Starting phenix.real_space_refine on Mon Sep 23 16:16:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ck0_16688/09_2024/8ck0_16688.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ck0_16688/09_2024/8ck0_16688.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ck0_16688/09_2024/8ck0_16688.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ck0_16688/09_2024/8ck0_16688.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ck0_16688/09_2024/8ck0_16688.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ck0_16688/09_2024/8ck0_16688.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 25 5.16 5 C 2351 2.51 5 N 659 2.21 5 O 727 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: 3762 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3762 Classifications: {'peptide': 478} Link IDs: {'PTRANS': 26, 'TRANS': 451} Chain breaks: 2 Time building chain proxies: 2.81, per 1000 atoms: 0.75 Number of scatterers: 3762 At special positions: 0 Unit cell: (89.1, 94.5, 152.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 25 16.00 O 727 8.00 N 659 7.00 C 2351 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: 0.89 Conformation dependent library (CDL) restraints added in 397.7 milliseconds 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 898 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 4 sheets defined 55.9% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 5 through 22 Processing helix chain 'A' and resid 24 through 35 Processing helix chain 'A' and resid 60 through 78 Processing helix chain 'A' and resid 91 through 97 removed outlier: 3.523A pdb=" N SER A 97 " --> pdb=" O GLU A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 118 Processing helix chain 'A' and resid 119 through 135 removed outlier: 3.553A pdb=" N GLN A 123 " --> pdb=" O ASN A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 187 Processing helix chain 'A' and resid 188 through 192 Processing helix chain 'A' and resid 193 through 202 Processing helix chain 'A' and resid 274 through 302 removed outlier: 4.725A pdb=" N GLY A 281 " --> pdb=" O HIS A 277 " (cutoff:3.500A) Proline residue: A 282 - end of helix Processing helix chain 'A' and resid 314 through 318 removed outlier: 4.546A pdb=" N LEU A 318 " --> pdb=" O PRO A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 364 removed outlier: 4.601A pdb=" N ILE A 349 " --> pdb=" O ASN A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 406 removed outlier: 4.145A pdb=" N THR A 405 " --> pdb=" O GLU A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 422 removed outlier: 3.557A pdb=" N GLY A 417 " --> pdb=" O ASP A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 467 removed outlier: 3.569A pdb=" N LEU A 451 " --> pdb=" O GLN A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 470 No H-bonds generated for 'chain 'A' and resid 468 through 470' Processing helix chain 'A' and resid 471 through 477 Processing helix chain 'A' and resid 479 through 492 removed outlier: 4.579A pdb=" N ASP A 485 " --> pdb=" O ASP A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 498 Processing helix chain 'A' and resid 500 through 523 removed outlier: 3.819A pdb=" N ALA A 518 " --> pdb=" O GLN A 514 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N MET A 521 " --> pdb=" O GLN A 517 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 86 through 88 Processing sheet with id=AA2, first strand: chain 'A' and resid 149 through 154 removed outlier: 3.984A pdb=" N MET A 154 " --> pdb=" O CYS A 138 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N CYS A 138 " --> pdb=" O MET A 154 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 159 through 163 removed outlier: 9.794A pdb=" N ASP A 170 " --> pdb=" O PRO A 217 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 305 through 306 214 hydrogen bonds defined for protein. 600 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: 0.89 Time building geometry restraints manager: 1.