Starting phenix.real_space_refine on Mon Sep 23 16:23:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zh0_14716/09_2024/7zh0_14716.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zh0_14716/09_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_14716/09_2024/7zh0_14716.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zh0_14716/09_2024/7zh0_14716.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zh0_14716/09_2024/7zh0_14716.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zh0_14716/09_2024/7zh0_14716.cif" } 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. Time to flip 4 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: 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: 3.68, per 1000 atoms: 0.95 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.00 Conformation dependent library (CDL) restraints added in 451.2 milliseconds 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: 0.42 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: 1.08 Time building geometry restraints manager: 1.15 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: 0.00 - 1.31: 5075 1.31 - 2.61: 234 2.61 - 3.92: 64 3.92 - 5.22: 15 5.22 - 6.53: 9 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 3.040 nonbonded pdb=" O CYS A 189 " pdb=" OG SER A 278 " model vdw 2.244 3.040 nonbonded pdb=" OE2 GLU A 232 " pdb=" NH1 ARG A 466 " model vdw 2.254 3.120 nonbonded pdb=" N ARG A 406 " pdb=" OE2 GLU A 519 " model vdw 2.293 3.120 nonbonded pdb=" NE ARG A 178 " pdb=" OD1 ASN A 335 " model vdw 2.296 3.120 ... (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: 2.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.430 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.160 ------------------------------------------------------------------------------- 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 : 0.385 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: 0.1581 time to fit residues: 16.0758 Evaluate side-chains 59 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 0.421 ------------------------------------------------------------------------------- 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: 2.9990 chunk 37 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 44 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 ASN A 158 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3965 Z= 0.232 Angle : 0.640 5.921 5397 Z= 0.328 Chirality : 0.041 0.136 629 Planarity : 0.005 0.068 669 Dihedral : 4.429 16.774 536 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 1.71 % Allowed : 13.20 % Favored : 85.09 % 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: 1.34 (0.39), residues: 487 helix: 1.76 (0.28), residues: 348 sheet: None (None), residues: 0 loop : -1.41 (0.52), residues: 139 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 0.013 0.001 TYR A 185 ARG 0.003 0.000 ARG A 406 *********************** 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 73 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 66 time to evaluate : 0.472 Fit side-chains REVERT: A 179 TYR cc_start: 0.7269 (m-10) cc_final: 0.7022 (m-10) REVERT: A 435 ARG cc_start: 0.7137 (mmt90) cc_final: 0.6796 (tpt-90) REVERT: A 478 ASP cc_start: 0.8075 (m-30) cc_final: 0.7644 (m-30) REVERT: A 515 MET cc_start: 0.6477 (ttm) cc_final: 0.5965 (mmp) outliers start: 7 outliers final: 6 residues processed: 72 average time/residue: 0.1321 time to fit residues: 12.4396 Evaluate side-chains 65 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 59 time to evaluate : 0.417 ------------------------------------------------------------------------------- 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 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: 2.9990 chunk 13 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 44 optimal weight: 0.4980 chunk 48 optimal weight: 4.9990 chunk 39 optimal weight: 0.2980 chunk 15 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.1775 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= 0.219 Angle : 0.620 7.152 5397 Z= 0.318 Chirality : 0.040 0.124 629 Planarity : 0.005 0.059 669 Dihedral : 4.362 17.540 536 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 2.44 % Allowed : 16.63 % Favored : 80.93 % 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: 1.25 (0.39), residues: 487 helix: 1.66 (0.28), residues: 350 sheet: None (None), residues: 0 loop : -1.36 (0.50), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 65 HIS 0.003 0.001 HIS A 137 PHE 0.010 0.001 PHE A 450 TYR 0.006 0.001 TYR A 49 ARG 0.002 0.000 ARG A 293 *********************** 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 75 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 65 time to evaluate : 0.422 Fit side-chains REVERT: A 459 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7044 (mp0) REVERT: A 478 ASP cc_start: 0.8109 (m-30) cc_final: 0.7704 (m-30) REVERT: A 515 MET cc_start: 0.6522 (ttm) cc_final: 0.6026 (mmp) outliers start: 10 outliers final: 8 residues processed: 74 average time/residue: 0.1215 time to fit residues: 11.9964 Evaluate side-chains 