Starting phenix.real_space_refine on Sun Mar 10 14:18:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rju_4906/03_2024/6rju_4906.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rju_4906/03_2024/6rju_4906.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/6rju_4906/03_2024/6rju_4906.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rju_4906/03_2024/6rju_4906.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rju_4906/03_2024/6rju_4906.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rju_4906/03_2024/6rju_4906.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= 0.002 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: 6 Type Number sf(0) Gaussians Se 3 7.20 5 S 1 5.16 5 C 625 2.51 5 N 178 2.21 5 O 188 1.98 5 H 997 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 417": "OE1" <-> "OE2" Residue "A ASP 432": "OD1" <-> "OD2" Residue "A GLU 509": "OE1" <-> "OE2" Time to flip residues: 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 1992 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1992 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 4, 'TRANS': 126} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Time building chain proxies: 1.47, per 1000 atoms: 0.74 Number of scatterers: 1992 At special positions: 0 Unit cell: (57.132, 40.204, 83.582, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Se 3 33.99 S 1 16.00 O 188 8.00 N 178 7.00 C 625 6.00 H 997 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 1.21 Conformation dependent library (CDL) restraints added in 174.3 milliseconds 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 254 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 0 sheets defined 72.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 404 through 406 No H-bonds generated for 'chain 'A' and resid 404 through 406' Processing helix chain 'A' and resid 407 through 412 removed outlier: 3.613A pdb=" N ASP A 412 " --> pdb=" O LEU A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 425 removed outlier: 3.590A pdb=" N LEU A 420 " --> pdb=" O THR A 416 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLN A 424 " --> pdb=" O LEU A 420 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA A 425 " --> pdb=" O SER A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 449 removed outlier: 4.511A pdb=" N ARG A 439 " --> pdb=" O ASN A 435 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LEU A 440 " --> pdb=" O TRP A 436 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR A 449 " --> pdb=" O VAL A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 467 removed outlier: 4.019A pdb=" N HIS A 457 " --> pdb=" O ASP A 453 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ARG A 465 " --> pdb=" O GLU A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 494 removed outlier: 3.674A pdb=" N VAL A 479 " --> pdb=" O GLU A 475 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU A 481 " --> pdb=" O GLU A 477 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG A 485 " --> pdb=" O GLU A 481 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU A 490 " --> pdb=" O ARG A 486 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ARG A 491 " --> pdb=" O LEU A 487 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N MSE A 492 " --> pdb=" O LYS A 488 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS A 493 " --> pdb=" O LEU A 489 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N SER A 494 " --> pdb=" O LEU A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 510 Processing helix chain 'A' and resid 510 through 517 removed outlier: 4.037A pdb=" N ILE A 516 " --> pdb=" O LEU A 512 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA A 517 " --> pdb=" O ALA A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 526 removed outlier: 3.626A pdb=" N ALA A 524 " --> pdb=" O ALA A 521 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL A 525 " --> pdb=" O ARG A 522 " (cutoff:3.500A) 40 hydrogen bonds defined for protein. 117 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.57 Time building geometry restraints manager: 1.