimal weight: 6.9990 chunk 53 optimal weight: 0.0570 chunk 30 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 62 optimal weight: 7.9990 chunk 7 optimal weight: 3.9990 chunk 36 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 overall best weight: 2.1704 ------------------------------------------------------------------------------- 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: 0.8458 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 5405 Z= 0.311 Angle : 0.727 11.114 7352 Z= 0.351 Chirality : 0.043 0.153 880 Planarity : 0.004 0.033 897 Dihedral : 4.104 21.272 732 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.33 % Allowed : 23.68 % Favored : 72.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 2.02 (0.33), residues: 678 helix: 2.40 (0.25), residues: 436 sheet: -0.62 (0.94), residues: 35 loop : -0.64 (0.43), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 108 HIS 0.005 0.001 HIS B 354 PHE 0.021 0.001 PHE B 229 TYR 0.012 0.001 TYR B 196 ARG 0.007 0.001 ARG B 392 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 109 time to evaluate : 0.664 Fit side-chains revert: symmetry clash REVERT: A 11 GLU cc_start: 0.8452 (pm20) cc_final: 0.7997 (pm20) REVERT: A 71 THR cc_start: 0.8447 (t) cc_final: 0.7890 (t) REVERT: A 75 ASP cc_start: 0.9258 (m-30) cc_final: 0.8959 (m-30) REVERT: B 118 GLN cc_start: 0.9076 (tm-30) cc_final: 0.8849 (tm-30) REVERT: B 130 ASP cc_start: 0.8339 (t70) cc_final: 0.7451 (t0) REVERT: B 268 GLU cc_start: 0.8883 (mm-30) cc_final: 0.8556 (mm-30) REVERT: B 294 GLN cc_start: 0.8100 (tp40) cc_final: 0.7851 (tp-100) REVERT: B 331 LEU cc_start: 0.9340 (tp) cc_final: 0.9120 (tm) REVERT: B 351 ASP cc_start: 0.8952 (p0) cc_final: 0.8692 (p0) REVERT: B 372 MET cc_start: 0.7784 (tpp) cc_final: 0.7208 (tmm) REVERT: B 384 ASN cc_start: 0.9080 (t0) cc_final: 0.8694 (t0) REVERT: B 418 LEU cc_start: 0.9316 (OUTLIER) cc_final: 0.9040 (tm) REVERT: C 46 GLU cc_start: 0.7757 (tm-30) cc_final: 0.6979 (tm-30) REVERT: C 82 MET cc_start: 0.9005 (mpt) cc_final: 0.8753 (mpp) REVERT: C 85 LEU cc_start: 0.9171 (mm) cc_final: 0.8866 (mm) REVERT: C 102 ASP cc_start: 0.8658 (t0) cc_final: 0.8259 (t0) REVERT: C 108 TRP cc_start: 0.8276 (m-10) cc_final: 0.8000 (m-10) outliers start: 19 outliers final: 12 residues processed: 121 average time/residue: 1.0332 time to fit residues: 131.7780 Evaluate side-chains 119 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 106 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 128 TYR Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 303 PHE Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 388 HIS Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 407 LEU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 112 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 36 optimal weight: 4.9990 chunk 54 optimal weight: 0.0770 chunk 64 optimal weight: 0.6980 chunk 40 optimal weight: 0.0070 chunk 39 optimal weight: 0.9980 chunk 29 optimal weight: 0.0270 chunk 25 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 overall best weight: 0.3614 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5405 Z= 0.197 Angle : 0.725 11.420 7352 Z= 0.345 Chirality : 0.040 0.144 880 Planarity : 0.004 0.032 897 Dihedral : 3.954 19.682 732 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.28 % Allowed : 26.84 % Favored : 70.