Starting phenix.real_space_refine on Sun Mar 10 21:10:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k5g_36905/03_2024/8k5g_36905.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k5g_36905/03_2024/8k5g_36905.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k5g_36905/03_2024/8k5g_36905.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k5g_36905/03_2024/8k5g_36905.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k5g_36905/03_2024/8k5g_36905.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k5g_36905/03_2024/8k5g_36905.pdb" } resolution = 3.41 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= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1744 atoms to isotropic. 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 18 5.16 5 C 2152 2.51 5 N 574 2.21 5 O 637 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 17": "OE1" <-> "OE2" Residue "A PHE 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 361": "OD1" <-> "OD2" Residue "A TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 513": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 3 Chain: "H" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 948 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 3, 'TRANS': 119} Chain: "L" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 816 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 99} Chain: "A" Number of atoms: 1617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1617 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 13, 'TRANS': 187} Time building chain proxies: 2.39, per 1000 atoms: 0.71 Number of scatterers: 3381 At special positions: 0 Unit cell: (60.3, 113.9, 75.04, 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 18 16.00 O 637 8.00 N 574 7.00 C 2152 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 101 " - pdb=" SG CYS H 105 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS A 333 " - pdb=" SG CYS A 358 " distance=2.02 Simple disulfide: pdb=" SG CYS A 376 " - pdb=" SG CYS A 429 " distance=2.04 Simple disulfide: pdb=" SG CYS A 388 " - pdb=" SG CYS A 522 " distance=2.03 Simple disulfide: pdb=" SG CYS A 477 " - pdb=" SG CYS A 485 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.15 Conformation dependent library (CDL) restraints added in 655.5 milliseconds 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 792 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 8 sheets defined 6.3% alpha, 32.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'H' and resid 87 through 91 removed outlier: 4.024A pdb=" N THR H 91 " --> pdb=" O PHE H 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 350 removed outlier: 3.802A pdb=" N TRP A 350 " --> pdb=" O VAL A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 366 removed outlier: 3.524A pdb=" N LEU A 365 " --> pdb=" O TYR A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 408 removed outlier: 3.918A pdb=" N ALA A 408 " --> pdb=" O ARG A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 419 removed outlier: 3.995A pdb=" N TYR A 418 " --> pdb=" O ASN A 414 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 5 through 6 Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.731A pdb=" N VAL H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N TRP H 50 " --> pdb=" O VAL H 34 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 12 Processing sheet with id=AA4, first strand: chain 'L' and resid 4 through 7 removed outlier: 4.562A pdb=" N PHE L 72 " --> pdb=" O CYS L 23 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASP L 71 " --> pdb=" O SER L 68 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 10 through 11 removed outlier: 6.689A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 351 through 355 removed outlier: 3.637A pdb=" N ASN A 351 " --> pdb=" O SER A 396 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL A 392 " --> pdb=" O ILE A 355 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL A 521 " --> pdb=" O PHE A 389 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N CYS