Starting phenix.real_space_refine on Fri Apr 5 16:33:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zh0_14716/04_2024/7zh0_14716.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zh0_14716/04_2024/7zh0_14716.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zh0_14716/04_2024/7zh0_14716.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zh0_14716/04_2024/7zh0_14716.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zh0_14716/04_2024/7zh0_14716.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zh0_14716/04_2024/7zh0_14716.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 22 5.16 5 C 2557 2.51 5 N 640 2.21 5 O 650 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 13": "OE1" <-> "OE2" Residue "A TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 61": "OE1" <-> "OE2" Residue "A TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 3869 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 495, 3869 Classifications: {'peptide': 495} Link IDs: {'PTRANS': 23, 'TRANS': 471} Chain breaks: 3 Time building chain proxies: 2.59, per 1000 atoms: 0.67 Number of scatterers: 3869 At special positions: 0 Unit cell: (102.3, 63.36, 75.9, 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 22 16.00 O 650 8.00 N 640 7.00 C 2557 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 51 " - pdb=" SG CYS A 127 " distance=2.03 Simple disulfide: pdb=" SG CYS A 90 " - pdb=" SG CYS A 148 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.66 Conformation dependent library (CDL) restraints added in 1.1 seconds 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 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: 28 helices and 2 sheets defined 80.4% alpha, 1.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 2 through 11 Processing helix chain 'A' and resid 15 through 38 removed outlier: 3.620A pdb=" N THR A 28 " --> pdb=" O LEU A 24 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL A 37 " --> pdb=" O ALA A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 42 Processing helix chain 'A' and resid 53 through 64 Processing helix chain 'A' and resid 66 through 74 Processing helix chain 'A' and resid 94 through 99 removed outlier: 4.162A pdb=" N ALA A 98 " --> pdb=" O LEU A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 145 Processing helix chain 'A' and resid 147 through 152 removed outlier: 3.614A pdb=" N TRP A 152 " --> pdb=" O VAL A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 179 removed outlier: 3.835A pdb=" N THR A 157 " --> pdb=" O MET A 153 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLN A 158 " --> pdb=" O LEU A 154 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N TYR A 174 " --> pdb=" O PHE A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 201 removed outlier: 3.629A pdb=" N ILE A 184 " --> pdb=" O GLY A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 234 removed outlier: 3.970A pdb=" N GLY A 221 " --> pdb=" O VAL A 217 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR A 222 " --> pdb=" O PHE A 218 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TRP A 223 " --> pdb=" O GLY A 219 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N VAL A 234 " --> pdb=" O VAL A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 264 Proline residue: A 258 - end of helix Processing helix chain 'A' and resid 266 through 276 Processing helix chain 'A' and resid 276 through 283 removed outlier: 3.776A pdb=" N LEU A 280 " --> pdb=" O LEU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 288 removed outlier: 3.575A pdb=" N VAL A 288 " --> pdb=" O TYR A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 296 removed outlier: 3.577A pdb=" N LEU A 295 " --> pdb=" O SER A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 312 Processing helix chain 'A' and resid 337 through 342 removed outlier: 3.641A pdb=" N VAL A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 373 removed outlier: 3.655A pdb=" N GLY A 373 " --> pdb=" O VAL A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 389 Processing helix chain 'A' and resid 389 through 405 removed outlier: 4.637A pdb=" N GLY A 393 " --> pdb=" O VAL A 389 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA A 394 " --> pdb=" O GLU A 390 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N