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.06: 996 1.06 - 1.29: 177 1.29 - 1.51: 452 1.51 - 1.73: 372 1.73 - 1.96: 7 Bond restraints: 2004 Sorted by residual: bond pdb=" CB ASN A 452 " pdb=" CG ASN A 452 " ideal model delta sigma weight residual 1.516 1.565 -0.049 2.50e-02 1.60e+03 3.90e+00 bond pdb=" CG GLU A 461 " pdb=" CD GLU A 461 " ideal model delta sigma weight residual 1.516 1.559 -0.043 2.50e-02 1.60e+03 2.99e+00 bond pdb=" CB GLU A 461 " pdb=" CG GLU A 461 " ideal model delta sigma weight residual 1.520 1.568 -0.048 3.00e-02 1.11e+03 2.56e+00 bond pdb=" CA ASN A 452 " pdb=" CB ASN A 452 " ideal model delta sigma weight residual 1.532 1.553 -0.021 1.51e-02 4.39e+03 1.90e+00 bond pdb=" CB TRP A 474 " pdb=" CG TRP A 474 " ideal model delta sigma weight residual 1.498 1.459 0.039 3.10e-02 1.04e+03 1.61e+00 ... (remaining 1999 not shown) Histogram of bond angle deviations from ideal: 98.22 - 105.39: 26 105.39 - 112.56: 2388 112.56 - 119.72: 552 119.72 - 126.89: 657 126.89 - 134.06: 15 Bond angle restraints: 3638 Sorted by residual: angle pdb=" C LYS A 451 " pdb=" N ASN A 452 " pdb=" CA ASN A 452 " ideal model delta sigma weight residual 122.61 128.50 -5.89 1.56e+00 4.11e-01 1.42e+01 angle pdb=" CA ASN A 452 " pdb=" CB ASN A 452 " pdb=" CG ASN A 452 " ideal model delta sigma weight residual 112.60 116.37 -3.77 1.00e+00 1.00e+00 1.42e+01 angle pdb=" CA GLN A 505 " pdb=" C GLN A 505 " pdb=" N PRO A 506 " ideal model delta sigma weight residual 118.44 122.27 -3.83 1.59e+00 3.96e-01 5.82e+00 angle pdb=" N ASN A 452 " pdb=" CA ASN A 452 " pdb=" C ASN A 452 " ideal model delta sigma weight residual 112.47 115.25 -2.78 1.24e+00 6.50e-01 5.04e+00 angle pdb=" N ARG A 468 " pdb=" CA ARG A 468 " pdb=" C ARG A 468 " ideal model delta sigma weight residual 108.23 105.14 3.09 1.38e+00 5.25e-01 5.02e+00 ... (remaining 3633 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.29: 817 16.29 - 32.59: 73 32.59 - 48.88: 19 48.88 - 65.17: 11 65.17 - 81.47: 2 Dihedral angle restraints: 922 sinusoidal: 509 harmonic: 413 Sorted by residual: dihedral pdb=" CA LEU A 469 " pdb=" C LEU A 469 " pdb=" N THR A 470 " pdb=" CA THR A 470 " ideal model delta harmonic sigma weight residual -180.00 -160.06 -19.94 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CA THR A 470 " pdb=" C THR A 470 " pdb=" N LEU A 471 " pdb=" CA LEU A 471 " ideal model delta harmonic sigma weight residual 180.00 -160.31 -19.69 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA THR A 449 " pdb=" C THR A 449 " pdb=" N GLY A 450 " pdb=" CA GLY A 450 " ideal model delta harmonic sigma weight residual 180.00 -161.97 -18.03 0 5.00e+00 4.00e-02 1.30e+01 ... (remaining 919 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 111 0.046 - 0.092: 46 0.092 - 0.137: 7 0.137 - 0.183: 0 0.183 - 0.229: 1 Chirality restraints: 165 Sorted by residual: chirality pdb=" CA ASN A 452 " pdb=" N ASN A 452 " pdb=" C ASN A 452 " pdb=" CB ASN A 452 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CA GLN A 505 " pdb=" N GLN A 505 " pdb=" C GLN A 505 " pdb=" CB GLN A 505 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.86e-01 chirality pdb=" CA ASN A 413 " pdb=" N ASN A 413 " pdb=" C ASN A 413 " pdb=" CB ASN A 413 " both_signs ideal model delta sigma weight residual False 2.51 2.40 0.11 2.00e-01 2.50e+01 3.17e-01 ... (remaining 162 not shown) Planarity restraints: 302 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 505 " -0.031 5.00e-02 4.00e+02 4.67e-02 3.49e+00 pdb=" N PRO A 506 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 506 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 506 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 451 " 0.007 2.00e-02 2.50e+03 1.51e-02 2.28e+00 pdb=" C LYS A 451 " -0.026 2.00e-02 2.50e+03 pdb=" O LYS A 451 " 0.010 2.00e-02 2.50e+03 pdb=" N ASN A 452 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 474 " -0.002 2.00e-02 2.50e+03 6.48e-03 1.68e+00 pdb=" CG TRP A 474 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 TRP A 474 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TRP A 474 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 474 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 474 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 474 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 474 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 474 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 474 " -0.001 2.00e-02 2.50e+03 pdb=" HD1 TRP A 474 " -0.016 2.00e-02 2.50e+03 pdb=" HE1 TRP A 474 " 0.003 2.00e-02 2.50e+03 pdb=" HE3 TRP A 474 " -0.000 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 474 " 0.003 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 474 " -0.004 2.00e-02 2.50e+03 pdb=" HH2 TRP A 474 " -0.002 2.00e-02 2.50e+03 ... (remaining 299 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.33: 400 2.33 - 2.94: 4685 2.94 - 3.56: 4919 3.56 - 4.18: 6409 4.18 - 4.80: 9891 Nonbonded interactions: 26304 Sorted by model distance: nonbonded pdb=" H VAL A 502 " pdb="HG22 VAL A 502 " model vdw 1.708 2.270 nonbonded pdb=" HA ARG A 468 " pdb=" HD2 ARG A 468 " model vdw 1.721 2.440 nonbonded pdb=" OG SER A 494 " pdb=" H ALA A 495 " model vdw 1.776 1.850 nonbonded pdb=" O THR A 497 " pdb=" HG1 THR A 497 " model vdw 1.783 1.850 nonbonded pdb=" H ILE A 516 " pdb="HG13 ILE