A 358 " --> pdb=" O CYS A 522 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 351 through 355 removed outlier: 3.637A pdb=" N ASN A 351 " --> pdb=" O SER A 396 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL A 392 " --> pdb=" O ILE A 355 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N ASN A 391 " --> pdb=" O GLU A 513 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N GLU A 513 " --> pdb=" O ASN A 391 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLY A 401 " --> pdb=" O GLN A 503 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N GLN A 503 " --> pdb=" O GLY A 401 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 449 through 451 94 hydrogen bonds defined for protein. 216 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: 0.85 Time building geometry restraints manager: 1.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1084 1.35 - 1.46: 908 1.46 - 1.58: 1456 1.58 - 1.70: 0 1.70 - 1.82: 22 Bond restraints: 3470 Sorted by residual: bond pdb=" N VAL A 442 " pdb=" CA VAL A 442 " ideal model delta sigma weight residual 1.459 1.472 -0.013 1.25e-02 6.40e+03 1.05e+00 bond pdb=" CA SER A 443 " pdb=" C SER A 443 " ideal model delta sigma weight residual 1.519 1.513 0.005 5.30e-03 3.56e+04 9.61e-01 bond pdb=" CA CYS A 333 " pdb=" CB CYS A 333 " ideal model delta sigma weight residual 1.536 1.524 0.012 1.25e-02 6.40e+03 8.56e-01 bond pdb=" CB CYS A 358 " pdb=" SG CYS A 358 " ideal model delta sigma weight residual 1.808 1.778 0.030 3.30e-02 9.18e+02 8.12e-01 bond pdb=" CG PRO L 96 " pdb=" CD PRO L 96 " ideal model delta sigma weight residual 1.512 1.488 0.024 2.70e-02 1.37e+03 7.86e-01 ... (remaining 3465 not shown) Histogram of bond angle deviations from ideal: 99.92 - 106.73: 104 106.73 - 113.55: 1788 113.55 - 120.36: 1251 120.36 - 127.17: 1529 127.17 - 133.98: 41 Bond angle restraints: 4713 Sorted by residual: angle pdb=" C LYS A 441 " pdb=" N VAL A 442 " pdb=" CA VAL A 442 " ideal model delta sigma weight residual 121.97 131.98 -10.01 1.80e+00 3.09e-01 3.09e+01 angle pdb=" CA SER A 443 " pdb=" C SER A 443 " pdb=" N GLY A 444 " ideal model delta sigma weight residual 119.56 116.68 2.88 5.80e-01 2.97e+00 2.46e+01 angle pdb=" N VAL A 442 " pdb=" CA VAL A 442 " pdb=" CB VAL A 442 " ideal model delta sigma weight residual 111.23 116.46 -5.23 1.65e+00 3.67e-01 1.01e+01 angle pdb=" N SER A 443 " pdb=" CA SER A 443 " pdb=" C SER A 443 " ideal model delta sigma weight residual 108.12 112.89 -4.77 1.59e+00 3.96e-01 9.00e+00 angle pdb=" N PHE A 335 " pdb=" CA PHE A 335 " pdb=" C PHE A 335 " ideal model delta sigma weight residual 112.88 109.15 3.73 1.29e+00 6.01e-01 8.38e+00 ... (remaining 4708 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.57: 1843 17.57 - 35.15: 173 35.15 - 52.72: 31 52.72 - 70.29: 5 70.29 - 87.87: 3 Dihedral angle restraints: 2055 sinusoidal: 809 harmonic: 1246 Sorted by residual: dihedral pdb=" CB CYS A 477 " pdb=" SG CYS A 477 " pdb=" SG CYS A 485 " pdb=" CB CYS A 485 " ideal model delta sinusoidal sigma weight residual 93.00 -179.13 -87.87 1 1.00e+01 1.00e-02 9.24e+01 dihedral pdb=" CA CYS A 358 " pdb=" C CYS A 358 " pdb=" N VAL A 359 " pdb=" CA VAL A 359 " ideal model delta harmonic sigma weight residual 180.00 153.20 26.80 0 5.00e+00 4.00e-02 2.87e+01 dihedral pdb=" CA PRO A 334 " pdb=" C PRO A 334 " pdb=" N PHE A 335 " pdb=" CA PHE A 335 " ideal model delta harmonic sigma weight residual 180.00 158.40 21.60 0 5.00e+00 4.00e-02 1.87e+01 ... (remaining 2052 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.027: 259 0.027 - 0.054: 145 0.054 - 0.081: 51 0.081 - 0.107: 26 0.107 - 0.134: 20 Chirality restraints: 501 Sorted by residual: chirality pdb=" CA PRO A 334 " pdb=" N PRO A 334 " pdb=" C PRO A 334 " pdb=" CB PRO A 334 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.13 2.00e-01 2.50e+01 4.50e-01 chirality pdb=" CA ASN A 391 " pdb=" N ASN A 391 " pdb=" C ASN A 391 " pdb=" CB ASN A 391 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.08e-01 chirality pdb=" CA