GLU A 402 " --> pdb=" O LEU A 398 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N ARG A 403 " --> pdb=" O LEU A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 426 Processing helix chain 'A' and resid 433 through 461 removed outlier: 4.268A pdb=" N THR A 437 " --> pdb=" O TRP A 433 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER A 458 " --> pdb=" O TYR A 454 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TYR A 461 " --> pdb=" O ASN A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 470 Processing helix chain 'A' and resid 471 through 495 Proline residue: A 485 - end of helix removed outlier: 3.669A pdb=" N VAL A 494 " --> pdb=" O ARG A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 509 Processing helix chain 'A' and resid 509 through 514 Processing helix chain 'A' and resid 527 through 532 removed outlier: 3.859A pdb=" N ASP A 531 " --> pdb=" O THR A 528 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 49 through 51 Processing sheet with id=AA2, first strand: chain 'A' and resid 91 through 93 262 hydrogen bonds defined for protein. 768 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: 1.16 Time building geometry restraints manager: 1.79 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: 1196 1.34 - 1.46: 633 1.46 - 1.57: 2106 1.57 - 1.69: 0 1.69 - 1.81: 30 Bond restraints: 3965 Sorted by residual: bond pdb=" N PHE A 450 " pdb=" CA PHE A 450 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.21e-02 6.83e+03 5.35e+00 bond pdb=" N MET A 448 " pdb=" CA MET A 448 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.21e-02 6.83e+03 5.10e+00 bond pdb=" N GLU A 451 " pdb=" CA GLU A 451 " ideal model delta sigma weight residual 1.459 1.487 -0.027 1.23e-02 6.61e+03 4.96e+00 bond pdb=" N ALA A 449 " pdb=" CA ALA A 449 " ideal model delta sigma weight residual 1.459 1.482 -0.023 1.21e-02 6.83e+03 3.67e+00 bond pdb=" N THR A 528 " pdb=" CA THR A 528 " ideal model delta sigma weight residual 1.457 1.481 -0.023 1.29e-02 6.01e+03 3.24e+00 ... (remaining 3960 not shown) Histogram of bond angle deviations from ideal: 100.02 - 106.81: 119 106.81 - 113.61: 2168 113.61 - 120.41: 1555 120.41 - 127.21: 1504 127.21 - 134.01: 51 Bond angle restraints: 5397 Sorted by residual: angle pdb=" N MET A 448 " pdb=" CA MET A 448 " pdb=" C MET A 448 " ideal model delta sigma weight residual 111.28 107.52 3.76 1.09e+00 8.42e-01 1.19e+01 angle pdb=" C VAL A 470 " pdb=" N SER A 471 " pdb=" CA SER A 471 " ideal model delta sigma weight residual 121.54 127.81 -6.27 1.91e+00 2.74e-01 1.08e+01 angle pdb=" N VAL A 529 " pdb=" CA VAL A 529 " pdb=" C VAL A 529 " ideal model delta sigma weight residual 112.80 109.18 3.62 1.15e+00 7.56e-01 9.90e+00 angle pdb=" C GLU A 13 " pdb=" CA GLU A 13 " pdb=" CB GLU A 13 " ideal model delta sigma weight residual 110.42 116.48 -6.06 1.99e+00 2.53e-01 9.27e+00 angle pdb=" C THR A 297 " pdb=" N ARG A 298 " pdb=" CA ARG A 298 " ideal model delta sigma weight residual 123.91 128.84 -4.93 1.66e+00 3.63e-01 8.82e+00 ... (remaining 5392 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 2089 17.90 - 35.79: 161 35.79 - 53.69: 39 53.69 - 71.58: 5 71.58 - 89.48: 4 Dihedral angle restraints: 2298 sinusoidal: 895 harmonic: 1403 Sorted by residual: dihedral pdb=" CA VAL A 532 " pdb=" C VAL A 532 " pdb=" N GLU A 533 " pdb=" CA GLU A 533 " ideal model delta harmonic sigma weight residual 180.00 164.26 15.74 0 5.00e+00 4.00e-02 9.92e+00 dihedral pdb=" N PHE A 450 " pdb=" CA PHE A 450 " pdb=" CB PHE A 450 " pdb=" CG PHE A 450 " ideal model delta sinusoidal sigma weight residual -60.00 -118.37 58.37 3 1.50e+01 4.44e-03 9.46e+00 dihedral pdb=" CB MET A 448 " pdb=" CG MET A 448 " pdb=" SD MET A 448 " pdb=" CE MET A 448 " ideal model delta sinusoidal sigma weight residual 60.00 1.88 58.12 3 1.50e+01 4.44e-03 9.46e+00 ... (remaining 2295 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 427 0.038 - 0.076: 149 0.076 - 0.114: 46 0.114 - 0.151: 3 0.151 - 0.189: 4 Chirality restraints: 629 Sorted by residual: chirality pdb=" CA PHE A 450 " pdb=" N PHE A 450 " pdb=" C PHE A 450 " pdb=" CB PHE A 450 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.96e-01 chirality pdb=" CA MET A 448 " pdb=" N MET A 448 " pdb=" C MET A 448 " pdb=" CB MET A 448 