A 516 " model vdw 1.796 2.270 ... (remaining 26299 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: 1.390 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: 0.030 Extract box with map and model: 6.890 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.220 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: -0.0287 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 : 0.007 0.049 1007 Z= 0.437 Angle : 0.929 6.431 1366 Z= 0.516 Chirality : 0.049 0.229 165 Planarity : 0.005 0.047 176 Dihedral : 15.358 81.468 373 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.63 % Favored : 88.37 % Rotamer: Outliers : 0.00 % Allowed : 11.11 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -7.10 (0.41), residues: 129 helix: -4.88 (0.19), residues: 79 sheet: None (None), residues: 0 loop : -4.14 (0.69), residues: 50 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 474 HIS 0.003 0.001 HIS A 457 PHE 0.011 0.004 PHE A 480 ARG 0.003 0.000 ARG A 522 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 400 is missing expected H atoms. Skipping. Residue LEU 401 is missing expected H atoms. Skipping. Residue SER 472 is missing expected H atoms. Skipping. Residue LYS 496 is missing expected H atoms. Skipping. Evaluate side-chains 13 residues out of total 109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.6195 time to fit residues: 8.5304 Evaluate side-chains 8 residues out of total 109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 8 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 13 random chunks: chunk 10 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 5 optimal weight: 0.5980 chunk 3 optimal weight: 0.0070 chunk 6 optimal weight: 0.7980 chunk 7 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 1 optimal weight: 4.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: -0.0036 moved from start: 0.3200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 1007 Z= 0.186 Angle : 0.621 5.775 1366 Z= 0.314 Chirality : 0.032 0.101 165 Planarity : 0.003 0.020 176 Dihedral : 5.653 14.359 139 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 3.03 % Allowed : 10.10 % Favored : 86.87 % 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: -5.40 (0.55), residues: 129 helix: -3.38 (0.41), residues: 81 sheet: None (None), residues: 0 loop : -3.70 (0.72), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 422 HIS 0.007 0.003 HIS A 457 PHE 0.005 0.002 PHE A 480 ARG 0.002 0.000 ARG A 468 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 400 is missing expected H atoms. Skipping. Residue LEU 401 is missing expected H atoms. Skipping. Residue SER 472 is missing expected H atoms. Skipping. Residue LYS 496 is missing expected H atoms. Skipping. Evaluate side-chains 11 residues out of total 109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 8 time to evaluate : 0.141 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 508 MSE cc_start: -0.1128 (ttm) cc_final: -0.1352 (tpp) outliers start: 3 outliers final: 0 residues processed: 10 average time/residue: 0.4844 time to fit residues: 5.2494 Evaluate side-chains 9 residues out of total 109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 9 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 13 random chunks: chunk 5 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 chunk 12 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 10 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 9 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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: 0.0153 moved from start: 0.4748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 1007 Z= 0.182 Angle : 0.575 5.060 1366 Z= 0.295 Chirality : 0.031 0.098 165 Planarity : 0.003 0.025 176 Dihedral : 4.694 13.013 139 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.01 % Allowed : 11.11 % Favored : 87.88 % 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: -4.15 (0.64), residues: 129 helix: -2.33 (0.48), residues: 85 sheet: None (None), residues: 0 loop : -3.35 (0.88), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 422 HIS 0.004 0.002 HIS A 457 PHE 0.004 0.001 PHE A 480 ARG 0.003 0.001 ARG A 486 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 400 is missing expected H atoms. Skipping. Residue LEU 401 is missing expected H atoms. Skipping. Residue SER 472 is missing expected H atoms. Skipping. Residue LYS 496 is missing expected H atoms. Skipping. Evaluate side-chains 11 residues out of total 109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 10 time to evaluate : 0.162 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 11 average time/residue: 0.3755 time to fit residues: 4.5917 Evaluate side-chains 10 residues