VAL A 508 " pdb=" N VAL A 508 " pdb=" C VAL A 508 " pdb=" CB VAL A 508 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.00e-01 ... (remaining 498 not shown) Planarity restraints: 611 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 441 " -0.009 2.00e-02 2.50e+03 1.85e-02 3.41e+00 pdb=" C LYS A 441 " 0.032 2.00e-02 2.50e+03 pdb=" O LYS A 441 " -0.012 2.00e-02 2.50e+03 pdb=" N VAL A 442 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 369 " 0.028 5.00e-02 4.00e+02 4.26e-02 2.91e+00 pdb=" N PRO A 370 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 370 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 370 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 517 " 0.027 5.00e-02 4.00e+02 4.13e-02 2.73e+00 pdb=" N PRO A 518 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 518 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 518 " 0.023 5.00e-02 4.00e+02 ... (remaining 608 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 553 2.77 - 3.30: 2862 3.30 - 3.83: 4873 3.83 - 4.37: 5694 4.37 - 4.90: 10813 Nonbonded interactions: 24795 Sorted by model distance: nonbonded pdb=" O SER A 443 " pdb=" NH1 ARG A 495 " model vdw 2.235 2.520 nonbonded pdb=" NH1 ARG A 454 " pdb=" OD2 ASP A 464 " model vdw 2.309 2.520 nonbonded pdb=" NE2 GLN L 39 " pdb=" O GLN L 43 " model vdw 2.348 2.520 nonbonded pdb=" NH2 ARG A 451 " pdb=" O SER A 466 " model vdw 2.367 2.520 nonbonded pdb=" OG SER H 106 " pdb=" OD2 ASP H 110 " model vdw 2.380 2.440 ... (remaining 24790 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: 1.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 5.070 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 14.060 Find NCS groups from input model: 0.100 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3470 Z= 0.191 Angle : 0.654 10.006 4713 Z= 0.353 Chirality : 0.045 0.134 501 Planarity : 0.004 0.043 611 Dihedral : 13.665 78.415 1242 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.00 % Favored : 91.76 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -2.07 (0.40), residues: 425 helix: -5.08 (0.53), residues: 8 sheet: -0.52 (0.46), residues: 150 loop : -1.85 (0.36), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 350 HIS 0.002 0.001 HIS A 516 PHE 0.005 0.001 PHE L 99 TYR 0.007 0.001 TYR L 92 ARG 0.005 0.000 ARG A 506 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 0.394 Fit side-chains REVERT: H 46 GLU cc_start: 0.7273 (mt-10) cc_final: 0.7070 (mt-10) REVERT: H 73 ASP cc_start: 0.8043 (t70) cc_final: 0.7605 (t0) REVERT: H 87 ARG cc_start: 0.7965 (mtm-85) cc_final: 0.7756 (mtm180) REVERT: L 5 THR cc_start: 0.9000 (m) cc_final: 0.8764 (p) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.2034 time to fit residues: 19.6840 Evaluate side-chains 64 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 12 optimal weight: 0.1980 chunk 20 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 6 GLN H 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3470 Z= 0.221 Angle : 0.636 12.172 4713 Z= 0.321 Chirality : 0.044 0.132 501 Planarity : 0.004 0.043 611 Dihedral : 4.787 26.912 478 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.76 % Favored : 92.00 % Rotamer: Outliers : 1.91 % Allowed : 7.63 % Favored : 90.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -1.98 (0.41), residues: 425 helix: -5.26 (0.33), residues: 14 sheet: -0.06 (0.48), residues: 142 loop : -1.90 (0.36), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 433 HIS 0.001 0.001 HIS A 516 PHE 0.006 0.001 PHE A 397 TYR 0.014 0.001 TYR L 50 ARG 0.004 0.000 ARG L 46 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 68 time to evaluate : 0.409 Fit side-chains REVERT: H 87 ARG cc_start: 0.8058 (mtm-85) cc_final: 0.7853 (mtm110) REVERT: L 5 THR cc_start: 0.8986 (m) cc_final: 0.8661 (p) REVERT: A 386 ASP cc_start: 0.7417 (t0) cc_final: 0.7138 (t0) outliers start: 7 outliers final: 5 residues processed: 72 average time/residue: 0.2018 time to fit residues: 17.0732 Evaluate side-chains 70 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 