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.75e-01 chirality pdb=" CB ILE A 523 " pdb=" CA ILE A 523 " pdb=" CG1 ILE A 523 " pdb=" CG2 ILE A 523 " both_signs ideal model delta sigma weight residual False 2.64 2.82 -0.18 2.00e-01 2.50e+01 7.82e-01 ... (remaining 626 not shown) Planarity restraints: 669 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 291 " -0.054 5.00e-02 4.00e+02 8.24e-02 1.09e+01 pdb=" N PRO A 292 " 0.142 5.00e-02 4.00e+02 pdb=" CA PRO A 292 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 292 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 519 " -0.010 2.00e-02 2.50e+03 1.95e-02 3.81e+00 pdb=" C GLU A 519 " 0.034 2.00e-02 2.50e+03 pdb=" O GLU A 519 " -0.012 2.00e-02 2.50e+03 pdb=" N THR A 520 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 131 " 0.010 2.00e-02 2.50e+03 9.61e-03 2.31e+00 pdb=" CG TRP A 131 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 TRP A 131 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP A 131 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 131 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 131 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 131 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 131 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 131 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 131 " 0.000 2.00e-02 2.50e+03 ... (remaining 666 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 240 2.73 - 3.27: 4304 3.27 - 3.82: 6583 3.82 - 4.36: 7315 4.36 - 4.90: 12549 Nonbonded interactions: 30991 Sorted by model distance: nonbonded pdb=" OG1 THR A 28 " pdb=" OH TYR A 185 " model vdw 2.191 2.440 nonbonded pdb=" O CYS A 189 " pdb=" OG SER A 278 " model vdw 2.244 2.440 nonbonded pdb=" OE2 GLU A 232 " pdb=" NH1 ARG A 466 " model vdw 2.254 2.520 nonbonded pdb=" N ARG A 406 " pdb=" OE2 GLU A 519 " model vdw 2.293 2.520 nonbonded pdb=" NE ARG A 178 " pdb=" OD1 ASN A 335 " model vdw 2.296 2.520 ... (remaining 30986 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 8.550 Check model and map are aligned: 0.060 Set scattering table: 0.030 Process input model: 15.270 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 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 : 0.004 0.035 3965 Z= 0.250 Angle : 0.719 6.530 5397 Z= 0.394 Chirality : 0.043 0.189 629 Planarity : 0.005 0.082 669 Dihedral : 13.972 89.476 1394 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 0.24 % Allowed : 0.24 % Favored : 99.51 % 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: 1.08 (0.39), residues: 487 helix: 1.50 (0.28), residues: 355 sheet: None (None), residues: 0 loop : -1.47 (0.52), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 131 HIS 0.002 0.001 HIS A 137 PHE 0.025 0.002 PHE A 410 TYR 0.009 0.001 TYR A 133 ARG 0.003 0.000 ARG A 212 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 82 time to evaluate : 0.373 Fit side-chains REVERT: A 306 GLN cc_start: 0.8006 (tm-30) cc_final: 0.7784 (tm-30) REVERT: A 478 ASP cc_start: 0.7985 (m-30) cc_final: 0.7611 (m-30) REVERT: A 515 MET cc_start: 0.6321 (ttm) cc_final: 0.5736 (mmp) outliers start: 1 outliers final: 0 residues processed: 82 average time/residue: 0.1615 time to fit residues: 16.3480 Evaluate side-chains 59 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 41 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 20 optimal weight: 0.0010 chunk 12 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 38 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 44 optimal weight: 0.7980 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3965 Z= 0.211 Angle : 0.619 5.865 5397 Z= 0.316 Chirality : 0.040 0.134 629 Planarity : 0.005 0.066 669 Dihedral : 4.383 16.445 536 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 1.96 % Allowed : 13.20 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.40), residues: 487 helix: 1.84 (0.29), residues: 347 sheet: None (None), residues: 0 loop : -1.43 (0.52), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 65 HIS 0.003 0.001 HIS A 137 PHE 0.013 0.001 PHE A 450 TYR 0.010 0.001 TYR A 185 ARG 0.002 0.000 ARG A 212 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 71 time to evaluate : 0.423 Fit side-chains REVERT: A 179 TYR cc_start: 0.7220 (m-10) cc_final: 0.6944 (m-10) REVERT: A 306 GLN