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1242 1.34 - 1.46: 508 1.46 - 1.57: 2040 1.57 - 1.69: 0 1.69 - 1.81: 46 Bond restraints: 3836 Sorted by residual: bond pdb=" CA PRO A 426 " pdb=" C PRO A 426 " ideal model delta sigma weight residual 1.514 1.534 -0.019 5.50e-03 3.31e+04 1.25e+01 bond pdb=" C PRO A 426 " pdb=" O PRO A 426 " ideal model delta sigma weight residual 1.246 1.218 0.027 8.50e-03 1.38e+04 1.04e+01 bond pdb=" N ARG A 150 " pdb=" CA ARG A 150 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.19e-02 7.06e+03 8.35e+00 bond pdb=" N ILE A 418 " pdb=" CA ILE A 418 " ideal model delta sigma weight residual 1.462 1.494 -0.032 1.18e-02 7.18e+03 7.50e+00 bond pdb=" N SER A 40 " pdb=" CA SER A 40 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.23e-02 6.61e+03 7.29e+00 ... (remaining 3831 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 4972 1.89 - 3.78: 185 3.78 - 5.67: 29 5.67 - 7.56: 4 7.56 - 9.45: 1 Bond angle restraints: 5191 Sorted by residual: angle pdb=" CA PRO A 426 " pdb=" C PRO A 426 " pdb=" O PRO A 426 " ideal model delta sigma weight residual 120.90 117.93 2.97 7.20e-01 1.93e+00 1.70e+01 angle pdb=" CA LYS A 477 " pdb=" C LYS A 477 " pdb=" O LYS A 477 " ideal model delta sigma weight residual 122.37 118.24 4.13 1.15e+00 7.56e-01 1.29e+01 angle pdb=" CA GLU A 143 " pdb=" C GLU A 143 " pdb=" O GLU A 143 " ideal model delta sigma weight residual 121.99 118.00 3.99 1.14e+00 7.69e-01 1.23e+01 angle pdb=" CA ILE A 480 " pdb=" C ILE A 480 " pdb=" O ILE A 480 " ideal model delta sigma weight residual 121.27 117.78 3.49 1.04e+00 9.25e-01 1.13e+01 angle pdb=" CA PRO A 426 " pdb=" C PRO A 426 " pdb=" N PRO A 427 " ideal model delta sigma weight residual 117.73 120.72 -2.99 9.00e-01 1.23e+00 1.10e+01 ... (remaining 5186 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 2036 17.95 - 35.89: 248 35.89 - 53.84: 55 53.84 - 71.78: 10 71.78 - 89.73: 7 Dihedral angle restraints: 2356 sinusoidal: 965 harmonic: 1391 Sorted by residual: dihedral pdb=" CA ALA A 81 " pdb=" C ALA A 81 " pdb=" N ARG A 82 " pdb=" CA ARG A 82 " ideal model delta harmonic sigma weight residual -180.00 -150.98 -29.02 0 5.00e+00 4.00e-02 3.37e+01 dihedral pdb=" CA PRO A 80 " pdb=" C PRO A 80 " pdb=" N ALA A 81 " pdb=" CA ALA A 81 " ideal model delta harmonic sigma weight residual 180.00 157.14 22.86 0 5.00e+00 4.00e-02 2.09e+01 dihedral pdb=" CA VAL A 444 " pdb=" C VAL A 444 " pdb=" N MET A 445 " pdb=" CA MET A 445 " ideal model delta harmonic sigma weight residual 180.00 159.52 20.48 0 5.00e+00 4.00e-02 1.68e+01 ... (remaining 2353 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 345 0.036 - 0.071: 131 0.071 - 0.107: 55 0.107 - 0.142: 23 0.142 - 0.178: 11 Chirality restraints: 565 Sorted by residual: chirality pdb=" CA LEU A 425 " pdb=" N LEU A 425 " pdb=" C LEU A 425 " pdb=" CB LEU A 425 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.92e-01 chirality pdb=" CA ILE A 418 " pdb=" N ILE A 418 " pdb=" C ILE A 418 " pdb=" CB ILE A 418 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.91e-01 chirality pdb=" CA MET A 420 " pdb=" N MET A 420 " pdb=" C MET A 420 " pdb=" CB MET A 420 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.10e-01 ... (remaining 562 not shown) Planarity restraints: 684 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 79 " -0.095 5.00e-02 4.00e+02 1.43e-01 3.25e+01 pdb=" N PRO A 80 " 0.247 5.00e-02 4.00e+02 pdb=" CA PRO A 80 " -0.078 5.00e-02 4.00e+02 pdb=" CD PRO A 80 " -0.073 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 416 " -0.025 2.00e-02 2.50e+03 2.55e-02 1.13e+01 pdb=" CG PHE A 416 " 0.058 2.00e-02 2.50e+03 pdb=" CD1 PHE A 416 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE A 416 " -0.020 2.00e-02 2.50e+03 pdb=" CE1 PHE A 416 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 PHE A 416 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A 416 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 84 " 0.014 2.00e-02 2.50e+03 1.55e-02 5.99e+00 pdb=" CG TRP A 84 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 TRP A 84 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP A 84 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 84 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 84 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 84 " 0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 84 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 84 