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.97 (0.33), residues: 678 helix: 2.39 (0.25), residues: 433 sheet: -0.83 (0.97), residues: 35 loop : -0.65 (0.42), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 108 HIS 0.003 0.001 HIS B 354 PHE 0.013 0.001 PHE B 229 TYR 0.010 0.001 TYR A 103 ARG 0.008 0.001 ARG B 392 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 107 time to evaluate : 0.593 Fit side-chains revert: symmetry clash REVERT: A 11 GLU cc_start: 0.8450 (pm20) cc_final: 0.8074 (pm20) REVERT: A 66 ASP cc_start: 0.8935 (m-30) cc_final: 0.8617 (m-30) REVERT: A 71 THR cc_start: 0.8314 (t) cc_final: 0.7759 (t) REVERT: A 75 ASP cc_start: 0.9231 (m-30) cc_final: 0.8922 (m-30) REVERT: B 118 GLN cc_start: 0.9056 (tm-30) cc_final: 0.8828 (tm-30) REVERT: B 130 ASP cc_start: 0.8269 (t70) cc_final: 0.7265 (t0) REVERT: B 331 LEU cc_start: 0.9303 (tp) cc_final: 0.9097 (tm) REVERT: B 351 ASP cc_start: 0.9001 (p0) cc_final: 0.8731 (p0) REVERT: B 372 MET cc_start: 0.7803 (tpp) cc_final: 0.7098 (tmm) REVERT: B 384 ASN cc_start: 0.9019 (t0) cc_final: 0.8640 (t0) REVERT: B 418 LEU cc_start: 0.9305 (OUTLIER) cc_final: 0.9018 (tm) REVERT: C 46 GLU cc_start: 0.7714 (tm-30) cc_final: 0.7010 (tm-30) REVERT: C 82 MET cc_start: 0.8919 (mpt) cc_final: 0.8392 (mpm) REVERT: C 85 LEU cc_start: 0.9101 (mm) cc_final: 0.8760 (mm) REVERT: C 108 TRP cc_start: 0.8221 (m-10) cc_final: 0.7268 (m-10) outliers start: 13 outliers final: 8 residues processed: 116 average time/residue: 0.9760 time to fit residues: 119.2076 Evaluate side-chains 113 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 104 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 128 TYR Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain B residue 303 PHE Chi-restraints excluded: chain B residue 388 HIS Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain C residue 95 CYS Chi-restraints excluded: chain C residue 112 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 43 optimal weight: 2.9990 chunk 31 optimal weight: 0.0870 chunk 6 optimal weight: 0.6980 chunk 50 optimal weight: 0.9980 chunk 58 optimal weight: 0.7980 chunk 61 optimal weight: 5.9990 chunk 56 optimal weight: 0.0050 chunk 60 optimal weight: 2.9990 chunk 36 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 overall best weight: 0.5172 ------------------------------------------------------------------------------- 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: 0.8385 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5405 Z= 0.200 Angle : 0.740 12.496 7352 Z= 0.348 Chirality : 0.041 0.143 880 Planarity : 0.004 0.031 897 Dihedral : 3.885 18.932 732 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.81 % Allowed : 26.67 % Favored : 70.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.96 (0.33), residues: 678 helix: 2.37 (0.25), residues: 433 sheet: -0.86 (0.96), residues: 35 loop : -0.62 (0.43), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 108 HIS 0.003 0.001 HIS B 354 PHE 0.014 0.001 PHE B 229 TYR 0.011 0.001 TYR B 425 ARG 0.008 0.001 ARG B 392 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 112 time to evaluate : 0.504 Fit side-chains revert: symmetry clash REVERT: A 11 GLU cc_start: 0.8441 (pm20) cc_final: 0.8060 (pm20) REVERT: A 66 ASP cc_start: 0.8936 (m-30) cc_final: 0.8616 (m-30) REVERT: A 71 THR cc_start: 0.8236 (t) cc_final: 0.7678 (t) REVERT: A 75 ASP cc_start: 0.9224 (m-30) cc_final: 0.8909 (m-30) REVERT: B 118 GLN cc_start: 0.9069 (tm-30) cc_final: 0.8841 (tm-30) REVERT: B 130 ASP cc_start: 0.8195 (t70) cc_final: 0.7176 (t0) REVERT: B 206 GLU cc_start: 0.8647 (pm20) cc_final: 0.8282 (pm20) REVERT: B 268 GLU cc_start: 0.8861 (mm-30) cc_final: 0.8523 (mm-30) REVERT: B 294 GLN cc_start: 0.8388 (tp-100) cc_final: 0.8051 (tp-100) REVERT: B 331 LEU cc_start: 0.9302 (tp) cc_final: 0.9096 (tm) REVERT: B 351 ASP cc_start: 0.8948 (p0) cc_final: 0.8687 (p0) REVERT: B 372 MET cc_start: 0.7834 (tpp) cc_final: 0.7207 (tmm) REVERT: B 384 ASN cc_start: 0.9017 (t0) cc_final: 0.8653 (t0) REVERT: B 418 