65 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain A residue 395 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 0.0060 chunk 25 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 13 optimal weight: 0.0370 chunk 30 optimal weight: 0.0000 chunk 28 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 overall best weight: 0.2878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 62 GLN L 101 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3470 Z= 0.142 Angle : 0.590 12.583 4713 Z= 0.291 Chirality : 0.043 0.124 501 Planarity : 0.004 0.044 611 Dihedral : 4.470 25.168 478 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.29 % Favored : 92.47 % Rotamer: Outliers : 2.45 % Allowed : 10.35 % Favored : 87.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -1.93 (0.40), residues: 425 helix: -5.32 (0.24), residues: 20 sheet: 0.06 (0.49), residues: 140 loop : -1.80 (0.35), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 350 HIS 0.000 0.000 HIS A 516 PHE 0.005 0.001 PHE A 397 TYR 0.009 0.001 TYR A 505 ARG 0.004 0.000 ARG L 46 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 73 time to evaluate : 0.414 Fit side-chains REVERT: H 46 GLU cc_start: 0.7707 (mt-10) cc_final: 0.7429 (mt-10) REVERT: H 87 ARG cc_start: 0.8048 (mtm-85) cc_final: 0.7827 (mtm110) REVERT: H 91 THR cc_start: 0.8270 (OUTLIER) cc_final: 0.7876 (t) REVERT: L 5 THR cc_start: 0.8851 (m) cc_final: 0.8561 (p) REVERT: L 61 ASP cc_start: 0.7224 (t70) cc_final: 0.6819 (t70) REVERT: A 336 ASP cc_start: 0.7692 (OUTLIER) cc_final: 0.7243 (p0) REVERT: A 386 ASP cc_start: 0.7471 (t0) cc_final: 0.7124 (t0) outliers start: 9 outliers final: 5 residues processed: 77 average time/residue: 0.1777 time to fit residues: 16.4118 Evaluate side-chains 74 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 67 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 395 ASP Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 430 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 0.5980 chunk 18 optimal weight: 0.3980 chunk 25 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 36 optimal weight: 0.0170 chunk 10 optimal weight: 4.9990 chunk 33 optimal weight: 0.0050 chunk 23 optimal weight: 0.0980 chunk 0 optimal weight: 4.9990 overall best weight: 0.2232 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 3470 Z= 0.132 Angle : 0.574 12.286 4713 Z= 0.282 Chirality : 0.042 0.124 501 Planarity : 0.004 0.044 611 Dihedral : 4.216 23.671 478 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.29 % Favored : 92.47 % Rotamer: Outliers : 2.45 % Allowed : 13.62 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -1.86 (0.40), residues: 425 helix: -5.31 (0.24), residues: 20 sheet: 0.04 (0.48), residues: 140 loop : -1.70 (0.36), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 350 HIS 0.001 0.000 HIS A 516 PHE 0.009 0.001 PHE A 389 TYR 0.015 0.001 TYR H 100 ARG 0.004 0.000 ARG L 55 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 68 time to evaluate : 0.417 Fit side-chains REVERT: H 2 MET cc_start: 0.5966 (ttp) cc_final: 0.5665 (ttp) REVERT: H 87 ARG cc_start: 0.8018 (mtm-85) cc_final: 0.7772 (mtm110) REVERT: H 91 THR cc_start: 0.8131 (OUTLIER) cc_final: 0.7785 (t) REVERT: L 5 THR cc_start: 0.8915 (m) cc_final: 0.8652 (p) REVERT: L 61 ASP cc_start: 0.7252 (t70) cc_final: 0.6850 (t70) REVERT: A 336 ASP cc_start: 0.7588 (OUTLIER) cc_final: 0.7073 (p0) REVERT: A 337 GLU cc_start: 0.6697 (mp0) cc_final: 0.6212 (mp0) REVERT: A 386 ASP cc_start: 0.7500 (t0) cc_final: 0.7191 (t0) outliers start: 9 outliers final: 5 residues processed: 73 average time/residue: 0.2031 time to fit residues: 17.5368 Evaluate side-chains 74 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 67 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 395 ASP Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 508 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 0.0770 chunk 16 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 20 optimal weight: 0.0170 