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 84 " 0.001 2.00e-02 2.50e+03 ... (remaining 681 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 888 2.79 - 3.32: 3797 3.32 - 3.84: 6117 3.84 - 4.37: 6845 4.37 - 4.90: 11622 Nonbonded interactions: 29269 Sorted by model distance: nonbonded pdb=" O GLY A 76 " pdb=" OG SER A 443 " model vdw 2.259 3.040 nonbonded pdb=" NH1 ARG A 402 " pdb=" OE1 GLU A 406 " model vdw 2.286 3.120 nonbonded pdb=" O ASP A 46 " pdb=" OD1 ASP A 46 " model vdw 2.293 3.040 nonbonded pdb=" NH1 ARG A 7 " pdb=" O GLU A 244 " model vdw 2.322 3.120 nonbonded pdb=" OD1 ASP A 144 " pdb=" N LYS A 145 " model vdw 2.323 3.120 ... (remaining 29264 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.260 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 12.610 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 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 : 0.005 0.066 3836 Z= 0.349 Angle : 0.804 9.449 5191 Z= 0.498 Chirality : 0.052 0.178 565 Planarity : 0.007 0.143 684 Dihedral : 16.634 89.728 1458 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 15.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 0.00 % Allowed : 22.71 % Favored : 77.29 % 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: 0.79 (0.39), residues: 472 helix: 1.61 (0.34), residues: 224 sheet: -0.28 (0.61), residues: 62 loop : -0.47 (0.49), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP A 84 HIS 0.003 0.001 HIS A 125 PHE 0.058 0.003 PHE A 416 TYR 0.023 0.002 TYR A 325 ARG 0.005 0.001 ARG A 67 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 SER cc_start: 0.9522 (m) cc_final: 0.9203 (t) REVERT: A 298 GLU cc_start: 0.8180 (tt0) cc_final: 0.7548 (mm-30) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.1805 time to fit residues: 28.1093 Evaluate side-chains 120 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 39 optimal weight: 8.9990 chunk 35 optimal weight: 0.9990 chunk 19 optimal weight: 20.0000 chunk 12 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 36 optimal weight: 6.9990 chunk 14 optimal weight: 9.9990 chunk 22 optimal weight: 10.0000 chunk 27 optimal weight: 3.9990 chunk 42 optimal weight: 20.0000 chunk 23 optimal weight: 8.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 HIS A 345 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3836 Z= 0.220 Angle : 0.603 5.665 5191 Z= 0.316 Chirality : 0.043 0.173 565 Planarity : 0.005 0.073 684 Dihedral : 4.697 26.825 520 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 4.59 % Allowed : 20.29 % Favored : 75.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.39), residues: 472 helix: 1.71 (0.33), residues: 230 sheet: 0.30 (0.65), residues: 64 loop : -0.06 (0.50), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 84 HIS 0.003 0.001 HIS A 34 PHE 0.010 0.002 PHE A 42 TYR 0.014 0.001 TYR A 237 ARG 0.004 0.001 ARG A 29 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 128 time to evaluate : 0.443 Fit side-chains REVERT: A 8 GLN cc_start: 0.8409 (mt0) cc_final: 0.8145 (mt0) REVERT: A 27 SER cc_start: 0.9495 (m) cc_final: 0.9144 (t) REVERT: A 69 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8801 (tt) REVERT: A 84 TRP cc_start: 0.8818 (p-90) cc_final: 0.8385 (p-90) REVERT: A 177 ARG cc_start: 0.8357 (ttm-80) cc_final: 0.7984 (ttm-80) REVERT: A 183 LEU cc_start: 0.9596 (OUTLIER) cc_final: 0.9351 (mm) REVERT: A 352 ASP cc_start: 0.8614 (t0) cc_final: 0.8347 (t0) REVERT: A 440 GLN cc_start: 0.7691 (tm-30) cc_final: 0.7408 (tm-30) outliers start: 19 outliers final: 12 residues processed: 136 average time/residue: 0.1480 time to fit residues: 24.8303 Evaluate side-chains 130 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 116 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 239 GLU Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 445 MET Chi-restraints excluded: chain A residue 480 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 13 optimal weight: 4.9990 chunk 35 optimal weight: 8.9990 chunk 29 optimal weight: 0.8980 chunk 11 optimal weight: 6.9990 chunk 42 optimal weight: 0.7980 chunk 46 optimal weight: 5.9990 chunk 38 optimal weight: 8.9990 chunk 14 optimal weight: 8.9990 chunk 34 optimal weight: 10.0000 chunk 32 optimal weight: 4.9990 chunk 22 optimal weight: 20.0000 overall best weight: 3.