out of total 109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 9 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 462 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 13 random chunks: chunk 11 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 7 optimal weight: 0.0070 chunk 3 optimal weight: 0.6980 chunk 12 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 1 optimal weight: 0.5980 chunk 4 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 overall best weight: 0.5398 ------------------------------------------------------------------------------- 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: 0.0133 moved from start: 0.5420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 1007 Z= 0.141 Angle : 0.502 4.221 1366 Z= 0.258 Chirality : 0.030 0.093 165 Planarity : 0.003 0.025 176 Dihedral : 4.459 12.977 139 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 1.01 % Allowed : 16.16 % Favored : 82.83 % 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: -3.50 (0.69), residues: 129 helix: -1.83 (0.52), residues: 88 sheet: None (None), residues: 0 loop : -3.14 (0.92), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 474 HIS 0.004 0.001 HIS A 457 PHE 0.002 0.001 PHE A 480 ARG 0.002 0.000 ARG A 491 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 400 is missing expected H atoms. Skipping. Residue LEU 401 is missing expected H atoms. Skipping. Residue SER 472 is missing expected H atoms. Skipping. Residue LYS 496 is missing expected H atoms. Skipping. Evaluate side-chains 9 residues out of total 109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 8 time to evaluate : 0.114 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 9 average time/residue: 0.3564 time to fit residues: 3.5615 Evaluate side-chains 8 residues out of total 109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 7 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 462 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 13 random chunks: chunk 7 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 2 optimal weight: 0.0470 chunk 8 optimal weight: 0.5980 chunk 6 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 overall best weight: 0.5278 ------------------------------------------------------------------------------- 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: 0.0167 moved from start: 0.5901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 1007 Z= 0.136 Angle : 0.482 4.137 1366 Z= 0.250 Chirality : 0.030 0.094 165 Planarity : 0.003 0.024 176 Dihedral : 4.132 12.681 139 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 1.01 % Allowed : 14.14 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.75), residues: 129 helix: -1.06 (0.58), residues: 85 sheet: None (None), residues: 0 loop : -2.72 (0.95), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 474 HIS 0.003 0.002 HIS A 457 PHE 0.002 0.001 PHE A 480 ARG 0.001 0.000 ARG A 491 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 400 is missing expected H atoms. Skipping. Residue LEU 401 is missing expected H atoms. Skipping. Residue SER 472 is missing expected H atoms. Skipping. Residue LYS 496 is missing expected H atoms. Skipping. Evaluate side-chains 10 residues out of total 109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 9 time to evaluate : 0.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 474 TRP cc_start: 0.1489 (OUTLIER) cc_final: 0.0794 (m-10) outliers start: 1 outliers final: 0 residues processed: 10 average time/residue: 0.4070 time to fit residues: 4.5004 Evaluate side-chains 10 residues out of total 109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 9 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 474 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 13 random chunks: chunk 12 optimal weight: 8.9990 chunk 10 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 1 optimal weight: 0.4980 chunk 6 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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: 0.0184 moved from start: 0.6204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 1007 Z= 0.145 Angle : 0.488 4.157 1366 Z= 0.250 Chirality : 0.030 0.094 165 Planarity : 0.002 0.021 176 Dihedral : 4.061 13.092 139 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.02 % Allowed : 14.14 % Favored : 83.84 % 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: -2.03 (0.77), residues: 129 helix: -0.67 (0.59), residues: 85 sheet: None (None), residues: 0 loop : -2.58 (0.97), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 474 HIS 0.003 0.001 HIS A 457 PHE 0.001 0.000 PHE A 480 ARG 0.001 0.000 ARG A 491 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 400 is