cc_start: 0.7956 (tm-30) cc_final: 0.7744 (tm-30) REVERT: A 478 ASP cc_start: 0.8073 (m-30) cc_final: 0.7662 (m-30) outliers start: 8 outliers final: 7 residues processed: 77 average time/residue: 0.1329 time to fit residues: 13.3065 Evaluate side-chains 71 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 64 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 TRP Chi-restraints excluded: chain A residue 152 TRP Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 330 ASP Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 433 TRP Chi-restraints excluded: chain A residue 483 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 24 optimal weight: 0.9980 chunk 13 optimal weight: 0.5980 chunk 37 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 12 optimal weight: 0.4980 chunk 44 optimal weight: 0.5980 chunk 48 optimal weight: 0.0770 chunk 39 optimal weight: 0.5980 chunk 15 optimal weight: 0.8980 chunk 35 optimal weight: 0.4980 chunk 33 optimal weight: 3.9990 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3965 Z= 0.186 Angle : 0.584 7.103 5397 Z= 0.298 Chirality : 0.039 0.130 629 Planarity : 0.005 0.060 669 Dihedral : 4.219 16.970 536 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.69 % Allowed : 17.11 % Favored : 80.20 % 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: 1.48 (0.39), residues: 487 helix: 1.89 (0.29), residues: 345 sheet: None (None), residues: 0 loop : -1.37 (0.48), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 65 HIS 0.002 0.001 HIS A 137 PHE 0.014 0.001 PHE A 384 TYR 0.022 0.001 TYR A 185 ARG 0.002 0.000 ARG A 73 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 70 time to evaluate : 0.436 Fit side-chains REVERT: A 152 TRP cc_start: 0.8400 (OUTLIER) cc_final: 0.8115 (p-90) REVERT: A 459 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.7015 (mp0) REVERT: A 478 ASP cc_start: 0.8049 (m-30) cc_final: 0.7665 (m-30) REVERT: A 515 MET cc_start: 0.6336 (ttm) cc_final: 0.5899 (mmp) outliers start: 11 outliers final: 7 residues processed: 78 average time/residue: 0.1178 time to fit residues: 12.2513 Evaluate side-chains 71 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 62 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 TRP Chi-restraints excluded: chain A residue 152 TRP Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 330 ASP Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 433 TRP Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain A residue 483 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 23 optimal weight: 0.9980 chunk 4 optimal weight: 0.0170 chunk 21 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 47 optimal weight: 0.0010 chunk 42 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 overall best weight: 0.5624 ------------------------------------------------------------------------------- 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: 0.7455 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 0.030 3965 Z= 0.200 Angle : 0.588 7.927 5397 Z= 0.301 Chirality : 0.039 0.164 629 Planarity : 0.005 0.054 669 Dihedral : 4.227 16.088 536 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 3.91 % Allowed : 19.07 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.39), residues: 487 helix: 1.80 (0.29), residues: 349 sheet: None (None), residues: 0 loop : -1.32 (0.49), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 152 HIS 0.002 0.001 HIS A 137 PHE 0.024 0.001 PHE A 356 TYR 0.024 0.001 TYR A 185 ARG 0.001 0.000 ARG A 298 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 70 time to evaluate : 0.448 Fit side-chains REVERT: A 14 PHE cc_start: 0.9054 (OUTLIER) cc_final: 0.8671 (m-80) REVERT: A 140 ILE cc_start: 0.7567 (pt) cc_final: 0.7263 (pt) REVERT: A 177 ASP cc_start: 0.7340 (t70) cc_final: 0.6992 (t70) REVERT: A 459 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.7089 (mp0) REVERT: A 478 ASP cc_start: 0.8130 (m-30) cc_final: 0.7722 (m-30) REVERT: A 515 MET cc_start: 0.6342 (ttm) cc_final: 0.5924 (mmp) outliers start: 16 outliers final: 12 residues processed: 83 average time/residue: 0.1358 time to fit residues: 14.7291 Evaluate side-chains 81 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 67 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 