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3836 Z= 0.221 Angle : 0.596 5.704 5191 Z= 0.305 Chirality : 0.043 0.175 565 Planarity : 0.004 0.034 684 Dihedral : 4.745 23.838 520 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 5.31 % Allowed : 21.01 % Favored : 73.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.40), residues: 472 helix: 1.78 (0.33), residues: 234 sheet: 0.54 (0.66), residues: 64 loop : 0.07 (0.51), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 84 HIS 0.006 0.001 HIS A 125 PHE 0.011 0.002 PHE A 42 TYR 0.013 0.001 TYR A 237 ARG 0.003 0.000 ARG A 174 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 121 time to evaluate : 0.459 Fit side-chains revert: symmetry clash REVERT: A 8 GLN cc_start: 0.8460 (mt0) cc_final: 0.8120 (mt0) REVERT: A 27 SER cc_start: 0.9504 (m) cc_final: 0.9127 (t) REVERT: A 69 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8552 (tt) REVERT: A 183 LEU cc_start: 0.9623 (OUTLIER) cc_final: 0.9382 (mm) REVERT: A 189 LEU cc_start: 0.8982 (tp) cc_final: 0.8756 (tp) REVERT: A 255 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7746 (pm20) REVERT: A 352 ASP cc_start: 0.8561 (t0) cc_final: 0.8261 (t0) REVERT: A 402 ARG cc_start: 0.2305 (mmt-90) cc_final: 0.1668 (mmt180) REVERT: A 421 ARG cc_start: 0.8161 (mmm160) cc_final: 0.7657 (mpp80) REVERT: A 521 MET cc_start: 0.5882 (mtt) cc_final: 0.5655 (mtp) outliers start: 22 outliers final: 13 residues processed: 134 average time/residue: 0.1366 time to fit residues: 23.0525 Evaluate side-chains 130 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 114 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 239 GLU Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 283 SER Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 480 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 4 optimal weight: 10.0000 chunk 20 optimal weight: 9.9990 chunk 28 optimal weight: 0.5980 chunk 42 optimal weight: 20.0000 chunk 45 optimal weight: 1.9990 chunk 22 optimal weight: 10.0000 chunk 40 optimal weight: 20.0000 chunk 12 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 ASN A 345 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3836 Z= 0.207 Angle : 0.593 7.289 5191 Z= 0.302 Chirality : 0.043 0.175 565 Planarity : 0.004 0.035 684 Dihedral : 4.730 24.631 520 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 4.83 % Allowed : 20.77 % Favored : 74.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.40), residues: 472 helix: 1.82 (0.33), residues: 240 sheet: 0.55 (0.66), residues: 64 loop : 0.09 (0.52), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 84 HIS 0.003 0.001 HIS A 213 PHE 0.007 0.001 PHE A 416 TYR 0.013 0.001 TYR A 237 ARG 0.003 0.000 ARG A 174 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 119 time to evaluate : 0.448 Fit side-chains revert: symmetry clash REVERT: A 8 GLN cc_start: 0.8470 (mt0) cc_final: 0.8103 (mt0) REVERT: A 27 SER cc_start: 0.9501 (m) cc_final: 0.9104 (t) REVERT: A 59 ASP cc_start: 0.7673 (t0) cc_final: 0.7408 (t0) REVERT: A 95 MET cc_start: 0.6668 (mmm) cc_final: 0.6346 (mmm) REVERT: A 183 LEU cc_start: 0.9611 (OUTLIER) cc_final: 0.9341 (mm) REVERT: A 255 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.7588 (pm20) REVERT: A 352 ASP cc_start: 0.8523 (t0) cc_final: 0.8222 (t0) REVERT: A 402 ARG cc_start: 0.1519 (mmt-90) cc_final: 0.0867 (mmt180) REVERT: A 419 MET cc_start: 0.9401 (mtp) cc_final: 0.9150 (mtt) REVERT: A 421 ARG cc_start: 0.8032 (mmm160) cc_final: 0.7696 (mtm-85) REVERT: A 521 MET cc_start: 0.5877 (mtt) cc_final: 0.5647 (mtp) outliers start: 20 outliers final: 17 residues processed: 132 average time/residue: 0.1415 time to fit residues: 23.3123 Evaluate side-chains 131 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 112 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 239 GLU Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 283 SER Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 500 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 33 optimal weight: 3.9990 chunk 18 optimal weight: 9.9990 chunk 38 optimal weight: 8.9990 chunk 31 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 23 optimal weight: 6.9990 chunk 40 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 8 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3836 Z= 0.217 Angle : 0.596 6.892 5191 Z= 0.302 Chirality : 0.042 0.172 565 Planarity : 0.005 0.034 684 Dihedral : 4.729 23.505 520 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 4.83 % Allowed : 21.26 % Favored : 73.