71 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 62 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 0.6980 chunk 4 optimal weight: 0.2980 chunk 21 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 47 optimal weight: 0.0170 chunk 42 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 0 optimal weight: 0.5980 overall best weight: 0.4418 ------------------------------------------------------------------------------- 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: 0.7440 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3965 Z= 0.193 Angle : 0.606 7.929 5397 Z= 0.308 Chirality : 0.040 0.124 629 Planarity : 0.005 0.057 669 Dihedral : 4.243 16.458 536 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 3.42 % Allowed : 18.58 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.39), residues: 487 helix: 1.65 (0.28), residues: 351 sheet: None (None), residues: 0 loop : -1.35 (0.49), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 358 HIS 0.002 0.001 HIS A 137 PHE 0.022 0.001 PHE A 356 TYR 0.006 0.001 TYR A 49 ARG 0.001 0.000 ARG A 466 *********************** 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 88 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 74 time to evaluate : 0.437 Fit side-chains REVERT: A 14 PHE cc_start: 0.9055 (OUTLIER) cc_final: 0.8835 (m-80) REVERT: A 140 ILE cc_start: 0.7475 (pt) cc_final: 0.7150 (pt) REVERT: A 177 ASP cc_start: 0.7222 (t70) cc_final: 0.6880 (t70) REVERT: A 435 ARG cc_start: 0.7180 (tpt-90) cc_final: 0.6855 (tpt-90) REVERT: A 459 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.7112 (mp0) REVERT: A 478 ASP cc_start: 0.8090 (m-30) cc_final: 0.7685 (m-30) REVERT: A 515 MET cc_start: 0.6555 (ttm) cc_final: 0.6048 (mmp) outliers start: 14 outliers final: 10 residues processed: 86 average time/residue: 0.1390 time to fit residues: 15.7203 Evaluate side-chains 76 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 64 time to evaluate : 0.443 ------------------------------------------------------------------------------- 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 305 LEU 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 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: 1.9990 chunk 19 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 9 optimal weight: 0.0070 chunk 27 optimal weight: 0.7980 overall best weight: 0.6598 ------------------------------------------------------------------------------- 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: 0.7474 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3965 Z= 0.217 Angle : 0.613 8.265 5397 Z= 0.317 Chirality : 0.040 0.167 629 Planarity : 0.005 0.051 669 Dihedral : 4.265 16.301 536 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 4.65 % Allowed : 18.58 % Favored : 76.77 % 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: 1.22 (0.39), residues: 487 helix: 1.62 (0.28), residues: 349 sheet: None (None), residues: 0 loop : -1.32 (0.49), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 152 HIS 0.005 0.002 HIS A 137 PHE 0.015 0.001 PHE A 384 TYR 0.013 0.001 TYR A 133 ARG 0.002 0.000 ARG A 466 *********************** 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 91 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 72 time to evaluate : 0.426 Fit side-chains REVERT: A 14 PHE cc_start: 0.9099 (OUTLIER) cc_final: 0.8842 (m-80) REVERT: A 140 ILE cc_start: 0.7544 (pt) cc_final: 0.7206 (pt) REVERT: A 177 ASP cc_start: 0.7265 (t70) cc_final: 0.6930 (t70) REVERT: A 435 ARG cc_start: 0.7204 (tpt-90) cc_final: 0.6902 (tpt-90) REVERT: A 459 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7196 (mp0) REVERT: A 478 ASP cc_start: 0.8168 (m-30) cc_final: 0.7750 (m-30) REVERT: A 515 MET cc_start: 0.6574 (ttm) cc_final: 0.6122 (mmp) outliers start: 19 outliers final: 12 residues processed: 87 average time/residue: 0.1350 time to fit residues: 15.4833 Evaluate side-chains 78 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 64 time to evaluate : 0.613 ------------------------------------------------------------------------------- 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 302 ASP Chi-restraints excluded: chain A residue 305 LEU 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 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: 0.9990 chunk 47 optimal weight: 0.4980 chunk 39 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 5 optimal weight: 0.4980 chunk 27 optimal weight: 4.9990 chunk 34 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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: 0.7481 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3965 Z= 0.219 Angle : 0.616 7.274 5397 Z= 0.318 Chirality : 0.041 0.148 629 Planarity : 0.005 0.051 669 Dihedral : 4.284 16.340 536 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 4.65 % Allowed : 20.29 % Favored : 75.06 % 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: 1.57 (0.28), residues: 349 sheet: None (None), residues: 0 loop : -1.35 (0.49), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 152 HIS 0.003 0.001 HIS A 137 PHE 