PHE Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 131 TRP Chi-restraints excluded: chain A residue 152 TRP Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 330 ASP Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 433 TRP Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain A residue 477 CYS Chi-restraints excluded: chain A residue 483 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 35 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 32 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 GLN A 457 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3965 Z= 0.229 Angle : 0.614 8.233 5397 Z= 0.312 Chirality : 0.040 0.137 629 Planarity : 0.005 0.051 669 Dihedral : 4.304 16.521 536 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 5.13 % Allowed : 20.54 % Favored : 74.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.39), residues: 487 helix: 1.70 (0.28), residues: 349 sheet: None (None), residues: 0 loop : -1.30 (0.49), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 152 HIS 0.002 0.001 HIS A 137 PHE 0.012 0.001 PHE A 356 TYR 0.026 0.001 TYR A 185 ARG 0.002 0.000 ARG A 407 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 69 time to evaluate : 0.454 Fit side-chains REVERT: A 14 PHE cc_start: 0.9088 (OUTLIER) cc_final: 0.8808 (m-80) REVERT: A 140 ILE cc_start: 0.7621 (pt) cc_final: 0.7303 (pt) REVERT: A 385 ILE cc_start: 0.9072 (OUTLIER) cc_final: 0.8871 (mp) REVERT: A 459 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7175 (mp0) REVERT: A 478 ASP cc_start: 0.8140 (m-30) cc_final: 0.7781 (m-30) REVERT: A 515 MET cc_start: 0.6506 (ttm) cc_final: 0.6007 (mmp) outliers start: 21 outliers final: 15 residues processed: 85 average time/residue: 0.1293 time to fit residues: 14.2483 Evaluate side-chains 76 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 58 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ASP Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 14 PHE Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 131 TRP Chi-restraints excluded: chain A residue 152 TRP Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 330 ASP Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 433 TRP Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain A residue 477 CYS Chi-restraints excluded: chain A residue 483 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 11 optimal weight: 0.7980 chunk 47 optimal weight: 0.8980 chunk 39 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 3 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 5 optimal weight: 0.4980 chunk 27 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3965 Z= 0.220 Angle : 0.604 7.369 5397 Z= 0.311 Chirality : 0.040 0.129 629 Planarity : 0.005 0.053 669 Dihedral : 4.312 16.398 536 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 5.38 % Allowed : 23.47 % Favored : 71.15 % 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: 1.33 (0.39), residues: 487 helix: 1.74 (0.28), residues: 349 sheet: None (None), residues: 0 loop : -1.37 (0.49), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 152 HIS 0.002 0.001 HIS A 137 PHE 0.009 0.001 PHE A 211 TYR 0.027 0.002 TYR A 185 ARG 0.002 0.000 ARG A 407 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 64 time to evaluate : 0.397 Fit side-chains REVERT: A 14 PHE cc_start: 0.9085 (OUTLIER) cc_final: 0.8807 (m-80) REVERT: A 384 PHE cc_start: 0.7800 (t80) cc_final: 0.7170 (t80) REVERT: A 385 ILE cc_start: 0.9067 (OUTLIER) cc_final: 0.8855 (mp) REVERT: A 456 VAL cc_start: 0.8646 (p) cc_final: 0.8384 (t) REVERT: A 459 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7191 (mp0) REVERT: A 478 ASP cc_start: 0.8140 (m-30) cc_final: 0.7774 (m-30) REVERT: A 515 MET cc_start: 0.6509 (ttm) cc_final: 0.6043 (mmp) outliers start: 22 outliers final: 16 residues processed: 82 average time/residue: 0.1281 time to fit residues: 13.6803 Evaluate side-chains 81 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 62 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 14 PHE Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 131 TRP Chi-restraints excluded: chain A residue 152 TRP Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 330 ASP Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 433 TRP Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 477 