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.39), residues: 472 helix: 2.01 (0.33), residues: 237 sheet: 0.54 (0.66), residues: 64 loop : -0.01 (0.50), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 84 HIS 0.003 0.001 HIS A 213 PHE 0.007 0.001 PHE A 42 TYR 0.011 0.001 TYR A 237 ARG 0.008 0.000 ARG A 177 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 115 time to evaluate : 0.444 Fit side-chains revert: symmetry clash REVERT: A 8 GLN cc_start: 0.8462 (mt0) cc_final: 0.8085 (mt0) REVERT: A 27 SER cc_start: 0.9501 (m) cc_final: 0.9107 (t) REVERT: A 59 ASP cc_start: 0.7708 (t0) cc_final: 0.7399 (t0) REVERT: A 69 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8513 (tt) REVERT: A 95 MET cc_start: 0.6730 (mmm) cc_final: 0.6316 (mmm) REVERT: A 183 LEU cc_start: 0.9587 (OUTLIER) cc_final: 0.9326 (mm) REVERT: A 189 LEU cc_start: 0.8950 (tp) cc_final: 0.8726 (tp) REVERT: A 255 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.7600 (pm20) REVERT: A 313 SER cc_start: 0.8941 (p) cc_final: 0.8663 (t) REVERT: A 352 ASP cc_start: 0.8508 (t0) cc_final: 0.8205 (t0) REVERT: A 402 ARG cc_start: 0.1572 (mmt-90) cc_final: 0.0964 (mmt180) REVERT: A 419 MET cc_start: 0.9352 (mtp) cc_final: 0.9147 (mtt) REVERT: A 421 ARG cc_start: 0.8081 (mmm160) cc_final: 0.7679 (mtm-85) REVERT: A 521 MET cc_start: 0.5884 (mtt) cc_final: 0.5651 (mtp) outliers start: 20 outliers final: 16 residues processed: 126 average time/residue: 0.1477 time to fit residues: 23.1505 Evaluate side-chains 128 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 109 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 239 GLU Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 283 SER Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 411 MET Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 500 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 11 optimal weight: 3.9990 chunk 45 optimal weight: 8.9990 chunk 37 optimal weight: 7.9990 chunk 21 optimal weight: 10.0000 chunk 3 optimal weight: 5.9990 chunk 15 optimal weight: 0.9990 chunk 23 optimal weight: 5.9990 chunk 43 optimal weight: 10.0000 chunk 5 optimal weight: 7.9990 chunk 25 optimal weight: 10.0000 chunk 33 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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: 0.7830 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3836 Z= 0.248 Angle : 0.605 7.175 5191 Z= 0.305 Chirality : 0.043 0.170 565 Planarity : 0.005 0.035 684 Dihedral : 4.722 23.871 520 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 5.07 % Allowed : 21.01 % Favored : 73.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.40), residues: 472 helix: 2.16 (0.33), residues: 237 sheet: 0.44 (0.65), residues: 64 loop : -0.04 (0.50), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 84 HIS 0.003 0.001 HIS A 213 PHE 0.009 0.001 PHE A 42 TYR 0.011 0.001 TYR A 237 ARG 0.006 0.000 ARG A 177 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 113 time to evaluate : 0.437 Fit side-chains revert: symmetry clash REVERT: A 8 GLN cc_start: 0.8450 (mt0) cc_final: 0.8068 (mt0) REVERT: A 27 SER cc_start: 0.9503 (m) cc_final: 0.9040 (t) REVERT: A 31 ILE cc_start: 0.9689 (OUTLIER) cc_final: 0.9449 (mt) REVERT: A 59 ASP cc_start: 0.7771 (t0) cc_final: 0.7453 (t0) REVERT: A 69 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8823 (tt) REVERT: A 95 MET cc_start: 0.6827 (mmm) cc_final: 0.6515 (mmm) REVERT: A 183 LEU cc_start: 0.9591 (OUTLIER) cc_final: 0.9324 (mm) REVERT: A 189 LEU cc_start: 0.8917 (tp) cc_final: 0.8693 (tp) REVERT: A 255 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.7808 (pm20) REVERT: A 313 SER cc_start: 0.8992 (p) cc_final: 0.8694 (t) REVERT: A 352 ASP cc_start: 0.8507 (t0) cc_final: 0.8209 (t0) REVERT: A 521 MET cc_start: 0.5986 (mtt) cc_final: 0.5723 (mtp) outliers start: 21 outliers final: 16 residues processed: 124 average time/residue: 0.1291 time to fit residues: 20.4292 Evaluate side-chains 128 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 108 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 239 GLU Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 283 SER Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 411 MET Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 500 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 25 optimal weight: 9.9990 chunk 38 optimal weight: 8.9990 chunk 45 optimal weight: 30.0000 chunk 28 optimal weight: 0.2980 chunk 27 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 18 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 8 optimal weight: 7.9990 chunk 30 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 overall best weight: 3.2588 ------------------------------------------------------------------------------- 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: 0.7817 moved from start: 0.3344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3836 Z= 0.204 Angle : 0.599 8.988 5191 Z= 0.299 Chirality : 0.041 0.169 565 Planarity : 0.004 0.034 684 Dihedral : 4.589 20.010 520 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 5.56 % Allowed : 20.53 % Favored : 73.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.40), residues: 472 helix: 2.26 (0.33), residues: 237 sheet: 0.50 (0.65), residues: 64 loop : 0.08 (0.51), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 84 HIS 0.003 0.001 HIS A 213 PHE 0.009 0.001 PHE A 42 TYR 0.012 0.001 TYR A 237 ARG 0.011 0.001 ARG A 421 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 113 time to evaluate : 0.446 Fit side-chains revert: symmetry clash REVERT: A 8 GLN cc_start: 0.8474 (mt0) cc_final: 0.8150 (mt0) REVERT: A 27 SER cc_start: 0.9498 (m) cc_final: 0.9089 (t) REVERT: A 59 ASP cc_start: 0.7922 (t0) cc_final: 0.7632 (t0) REVERT: A 69 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8589 (tt) REVERT: A 93 GLU cc_start: 0.6282 (OUTLIER) cc_final: 0.5994 (mm-30) REVERT: A 95 MET cc_start: 0.6808 (mmm) cc_final: 0.6478 (mmm) REVERT: A 183 LEU cc_start: 0.9457 (OUTLIER) cc_final: 0.9216 (mm) REVERT: A 189 LEU cc_start: 0.8884 (tp) cc_final: 0.8671 (tp) REVERT: A 255 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7705 (pm20) REVERT: A 313 SER cc_start: 0.8989 (p) cc_final: 0.8678 (t) REVERT: A 352 ASP cc_start: 0.8485 (t0) cc_final: 0.8189 (t0) REVERT: A 401 GLU cc_start: 0.7332 (pm20) cc_final: 0.6804 (pt0) REVERT: A 521 MET cc_start: 0.5990 (mtt) cc_final: 0.5734 (mtp) outliers start: 23 outliers final: 17 residues processed: 126 average time/residue: 0.1382 time to fit residues: 22.0176 Evaluate side-chains 130 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 109 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 239 GLU Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 283 SER Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 411 MET Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 445 MET Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 500 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 4 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 chunk 41 optimal weight: 9.9990 chunk 43 optimal weight: 0.1980 chunk 39 optimal weight: 6.9990 chunk 42 optimal weight: 0.0040 chunk 25 optimal weight: 3.9990 chunk 18 optimal weight: 9.9990 chunk 33 optimal weight: 7.9990 chunk 12 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 overall best weight: 2.2398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.3497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3836 Z= 0.176 Angle : 0.603 8.941 5191 Z= 0.300 Chirality : 0.042 0.168 565 Planarity : 0.004 0.035 684 Dihedral : 4.589 23.484 520 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 5.07 % Allowed : 21.26 % Favored : 73.