0.009 0.001 PHE A 211 TYR 0.007 0.001 TYR A 285 ARG 0.002 0.000 ARG A 466 *********************** 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 95 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 76 time to evaluate : 0.443 Fit side-chains REVERT: A 14 PHE cc_start: 0.9105 (OUTLIER) cc_final: 0.8862 (m-80) REVERT: A 177 ASP cc_start: 0.7229 (t70) cc_final: 0.6917 (t70) REVERT: A 459 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7209 (mp0) REVERT: A 478 ASP cc_start: 0.8166 (m-30) cc_final: 0.7768 (m-30) REVERT: A 515 MET cc_start: 0.6555 (ttm) cc_final: 0.6222 (mmp) outliers start: 19 outliers final: 14 residues processed: 91 average time/residue: 0.1322 time to fit residues: 15.6332 Evaluate side-chains 84 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 68 time to evaluate : 0.420 ------------------------------------------------------------------------------- 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 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 302 ASP Chi-restraints excluded: chain A residue 305 LEU 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 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: 0.5980 chunk 39 optimal weight: 0.8980 chunk 47 optimal weight: 0.7980 chunk 29 optimal weight: 0.0270 chunk 28 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 GLN ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3965 Z= 0.208 Angle : 0.627 9.065 5397 Z= 0.321 Chirality : 0.040 0.141 629 Planarity : 0.005 0.052 669 Dihedral : 4.237 15.943 536 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 4.89 % Allowed : 21.76 % Favored : 73.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.38), residues: 487 helix: 1.55 (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 0.011 0.001 TRP A 358 HIS 0.003 0.001 HIS A 137 PHE 0.035 0.001 PHE A 356 TYR 0.005 0.001 TYR A 49 ARG 0.002 0.000 ARG A 466 *********************** 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: 20 poor density : 68 time to evaluate : 0.421 Fit side-chains REVERT: A 14 PHE cc_start: 0.9100 (OUTLIER) cc_final: 0.8853 (m-80) REVERT: A 459 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7201 (mp0) REVERT: A 478 ASP cc_start: 0.8196 (m-30) cc_final: 0.7804 (m-30) REVERT: A 515 MET cc_start: 0.6550 (ttm) cc_final: 0.6251 (mmp) outliers start: 20 outliers final: 15 residues processed: 84 average time/residue: 0.1277 time to fit residues: 14.1294 Evaluate side-chains 81 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 64 time to evaluate : 0.433 ------------------------------------------------------------------------------- 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 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 276 LEU Chi-restraints excluded: chain A residue 302 ASP 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 23 optimal weight: 0.9980 chunk 4 optimal weight: 0.0270 chunk 37 optimal weight: 0.5980 chunk 42 optimal weight: 0.5980 chunk 45 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 overall best weight: 0.5638 ------------------------------------------------------------------------------- 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: 0.7465 moved from start: 0.2615 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= 0.210 Angle : 0.624 9.142 5397 Z= 0.320 Chirality : 0.040 0.133 629 Planarity : 0.005 0.051 669 Dihedral : 4.228 15.698 536 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 5.13 % Allowed : 22.25 % Favored : 72.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.38), residues: 487 helix: 1.61 (0.28), residues: 345 sheet: None (None), residues: 0 loop : -1.31 (0.48), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 358 HIS 0.003 0.001 HIS A 137 PHE 0.026 0.001 PHE A 356 TYR 0.014 0.001 TYR A 179 ARG 0.002 0.000 ARG A 466 *********************** 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 90 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 69 time to evaluate : 0.440 Fit side-chains REVERT: A 14 PHE cc_start: 0.9099 (OUTLIER) cc_final: 0.8850 (m-80) REVERT: A 459 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7184 (mp0) REVERT: A 478 ASP cc_start: 0.8187 (m-30) cc_final: 0.7783 (m-30) REVERT: A 515 MET cc_start: 0.6596 (ttm) cc_final: 0.6306 (mmp) outliers start: 21 outliers final: 16 residues processed: 85 average time/residue: 0.1354 time to fit residues: 15.0230 Evaluate side-chains 82 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 64 time to evaluate : 0.499 ------------------------------------------------------------------------------- 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 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 276 LEU Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 390 GLU 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: 1.9990 chunk 41 optimal weight: 0.6980 chunk 43 optimal weight: 0.1980 chunk 28 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 48 optimal weight: 0.0970 chunk 44 optimal weight: 0.0370 chunk 38 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 overall best weight: 0.3456 ------------------------------------------------------------------------------- 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: 0.7422 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3965 Z= 0.192 Angle : 0.621 9.185 5397 Z= 0.317 Chirality : 0.040 0.137 629 Planarity : 0.005 0.050 669 Dihedral : 4.201 15.267 536 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 4.89 % Allowed : 22.49 % Favored : 72.62 % 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 (0.38), residues: 487 helix: 1.75 (0.28), residues: 341 sheet: None (None), residues: 0 loop : -1.28 (0.47), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP A 65 HIS 0.003 0.001 HIS A 137 PHE 0.023 0.001 PHE A 356 TYR 0.005 0.001 TYR A 49 ARG 0.006 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 91 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 71 time to evaluate : 0.408 Fit side-chains REVERT: A 14 PHE cc_start: 0.9078 (OUTLIER) cc_final: 0.8869 (m-80) REVERT: A 384 PHE cc_start: 0.7727 (t80) cc_final: 0.7169 (t80) REVERT: A 459 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7150 (mp0) REVERT: A 478 ASP cc_start: 0.8239 (m-30) cc_final: 0.7859 (m-30) REVERT: A 515 MET cc_start: 0.6505 (ttm) cc_final: 0.6258 (mmp) outliers start: 20 outliers final: 17 residues processed: 86 average time/residue: 0.1305 time to fit residues: 14.6411 Evaluate side-chains 82 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 63 time to evaluate : 0.436 ------------------------------------------------------------------------------- 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 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 230 VAL Chi-restraints excluded: chain A residue 264 ILE 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 344 THR Chi-restraints excluded: chain A residue 390 GLU 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: 2.9990 chunk 23 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 35 optimal weight: 0.5980 chunk 5 optimal weight: 0.0970 chunk 10 optimal weight: 0.9990 chunk 38 optimal weight: 0.0970 chunk 16 optimal weight: 0.5980 chunk 39 optimal weight: 10.0000 chunk 4 optimal weight: 0.8980 overall best weight: 0.4176 ------------------------------------------------------------------------------- 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: 0.7427 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3965 Z= 0.194 Angle : 0.623 9.149 5397 Z= 0.320 Chirality : 0.040 0.147 629 Planarity : 0.005 0.052 669 Dihedral : 4.193 14.796 536 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 4.65 % Allowed : 22.74 % Favored : 72.62 % 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: 1.16 (0.38), residues: 487 helix: 1.59 (0.28), residues: 347 sheet: None (None), residues: 0 loop : -1.33 (0.49), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP A 65 HIS 0.003 0.001 HIS A 137 PHE 0.021 0.001 PHE A 356 TYR 0.016 0.001 TYR A 179 ARG 0.005 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 85 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 66 time to evaluate : 0.384 Fit side-chains REVERT: A 14 PHE cc_start: 0.9073 (OUTLIER) cc_final: 0.8868 (m-80) REVERT: A 384 PHE cc_start: 0.7743 (t80) cc_final: 0.7187 (t80) REVERT: A 459 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7164 (mp0) REVERT: A 478 ASP cc_start: 0.8254 (m-30) cc_final: 0.7877 (m-30) REVERT: A 515 MET cc_start: 0.6553 (ttm) cc_final: 0.6284 (mmp) outliers start: 19 outliers final: 16 residues processed: 80 average time/residue: 0.1242 time to fit residues: 13.4644 Evaluate side-chains 80 residues out of total 409 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 62 time to evaluate : 0.394 ------------------------------------------------------------------------------- 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 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 230 VAL Chi-restraints excluded: chain A residue 264 ILE 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 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: 0.9980 chunk 34 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.4038 r_free = 0.4038 target = 0.138419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.118567 restraints weight = 6786.668| |-----------------------------------------------------------------------------| r_work (start): 0.3765 rms_B_bonded: 3.05 r_work: 0.3650 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3965 Z= 0.255 Angle : 0.649 9.025 5397 Z= 0.335 Chirality : 0.041 0.167 629 Planarity : 0.005 0.051 669 Dihedral : 4.380 15.536 536 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 4.65 % Allowed : 22.98 % Favored : 72.37 % 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: 0.98 (0.38), residues: 487 helix: 1.48 (0.28), residues: 346 sheet: None (None), residues: 0 loop : -1.44 (0.48), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 65 HIS 0.003 0.001 HIS A 137 PHE 0.017 0.002 PHE A 356 TYR 0.009 0.001 TYR A 454 ARG 0.005 0.000 ARG A 73 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1309.59 seconds wall clock time: 28 minutes 37.85 seconds (1717.85 seconds total)