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.9033 (tm) REVERT: C 46 GLU cc_start: 0.7668 (tm-30) cc_final: 0.7048 (tm-30) REVERT: C 82 MET cc_start: 0.8901 (mpt) cc_final: 0.8365 (mpm) REVERT: C 85 LEU cc_start: 0.9069 (mm) cc_final: 0.8732 (mm) REVERT: C 108 TRP cc_start: 0.8243 (m-10) cc_final: 0.7266 (m-10) outliers start: 16 outliers final: 11 residues processed: 121 average time/residue: 0.9183 time to fit residues: 117.1510 Evaluate side-chains 120 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 108 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 128 TYR Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 303 PHE Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 388 HIS Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain C residue 95 CYS Chi-restraints excluded: chain C residue 112 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 18 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 chunk 56 optimal weight: 0.3980 chunk 59 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 61 optimal weight: 6.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5405 Z= 0.213 Angle : 0.756 11.859 7352 Z= 0.355 Chirality : 0.041 0.145 880 Planarity : 0.004 0.033 897 Dihedral : 3.902 18.876 732 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.63 % Allowed : 27.37 % Favored : 70.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.94 (0.33), residues: 678 helix: 2.35 (0.25), residues: 433 sheet: -0.89 (0.96), residues: 35 loop : -0.61 (0.43), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 108 HIS 0.003 0.000 HIS B 354 PHE 0.018 0.001 PHE B 229 TYR 0.010 0.001 TYR B 196 ARG 0.008 0.001 ARG B 392 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 110 time to evaluate : 0.596 Fit side-chains revert: symmetry clash REVERT: A 11 GLU cc_start: 0.8439 (pm20) cc_final: 0.7972 (pm20) REVERT: A 66 ASP cc_start: 0.8940 (m-30) cc_final: 0.8602 (m-30) REVERT: A 71 THR cc_start: 0.8219 (t) cc_final: 0.7660 (t) REVERT: A 75 ASP cc_start: 0.9222 (m-30) cc_final: 0.8905 (m-30) REVERT: B 118 GLN cc_start: 0.9076 (tm-30) cc_final: 0.8859 (tm-30) REVERT: B 130 ASP cc_start: 0.8154 (t70) cc_final: 0.7106 (t0) REVERT: B 206 GLU cc_start: 0.8648 (pm20) cc_final: 0.8279 (pm20) REVERT: B 268 GLU cc_start: 0.8865 (mm-30) cc_final: 0.8502 (mm-30) REVERT: B 294 GLN cc_start: 0.8396 (tp-100) cc_final: 0.8106 (tp-100) REVERT: B 331 LEU cc_start: 0.9313 (tp) cc_final: 0.9110 (tm) REVERT: B 351 ASP cc_start: 0.8960 (p0) cc_final: 0.8695 (p0) REVERT: B 372 MET cc_start: 0.7870 (tpp) cc_final: 0.7244 (tmm) REVERT: B 418 LEU cc_start: 0.9279 (OUTLIER) cc_final: 0.9066 (tm) REVERT: C 46 GLU cc_start: 0.7667 (tm-30) cc_final: 0.7033 (tm-30) REVERT: C 82 MET cc_start: 0.8896 (mpt) cc_final: 0.8625 (mpp) REVERT: C 85 LEU cc_start: 0.9037 (mm) cc_final: 0.8741 (mm) REVERT: C 108 TRP cc_start: 0.8240 (m-10) cc_final: 0.7264 (m-10) outliers start: 15 outliers final: 12 residues processed: 119 average time/residue: 0.9161 time to fit residues: 114.8351 Evaluate side-chains 121 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 108 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 128 TYR Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 303 PHE Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 388 HIS Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain C residue 95 CYS Chi-restraints excluded: chain C residue 112 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 53 optimal weight: 0.0980 chunk 5 optimal weight: 0.5980 chunk 41 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 49 optimal weight: 0.2980 chunk 7 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 22 optimal weight: 5.