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.40), residues: 472 helix: 2.38 (0.33), residues: 237 sheet: 0.69 (0.66), residues: 62 loop : 0.02 (0.50), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 84 HIS 0.003 0.001 HIS A 213 PHE 0.009 0.001 PHE A 42 TYR 0.012 0.001 TYR A 237 ARG 0.004 0.000 ARG A 177 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 118 time to evaluate : 0.430 Fit side-chains revert: symmetry clash REVERT: A 8 GLN cc_start: 0.8472 (mt0) cc_final: 0.8145 (mt0) REVERT: A 27 SER cc_start: 0.9495 (m) cc_final: 0.9085 (t) REVERT: A 69 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8519 (tt) REVERT: A 93 GLU cc_start: 0.6265 (OUTLIER) cc_final: 0.5821 (mm-30) REVERT: A 95 MET cc_start: 0.6786 (mmm) cc_final: 0.6450 (mmm) REVERT: A 177 ARG cc_start: 0.8046 (ttm-80) cc_final: 0.7750 (ttm-80) REVERT: A 183 LEU cc_start: 0.9449 (OUTLIER) cc_final: 0.9212 (mm) REVERT: A 255 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7680 (pm20) REVERT: A 313 SER cc_start: 0.8974 (p) cc_final: 0.8660 (t) REVERT: A 352 ASP cc_start: 0.8455 (t0) cc_final: 0.8158 (t0) REVERT: A 401 GLU cc_start: 0.7271 (pm20) cc_final: 0.6698 (pt0) REVERT: A 521 MET cc_start: 0.5975 (mtt) cc_final: 0.5725 (mtp) outliers start: 21 outliers final: 15 residues processed: 128 average time/residue: 0.1408 time to fit residues: 22.5198 Evaluate side-chains 128 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 109 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 283 SER Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 411 MET Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 445 MET Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 500 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 39 optimal weight: 9.9990 chunk 42 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 chunk 44 optimal weight: 9.9990 chunk 21 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 46 optimal weight: 6.9990 chunk 43 optimal weight: 7.9990 chunk 37 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 overall best weight: 1.5784 ------------------------------------------------------------------------------- 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: 0.7782 moved from start: 0.3663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3836 Z= 0.158 Angle : 0.615 9.610 5191 Z= 0.303 Chirality : 0.042 0.168 565 Planarity : 0.004 0.036 684 Dihedral : 4.523 23.412 520 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.14 % Allowed : 23.19 % Favored : 73.67 % 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: 2.01 (0.40), residues: 472 helix: 2.48 (0.34), residues: 237 sheet: 0.69 (0.66), residues: 62 loop : -0.00 (0.50), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 84 HIS 0.003 0.001 HIS A 213 PHE 0.010 0.001 PHE A 42 TYR 0.014 0.001 TYR A 237 ARG 0.004 0.000 ARG A 177 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 115 time to evaluate : 0.441 Fit side-chains revert: symmetry clash REVERT: A 8 GLN cc_start: 0.8385 (mt0) cc_final: 0.8063 (mt0) REVERT: A 27 SER cc_start: 0.9478 (m) cc_final: 0.9118 (t) REVERT: A 74 MET cc_start: 0.8243 (ttp) cc_final: 0.7992 (ttm) REVERT: A 95 MET cc_start: 0.6896 (mmm) cc_final: 0.6540 (mmm) REVERT: A 117 LYS cc_start: 0.8719 (tptm) cc_final: 0.8495 (tptm) REVERT: A 177 ARG cc_start: 0.7914 (ttm-80) cc_final: 0.7670 (ttm-80) REVERT: A 183 LEU cc_start: 0.9443 (OUTLIER) cc_final: 0.9213 (mm) REVERT: A 201 ASP cc_start: 0.8999 (m-30) cc_final: 0.8152 (p0) REVERT: A 206 GLU cc_start: 0.8521 (mm-30) cc_final: 0.7799 (mm-30) REVERT: A 255 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7663 (pm20) REVERT: A 352 ASP cc_start: 0.8408 (t0) cc_final: 0.8101 (t0) REVERT: A 401 GLU cc_start: 0.7196 (pm20) cc_final: 0.6646 (pt0) REVERT: A 421 ARG cc_start: 0.7842 (mmm160) cc_final: 0.7607 (mmp80) REVERT: A 521 MET cc_start: 0.6049 (mtt) cc_final: 0.5833 (mtp) outliers start: 13 outliers final: 11 residues processed: 123 average time/residue: 0.1482 time to fit residues: 22.7128 Evaluate side-chains 124 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 111 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 283 SER Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 411 MET Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 500 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 22 optimal weight: 6.9990 chunk 29 optimal weight: 0.3980 chunk 39 optimal weight: 20.0000 chunk 11 