CYS Chi-restraints excluded: chain A residue 483 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 26 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 9 optimal weight: 8.9990 chunk 30 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 158 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3965 Z= 0.243 Angle : 0.628 8.820 5397 Z= 0.321 Chirality : 0.040 0.142 629 Planarity : 0.005 0.052 669 Dihedral : 4.373 16.468 536 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 6.11 % Allowed : 23.47 % Favored : 70.42 % 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: 1.26 (0.38), residues: 487 helix: 1.70 (0.28), residues: 347 sheet: None (None), residues: 0 loop : -1.41 (0.48), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 152 HIS 0.004 0.001 HIS A 137 PHE 0.010 0.001 PHE A 211 TYR 0.028 0.002 TYR A 185 ARG 0.002 0.000 ARG A 407 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 63 time to evaluate : 0.434 Fit side-chains REVERT: A 14 PHE cc_start: 0.9075 (OUTLIER) cc_final: 0.8806 (m-80) REVERT: A 456 VAL cc_start: 0.8648 (p) cc_final: 0.8388 (t) REVERT: A 459 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7192 (mp0) REVERT: A 478 ASP cc_start: 0.8137 (m-30) cc_final: 0.7794 (m-30) REVERT: A 515 MET cc_start: 0.6642 (ttm) cc_final: 0.6185 (mmp) outliers start: 25 outliers final: 18 residues processed: 83 average time/residue: 0.1273 time to fit residues: 13.7396 Evaluate side-chains 80 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 60 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ASP Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 14 PHE Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 131 TRP Chi-restraints excluded: chain A residue 152 TRP Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 330 ASP Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 433 TRP Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 477 CYS Chi-restraints excluded: chain A residue 483 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 23 optimal weight: 0.0870 chunk 4 optimal weight: 0.0570 chunk 37 optimal weight: 0.5980 chunk 42 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 chunk 44 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 34 optimal weight: 0.5980 chunk 13 optimal weight: 0.8980 overall best weight: 0.4076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3965 Z= 0.189 Angle : 0.603 9.164 5397 Z= 0.309 Chirality : 0.039 0.130 629 Planarity : 0.005 0.052 669 Dihedral : 4.241 16.025 536 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 5.13 % Allowed : 23.96 % Favored : 70.90 % 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: 1.37 (0.39), residues: 487 helix: 1.78 (0.29), residues: 347 sheet: None (None), residues: 0 loop : -1.35 (0.49), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP A 65 HIS 0.002 0.001 HIS A 137 PHE 0.011 0.001 PHE A 22 TYR 0.028 0.002 TYR A 185 ARG 0.006 0.000 ARG A 73 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 74 time to evaluate : 0.486 Fit side-chains REVERT: A 177 ASP cc_start: 0.7254 (OUTLIER) cc_final: 0.7048 (t70) REVERT: A 459 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7182 (mp0) REVERT: A 478 ASP cc_start: 0.8120 (m-30) cc_final: 0.7770 (m-30) REVERT: A 515 MET cc_start: 0.6567 (ttm) cc_final: 0.6145 (mmp) outliers start: 21 outliers final: 17 residues processed: 91 average time/residue: 0.1322 time to fit residues: 15.5627 Evaluate side-chains 82 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 63 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 131 TRP Chi-restraints excluded: chain A residue 152 TRP Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 315 ASN Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 433 TRP Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 477 CYS Chi-restraints excluded: chain A residue 483 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 39 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 chunk 43 optimal weight: 0.2980 chunk 28 optimal weight: 4.9990 chunk 46 optimal weight: 0.8980 chunk 22 optimal weight: 0.5980 chunk 32 optimal weight: 0.8980 chunk 48 optimal weight: 0.5980 chunk 44 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3965 Z= 0.208 Angle : 0.612 9.077 5397 Z= 0.315 Chirality : 0.039 0.136 