missing expected H atoms. Skipping. Residue LEU 401 is missing expected H atoms. Skipping. Residue SER 472 is missing expected H atoms. Skipping. Residue LYS 496 is missing expected H atoms. Skipping. Evaluate side-chains 11 residues out of total 109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 9 time to evaluate : 0.159 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 474 TRP cc_start: 0.1523 (OUTLIER) cc_final: 0.0882 (m-10) outliers start: 2 outliers final: 1 residues processed: 11 average time/residue: 0.4222 time to fit residues: 5.1470 Evaluate side-chains 10 residues out of total 109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 8 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 474 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 13 random chunks: chunk 10 optimal weight: 0.9980 chunk 4 optimal weight: 4.9990 chunk 1 optimal weight: 0.3980 chunk 9 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 chunk 7 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 5 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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: 0.0230 moved from start: 0.6595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 1007 Z= 0.150 Angle : 0.510 4.195 1366 Z= 0.258 Chirality : 0.031 0.096 165 Planarity : 0.003 0.021 176 Dihedral : 4.061 13.807 139 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.02 % Allowed : 14.14 % Favored : 83.84 % 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: -1.64 (0.79), residues: 129 helix: -0.38 (0.61), residues: 85 sheet: None (None), residues: 0 loop : -2.39 (1.00), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 474 HIS 0.003 0.002 HIS A 510 PHE 0.002 0.001 PHE A 480 ARG 0.003 0.000 ARG A 491 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 400 is missing expected H atoms. Skipping. Residue LEU 401 is missing expected H atoms. Skipping. Residue SER 472 is missing expected H atoms. Skipping. Residue LYS 496 is missing expected H atoms. Skipping. Evaluate side-chains 11 residues out of total 109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 9 time to evaluate : 0.150 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 474 TRP cc_start: 0.1592 (OUTLIER) cc_final: 0.0758 (m-10) outliers start: 2 outliers final: 1 residues processed: 11 average time/residue: 0.4315 time to fit residues: 5.2775 Evaluate side-chains 11 residues out of total 109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 9 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 474 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 13 random chunks: chunk 0 optimal weight: 9.9990 chunk 12 optimal weight: 8.9990 chunk 2 optimal weight: 0.5980 chunk 1 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 5 optimal weight: 0.2980 chunk 3 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 4 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 9 optimal weight: 0.2980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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: 0.0231 moved from start: 0.6869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 1007 Z= 0.138 Angle : 0.497 4.907 1366 Z= 0.250 Chirality : 0.030 0.096 165 Planarity : 0.002 0.017 176 Dihedral : 3.927 13.589 139 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.02 % Allowed : 14.14 % Favored : 83.84 % 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: -1.22 (0.81), residues: 129 helix: -0.08 (0.62), residues: 85 sheet: None (None), residues: 0 loop : -2.18 (1.05), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 436 HIS 0.003 0.001 HIS A 457 PHE 0.001 0.001 PHE A 480 ARG 0.001 0.000 ARG A 486 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 400 is missing expected H atoms. Skipping. Residue LEU 401 is missing expected H atoms. Skipping. Residue SER 472 is missing expected H atoms. Skipping. Residue LYS 496 is missing expected H atoms. Skipping. Evaluate side-chains 11 residues out of total 109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 9 time to evaluate : 0.160 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 11 average time/residue: 0.3918 time to fit residues: 4.7773 Evaluate side-chains 10 residues out of total 109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 9 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 462 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 13 random chunks: chunk 10 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 4 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 chunk 7 optimal weight: 0.0470 chunk 5 optimal weight: 0.3980 chunk 6 optimal weight: 0.8980 overall best weight: 0.5878 ------------------------------------------------------------------------------- 