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 76 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5405 Z= 0.209 Angle : 0.762 12.956 7352 Z= 0.361 Chirality : 0.042 0.160 880 Planarity : 0.004 0.034 897 Dihedral : 3.901 18.459 732 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.81 % Allowed : 27.37 % Favored : 69.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.91 (0.33), residues: 678 helix: 2.31 (0.25), residues: 434 sheet: -0.85 (0.97), residues: 35 loop : -0.61 (0.43), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 108 HIS 0.004 0.001 HIS A 52 PHE 0.020 0.001 PHE B 229 TYR 0.011 0.001 TYR B 425 ARG 0.008 0.001 ARG B 392 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1356 Ramachandran restraints generated. 678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 107 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 ASP cc_start: 0.8936 (m-30) cc_final: 0.8604 (m-30) REVERT: A 71 THR cc_start: 0.8178 (t) cc_final: 0.7616 (t) REVERT: A 75 ASP cc_start: 0.9215 (m-30) cc_final: 0.8895 (m-30) REVERT: B 50 ASP cc_start: 0.8660 (t0) cc_final: 0.8420 (t0) REVERT: B 120 GLU cc_start: 0.8662 (mt-10) cc_final: 0.8164 (mp0) REVERT: B 130 ASP cc_start: 0.8091 (t70) cc_final: 0.7150 (t0) REVERT: B 206 GLU cc_start: 0.8658 (pm20) cc_final: 0.8302 (pm20) REVERT: B 268 GLU cc_start: 0.8864 (mm-30) cc_final: 0.8513 (mm-30) REVERT: B 294 GLN cc_start: 0.8414 (tp-100) cc_final: 0.7951 (tp-100) REVERT: B 297 GLN cc_start: 0.8498 (mp10) cc_final: 0.8174 (mp10) REVERT: B 331 LEU cc_start: 0.9294 (tp) cc_final: 0.9092 (tm) REVERT: B 351 ASP cc_start: 0.8958 (p0) cc_final: 0.8705 (p0) REVERT: B 372 MET cc_start: 0.8017 (tpp) cc_final: 0.7356 (tmm) REVERT: C 46 GLU cc_start: 0.7642 (tm-30) cc_final: 0.7065 (tm-30) REVERT: C 82 MET cc_start: 0.8899 (mpt) cc_final: 0.8630 (mpp) REVERT: C 85 LEU cc_start: 0.9025 (mm) cc_final: 0.8737 (mm) outliers start: 16 outliers final: 9 residues processed: 116 average time/residue: 0.8773 time to fit residues: 107.4358 Evaluate side-chains 115 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 106 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 TYR Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 303 PHE Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 388 HIS Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain C residue 95 CYS Chi-restraints excluded: chain C residue 112 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 54 optimal weight: 4.9990 chunk 6 optimal weight: 7.9990 chunk 9 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 60 optimal weight: 0.1980 chunk 35 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 1 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 GLN B 384 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.070855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.058489 restraints weight = 13937.026| |-----------------------------------------------------------------------------| r_work (start): 0.2817 rms_B_bonded: 3.63 r_work: 0.2688 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5405 Z= 0.222 Angle : 0.795 12.741 7352 Z= 0.372 Chirality : 0.042 0.200 880 Planarity : 0.004 0.036 897 Dihedral : 3.935 18.707 732 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.11 % Allowed : 27.89 % Favored : 70.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.94 (0.33), residues: 678 helix: 2.34 (0.25), residues: 433 sheet: -0.93 (0.95), residues: 35 loop : -0.56 (0.44), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 108 HIS 0.003 0.001 HIS B 354 PHE 0.025 0.001 PHE B 229 TYR 0.009 0.001 TYR C 94 ARG 0.008 0.001 ARG B 392 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2465.07 seconds wall clock time: 44 minutes 21.29 seconds (2661.29 seconds total)