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 15 optimal weight: 7.9990 chunk 38 optimal weight: 0.0050 chunk 4 optimal weight: 0.4980 overall best weight: 1.7798 ------------------------------------------------------------------------------- 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: 0.7773 moved from start: 0.3811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3836 Z= 0.165 Angle : 0.619 9.769 5191 Z= 0.304 Chirality : 0.042 0.173 565 Planarity : 0.004 0.036 684 Dihedral : 4.371 21.780 520 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.38 % Allowed : 23.43 % Favored : 73.19 % 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: 2.09 (0.40), residues: 472 helix: 2.56 (0.34), residues: 237 sheet: 0.73 (0.68), residues: 62 loop : 0.01 (0.50), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 84 HIS 0.003 0.001 HIS A 213 PHE 0.011 0.001 PHE A 42 TYR 0.014 0.001 TYR A 441 ARG 0.004 0.000 ARG A 177 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 944 Ramachandran restraints generated. 472 Oldfield, 0 Emsley, 472 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 114 time to evaluate : 0.436 Fit side-chains revert: symmetry clash REVERT: A 8 GLN cc_start: 0.8467 (mt0) cc_final: 0.8139 (mt0) REVERT: A 27 SER cc_start: 0.9474 (m) cc_final: 0.9113 (t) REVERT: A 93 GLU cc_start: 0.6556 (OUTLIER) cc_final: 0.6060 (mm-30) REVERT: A 95 MET cc_start: 0.6792 (mmm) cc_final: 0.6375 (mmm) REVERT: A 117 LYS cc_start: 0.8713 (tptm) cc_final: 0.8499 (tptm) REVERT: A 177 ARG cc_start: 0.7897 (ttm-80) cc_final: 0.7664 (ttm-80) REVERT: A 183 LEU cc_start: 0.9442 (OUTLIER) cc_final: 0.9211 (mm) REVERT: A 206 GLU cc_start: 0.8509 (mm-30) cc_final: 0.7785 (mm-30) REVERT: A 255 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7631 (pm20) REVERT: A 352 ASP cc_start: 0.8395 (t0) cc_final: 0.8086 (t0) REVERT: A 401 GLU cc_start: 0.7174 (pm20) cc_final: 0.6508 (pt0) REVERT: A 421 ARG cc_start: 0.7715 (mmm160) cc_final: 0.7466 (mmp80) REVERT: A 521 MET cc_start: 0.6022 (mtt) cc_final: 0.5801 (mtp) outliers start: 14 outliers final: 10 residues processed: 124 average time/residue: 0.1442 time to fit residues: 22.5690 Evaluate side-chains 123 residues out of total 414 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 110 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 283 SER Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 411 MET Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 500 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 47 random chunks: chunk 6 optimal weight: 3.9990 chunk 32 optimal weight: 30.0000 chunk 2 optimal weight: 9.9990 chunk 26 optimal weight: 0.9980 chunk 42 optimal weight: 8.9990 chunk 25 optimal weight: 8.9990 chunk 31 optimal weight: 0.0980 chunk 1 optimal weight: 10.0000 chunk 29 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 overall best weight: 3.0186 ------------------------------------------------------------------------------- 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 = 0.3643 r_free = 0.3643 target = 0.123726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.103877 restraints weight = 8974.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.106737 restraints weight = 4266.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.108632 restraints weight = 2611.632| |-----------------------------------------------------------------------------| r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.3877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3836 Z= 0.204 Angle : 0.664 9.852 5191 Z= 0.325 Chirality : 0.042 0.169 565 Planarity : 0.004 0.036 684 Dihedral : 4.394 19.799 520 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 4.11 % Allowed : 23.91 % Favored : 71.98 % 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: 2.05 (0.40), residues: 472 helix: 2.55 (0.34), residues: 237 sheet: 0.77 (0.68), residues: 62 loop : -0.07 (0.49), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 84 HIS 0.003 0.001 HIS A 213 PHE 0.011 0.001 PHE A 42 TYR 0.013 0.001 TYR A 441 ARG 0.004 0.000 ARG A 177 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1162.56 seconds wall clock time: 21 minutes 38.36 seconds (1298.36 seconds total)