chunk 36 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 13 optimal weight: 0.1980 chunk 8 optimal weight: 4.9990 chunk 23 optimal weight: 0.1980 overall best weight: 0.2978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 391 ASN ** A 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3470 Z= 0.138 Angle : 0.571 12.206 4713 Z= 0.278 Chirality : 0.041 0.124 501 Planarity : 0.004 0.045 611 Dihedral : 4.102 23.282 478 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.29 % Favored : 92.47 % Rotamer: Outliers : 3.27 % Allowed : 13.62 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -1.73 (0.40), residues: 425 helix: -5.29 (0.25), residues: 20 sheet: -0.04 (0.47), residues: 145 loop : -1.51 (0.36), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 350 HIS 0.001 0.000 HIS A 516 PHE 0.010 0.001 PHE A 389 TYR 0.016 0.001 TYR H 100 ARG 0.004 0.000 ARG L 46 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 70 time to evaluate : 0.395 Fit side-chains REVERT: H 46 GLU cc_start: 0.7693 (mt-10) cc_final: 0.7439 (mt-10) REVERT: H 87 ARG cc_start: 0.8010 (mtm-85) cc_final: 0.7767 (mtm110) REVERT: H 91 THR cc_start: 0.8145 (OUTLIER) cc_final: 0.7778 (t) REVERT: L 5 THR cc_start: 0.8916 (m) cc_final: 0.8669 (p) REVERT: L 61 ASP cc_start: 0.7214 (t70) cc_final: 0.6890 (t70) REVERT: A 336 ASP cc_start: 0.7557 (OUTLIER) cc_final: 0.7286 (p0) REVERT: A 386 ASP cc_start: 0.7503 (t0) cc_final: 0.7259 (t0) outliers start: 12 outliers final: 8 residues processed: 77 average time/residue: 0.1733 time to fit residues: 16.0605 Evaluate side-chains 77 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 67 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 395 ASP Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 508 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 33 optimal weight: 0.4980 chunk 18 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 13 optimal weight: 0.0010 chunk 21 optimal weight: 0.4980 chunk 39 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 overall best weight: 0.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 62 GLN ** A 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3470 Z= 0.165 Angle : 0.600 12.177 4713 Z= 0.296 Chirality : 0.043 0.140 501 Planarity : 0.004 0.044 611 Dihedral : 4.171 23.701 478 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.00 % Favored : 91.76 % Rotamer: Outliers : 2.72 % Allowed : 15.26 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -1.72 (0.40), residues: 425 helix: -5.28 (0.26), residues: 20 sheet: -0.05 (0.47), residues: 145 loop : -1.49 (0.36), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 350 HIS 0.002 0.001 HIS A 516 PHE 0.012 0.001 PHE A 389 TYR 0.016 0.001 TYR H 100 ARG 0.004 0.000 ARG L 46 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 67 time to evaluate : 0.406 Fit side-chains REVERT: H 46 GLU cc_start: 0.7454 (mt-10) cc_final: 0.7216 (mt-10) REVERT: H 87 ARG cc_start: 0.8049 (mtm-85) cc_final: 0.7814 (mtm110) REVERT: H 91 THR cc_start: 0.8366 (OUTLIER) cc_final: 0.7986 (t) REVERT: L 5 THR cc_start: 0.8956 (m) cc_final: 0.8714 (p) REVERT: L 61 ASP cc_start: 0.7347 (t70) cc_final: 0.7073 (t70) REVERT: A 336 ASP cc_start: 0.7670 (p0) cc_final: 0.7425 (p0) REVERT: A 386 ASP cc_start: 0.7522 (t0) cc_final: 0.7291 (t0) outliers start: 10 outliers final: 9 residues processed: 72 average time/residue: 0.1984 time to fit residues: 16.9313 Evaluate side-chains 75 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 65 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain A residue 395 ASP Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 508 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 25 optimal weight: 0.3980 chunk 24 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 7 optimal weight: 0.4980 chunk 27 optimal weight: 0.0040 chunk 20 optimal weight: 1.9990 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3470 Z= 0.162 Angle : 0.578 12.192 4713 Z= 0.286 Chirality : 0.042 0.135 501 Planarity : 0.004 0.046 