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: 0.0271 moved from start: 0.7443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 1007 Z= 0.142 Angle : 0.511 4.492 1366 Z= 0.257 Chirality : 0.031 0.098 165 Planarity : 0.002 0.018 176 Dihedral : 3.936 13.979 139 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 1.01 % Allowed : 15.15 % Favored : 83.84 % 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: -0.97 (0.81), residues: 129 helix: 0.25 (0.63), residues: 82 sheet: None (None), residues: 0 loop : -2.26 (0.98), residues: 47 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 436 HIS 0.003 0.001 HIS A 457 PHE 0.001 0.000 PHE A 480 ARG 0.001 0.000 ARG A 486 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 400 is missing expected H atoms. Skipping. Residue LEU 401 is missing expected H atoms. Skipping. Residue SER 472 is missing expected H atoms. Skipping. Residue LYS 496 is missing expected H atoms. Skipping. Evaluate side-chains 10 residues out of total 109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 9 time to evaluate : 0.153 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 10 average time/residue: 0.3952 time to fit residues: 4.3798 Evaluate side-chains 10 residues out of total 109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 9 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 462 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 13 random chunks: chunk 5 optimal weight: 0.5980 chunk 7 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 0 optimal weight: 9.9990 chunk 9 optimal weight: 0.9980 chunk 12 optimal weight: 10.0000 chunk 8 optimal weight: 0.7980 chunk 2 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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: 0.0357 moved from start: 0.8238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 1007 Z= 0.140 Angle : 0.526 4.903 1366 Z= 0.265 Chirality : 0.030 0.094 165 Planarity : 0.003 0.016 176 Dihedral : 4.133 15.323 139 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.01 % Allowed : 15.15 % Favored : 83.84 % 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: -0.96 (0.81), residues: 129 helix: 0.31 (0.63), residues: 82 sheet: None (None), residues: 0 loop : -2.37 (0.98), residues: 47 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 436 HIS 0.002 0.001 HIS A 457 PHE 0.001 0.000 PHE A 480 ARG 0.002 0.000 ARG A 486 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 258 Ramachandran restraints generated. 129 Oldfield, 0 Emsley, 129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 400 is missing expected H atoms. Skipping. Residue LEU 401 is missing expected H atoms. Skipping. Residue SER 472 is missing expected H atoms. Skipping. Residue LYS 496 is missing expected H atoms. Skipping. Evaluate side-chains 10 residues out of total 109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 9 time to evaluate : 0.156 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 10 average time/residue: 0.4033 time to fit residues: 4.4773 Evaluate side-chains 10 residues out of total 109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 9 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 462 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 13 random chunks: chunk 4 optimal weight: 4.9990 chunk 3 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 chunk 0 optimal weight: 9.9990 chunk 2 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4982 r_free = 0.4982 target = 0.197560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4812 r_free = 0.4812 target = 0.165413 restraints weight = 8018.377| |-----------------------------------------------------------------------------| r_work (start): 0.4800 rms_B_bonded: 12.05 r_work: 0.4674 rms_B_bonded: 11.40 restraints_weight: 2.0000 r_work: 0.4765 rms_B_bonded: 7.52 restraints_weight: 4.0000 r_work (final): 0.4765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0246 moved from start: 0.8752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 1007 Z= 0.169 Angle : 0.547 6.763 1366 Z= 0.270 Chirality : 0.031 0.099 165 Planarity : 0.003 0.016 176 Dihedral : 4.133 15.515 139 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 1.01 % Allowed : 15.15 % Favored : 83.84 % 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: -0.89 (0.81), residues: 129 helix: 0.35 (0.63), residues: 82 sheet: None (None), residues: 0 loop : -2.28 (0.99), residues: 47 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 474 HIS 0.002 0.001 HIS A 457 PHE 0.001 0.000 PHE A 480 ARG 0.004 0.001 ARG A 491 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1714.52 seconds wall clock time: 30 minutes 42.04 seconds (1842.04 seconds total)