629 Planarity : 0.005 0.049 669 Dihedral : 4.264 15.501 536 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 4.65 % Allowed : 27.63 % Favored : 67.73 % 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: 1.23 (0.38), residues: 487 helix: 1.67 (0.28), residues: 348 sheet: None (None), residues: 0 loop : -1.44 (0.49), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A 65 HIS 0.002 0.001 HIS A 137 PHE 0.008 0.001 PHE A 450 TYR 0.026 0.002 TYR A 185 ARG 0.004 0.000 ARG A 73 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 64 time to evaluate : 0.425 Fit side-chains REVERT: A 456 VAL cc_start: 0.8693 (t) cc_final: 0.8480 (p) REVERT: A 459 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7116 (mp0) REVERT: A 478 ASP cc_start: 0.8165 (m-30) cc_final: 0.7806 (m-30) REVERT: A 515 MET cc_start: 0.6602 (ttm) cc_final: 0.6194 (mmp) outliers start: 19 outliers final: 16 residues processed: 80 average time/residue: 0.1433 time to fit residues: 14.7501 Evaluate side-chains 79 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 62 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 131 TRP Chi-restraints excluded: chain A residue 152 TRP Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 315 ASN Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 433 TRP Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 477 CYS Chi-restraints excluded: chain A residue 483 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 30 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 41 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 5 optimal weight: 0.1980 chunk 10 optimal weight: 0.5980 chunk 38 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3965 Z= 0.212 Angle : 0.612 9.131 5397 Z= 0.316 Chirality : 0.039 0.154 629 Planarity : 0.005 0.050 669 Dihedral : 4.258 15.796 536 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 4.40 % Allowed : 28.36 % Favored : 67.24 % 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: 1.20 (0.38), residues: 487 helix: 1.65 (0.28), residues: 348 sheet: None (None), residues: 0 loop : -1.45 (0.49), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 65 HIS 0.002 0.001 HIS A 137 PHE 0.015 0.001 PHE A 22 TYR 0.022 0.002 TYR A 185 ARG 0.004 0.000 ARG A 73 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 70 time to evaluate : 0.411 Fit side-chains REVERT: A 347 MET cc_start: 0.8183 (tpt) cc_final: 0.7872 (tpt) REVERT: A 456 VAL cc_start: 0.8658 (t) cc_final: 0.8428 (p) REVERT: A 459 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.7118 (mp0) REVERT: A 478 ASP cc_start: 0.8183 (m-30) cc_final: 0.7816 (m-30) REVERT: A 515 MET cc_start: 0.6574 (ttm) cc_final: 0.6243 (mmp) outliers start: 18 outliers final: 17 residues processed: 85 average time/residue: 0.1388 time to fit residues: 15.1953 Evaluate side-chains 87 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 69 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 131 TRP Chi-restraints excluded: chain A residue 152 TRP Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 315 ASN Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 433 TRP Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 477 CYS Chi-restraints excluded: chain A residue 483 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 7 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 44 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.138807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.118903 restraints weight = 6799.049| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 3.06 r_work: 0.3648 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3965 Z= 0.233 Angle : 0.624 8.951 5397 Z= 0.323 Chirality : 0.040 0.158 629 Planarity : 0.005 0.052 669 Dihedral : 4.334 15.723 536 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 4.65 % Allowed : 27.87 % Favored : 67.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.38), residues: 487 helix: 1.63 (0.28), residues: 346 sheet: None (None), residues: 0 loop : -1.46 (0.48), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 65 HIS 0.002 0.001 HIS A 137 PHE 0.017 0.001 PHE A 22 TYR 0.021 0.002 TYR A 185 ARG 0.003 0.000 ARG A 73 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1293.95 seconds wall clock time: 24 minutes 6.00 seconds (1446.00 seconds total)