611 Dihedral : 4.167 23.809 478 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.53 % Favored : 92.24 % Rotamer: Outliers : 3.81 % Allowed : 14.71 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -1.67 (0.40), residues: 425 helix: -5.22 (0.34), residues: 14 sheet: -0.06 (0.47), residues: 145 loop : -1.54 (0.35), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 350 HIS 0.002 0.001 HIS A 516 PHE 0.013 0.001 PHE A 389 TYR 0.016 0.001 TYR H 100 ARG 0.005 0.000 ARG L 46 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 67 time to evaluate : 0.375 Fit side-chains REVERT: H 46 GLU cc_start: 0.7444 (mt-10) cc_final: 0.7215 (mt-10) REVERT: H 87 ARG cc_start: 0.8046 (mtm-85) cc_final: 0.7788 (mtm110) REVERT: H 91 THR cc_start: 0.8384 (OUTLIER) cc_final: 0.8008 (t) REVERT: L 5 THR cc_start: 0.8979 (m) cc_final: 0.8739 (p) REVERT: L 61 ASP cc_start: 0.7309 (t70) cc_final: 0.7045 (t70) REVERT: A 336 ASP cc_start: 0.7610 (p0) cc_final: 0.7368 (p0) REVERT: A 386 ASP cc_start: 0.7545 (t0) cc_final: 0.7309 (t0) outliers start: 14 outliers final: 11 residues processed: 75 average time/residue: 0.1792 time to fit residues: 16.1274 Evaluate side-chains 76 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 64 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain A residue 395 ASP Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 508 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 35 optimal weight: 0.0970 chunk 37 optimal weight: 0.0010 chunk 22 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 62 GLN ** A 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3470 Z= 0.173 Angle : 0.603 12.228 4713 Z= 0.295 Chirality : 0.042 0.132 501 Planarity : 0.004 0.045 611 Dihedral : 4.195 23.717 478 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.29 % Favored : 92.47 % Rotamer: Outliers : 3.54 % Allowed : 16.08 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -1.75 (0.40), residues: 425 helix: -5.27 (0.25), residues: 20 sheet: -0.17 (0.47), residues: 140 loop : -1.42 (0.36), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 350 HIS 0.001 0.001 HIS A 516 PHE 0.014 0.001 PHE A 389 TYR 0.017 0.001 TYR H 100 ARG 0.005 0.000 ARG L 46 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 65 time to evaluate : 0.389 Fit side-chains REVERT: H 46 GLU cc_start: 0.7449 (mt-10) cc_final: 0.7219 (mt-10) REVERT: H 87 ARG cc_start: 0.8051 (mtm-85) cc_final: 0.7771 (mtm110) REVERT: H 91 THR cc_start: 0.8420 (OUTLIER) cc_final: 0.8036 (t) REVERT: L 5 THR cc_start: 0.8995 (m) cc_final: 0.8751 (p) REVERT: A 336 ASP cc_start: 0.7583 (p0) cc_final: 0.7356 (p0) REVERT: A 386 ASP cc_start: 0.7550 (t0) cc_final: 0.7309 (t0) outliers start: 13 outliers final: 12 residues processed: 72 average time/residue: 0.1754 time to fit residues: 15.1429 Evaluate side-chains 78 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 65 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain A residue 366 TYR Chi-restraints excluded: chain A residue 395 ASP Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 508 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.0370 chunk 37 optimal weight: 0.0470 chunk 24 optimal weight: 0.6980 chunk 39 optimal weight: 0.0050 chunk 18 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 41 optimal weight: 0.4980 chunk 38 optimal weight: 0.9990 chunk 33 optimal weight: 0.0770 chunk 3 optimal weight: 4.9990 chunk 25 optimal weight: 0.0980 overall best weight: 0.0528 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 6 GLN H 39 GLN L 39 GLN ** A 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 3470 Z= 0.137 Angle : 0.583 11.586 4713 Z= 0.284 Chirality : 0.042 0.130 501 Planarity : 0.004 0.046 611 Dihedral : 3.953 21.309 478 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.82 % Favored : 92.94 % Rotamer: Outliers : 3.81 % Allowed : 16.35 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -1.54 (0.41), residues: 425 helix: -5.21 (0.24), residues: 20 sheet: 0.37 (0.48), residues: 136 loop : -1.50 (0.36), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 350 HIS 0.001 0.000 HIS A 516 PHE 0.011 0.001 PHE A 389 TYR 0.016 0.001 TYR H 100 ARG 0.005 0.000 ARG L 46 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 71 time to evaluate : 0.403 Fit side-chains REVERT: H 46 GLU cc_start: 0.7597 (mt-10) cc_final: 0.7388 (mt-10) REVERT: H 87 ARG cc_start: 0.8005 (mtm-85) cc_final: 0.7757 (mtm110) REVERT: H 91 THR cc_start: 0.7924 (OUTLIER) cc_final: 0.7562 (t) REVERT: L 5 THR cc_start: 0.8863 (m) cc_final: 0.8599 (p) REVERT: A 389 PHE cc_start: 0.7700 (m-80) cc_final: 0.7435 (m-80) outliers start: 14 outliers final: 11 residues processed: 79 average time/residue: 0.1741 time to fit residues: 16.5356 Evaluate side-chains 77 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 65 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 39 GLN Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain A residue 366 TYR Chi-restraints excluded: chain A residue 395 ASP Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 508 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 10 optimal weight: 0.0970 chunk 30 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 chunk 9 optimal weight: 0.3980 chunk 33 optimal weight: 0.7980 chunk 13 optimal weight: 0.0370 chunk 34 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 overall best weight: 0.3656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 3470 Z= 0.156 Angle : 0.590 11.533 4713 Z= 0.292 Chirality : 0.042 0.132 501 Planarity : 0.004 0.045 611 Dihedral : 3.960 22.022 478 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.82 % Favored : 92.94 % Rotamer: Outliers : 2.72 % Allowed : 17.44 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -1.50 (0.41), residues: 425 helix: -5.24 (0.25), residues: 20 sheet: 0.10 (0.47), residues: 147 loop : -1.34 (0.37), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 350 HIS 0.001 0.000 HIS A 516 PHE 0.013 0.001 PHE A 389 TYR 0.017 0.001 TYR H 100 ARG 0.004 0.000 ARG L 46 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 65 time to evaluate : 0.391 Fit side-chains REVERT: H 46 GLU cc_start: 0.7638 (mt-10) cc_final: 0.7428 (mt-10) REVERT: H 87 ARG cc_start: 0.8040 (mtm-85) cc_final: 0.7783 (mtm110) REVERT: H 91 THR cc_start: 0.8171 (OUTLIER) cc_final: 0.7819 (t) REVERT: L 5 THR cc_start: 0.8912 (m) cc_final: 0.8645 (p) outliers start: 10 outliers final: 9 residues processed: 70 average time/residue: 0.1823 time to fit residues: 15.2409 Evaluate side-chains 75 residues out of total 367 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 65 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain A residue 366 TYR Chi-restraints excluded: chain A residue 395 ASP Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 508 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 2.9990 chunk 1 optimal weight: 0.1980 chunk 24 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 25 optimal weight: 0.0870 chunk 16 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 39 GLN ** A 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.090553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.071045 restraints weight = 7596.932| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 3.71 r_work: 0.2807 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3470 Z= 0.176 Angle : 0.611 11.747 4713 Z= 0.301 Chirality : 0.043 0.133 501 Planarity : 0.004 0.046 611 Dihedral : 4.106 23.823 478 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.06 % Favored : 92.71 % Rotamer: Outliers : 3.00 % Allowed : 17.17 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: -1.49 (0.41), residues: 425 helix: -5.25 (0.26), residues: 20 sheet: 0.12 (0.47), residues: 147 loop : -1.34 (0.36), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 350 HIS 0.002 0.001 HIS A 516 PHE 0.013 0.001 PHE A 389 TYR 0.017 0.001 TYR H 100 ARG 0.004 0.000 ARG L 46 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1362.18 seconds wall clock time: 25 minutes 0.36 seconds (1500.36 seconds total)