Starting phenix.real_space_refine on Thu Dec 7 16:53:50 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e3c_30979/12_2023/7e3c_30979.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e3c_30979/12_2023/7e3c_30979.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e3c_30979/12_2023/7e3c_30979.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e3c_30979/12_2023/7e3c_30979.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e3c_30979/12_2023/7e3c_30979.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e3c_30979/12_2023/7e3c_30979.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 15 5.16 5 C 1865 2.51 5 N 493 2.21 5 O 564 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 357": "NH1" <-> "NH2" Residue "C GLU 106": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 2937 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1536 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 10, 'TRANS': 183} Chain: "C" Number of atoms: 655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 655 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 7, 'TRANS': 94} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 128 Unresolved non-hydrogen angles: 160 Unresolved non-hydrogen dihedrals: 104 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 4, 'PHE:plan': 3, 'ARG:plan': 3, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 56 Chain: "B" Number of atoms: 732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 732 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 2, 'TRANS': 106} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 46 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.20, per 1000 atoms: 0.75 Number of scatterers: 2937 At special positions: 0 Unit cell: (64.133, 56.524, 95.656, 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 15 16.00 O 564 8.00 N 493 7.00 C 1865 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.05 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 95 " 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 Links applied NAG-ASN " NAG A 601 " - " ASN A 343 " Time building additional restraints: 1.18 Conformation dependent library (CDL) restraints added in 802.1 milliseconds 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 732 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 9 sheets defined 9.9% alpha, 26.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.962A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 370 removed outlier: 3.880A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 408 removed outlier: 4.456A pdb=" N ARG A 408 " --> pdb=" O GLY A 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 404 through 408' Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'C' and resid 57 through 61 removed outlier: 4.282A pdb=" N ARG C 61 " --> pdb=" O VAL C 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 90 Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA2, first strand: chain 'A' and resid 361 through 362 removed outlier: 7.206A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'C' and resid 5 through 6 Processing sheet with id=AA5, first strand: chain 'C' and resid 11 through 13 Processing sheet with id=AA6, first strand: chain 'C' and resid 45 through 48 removed outlier: 6.173A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 18 through 23 removed outlier: 3.613A pdb=" N TYR B 79 " --> pdb=" O ILE B 69 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 57 through 59 removed outlier: 4.167A pdb=" N TYR B 33 " --> pdb=" O ASP B 98 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ALA B 96 " --> pdb=" O THR B 35 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ARG B 97 " --> pdb=" O ASP B 105 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 57 through 59 92 hydrogen bonds defined for protein. 222 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: 0.80 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: 1.22 - 1.52: 2204 1.52 - 1.81: 801 1.81 - 2.11: 2 2.11 - 2.40: 0 2.40 - 2.69: 1 Bond restraints: 3008 Sorted by residual: bond pdb=" C HIS B 72 " pdb=" N ASN B 76 " ideal model delta sigma weight residual 1.332 2.695 -1.362 1.40e-02 5.10e+03 9.47e+03 bond pdb=" CA ILE B 69 " pdb=" CB ILE B 69 " ideal model delta sigma weight residual 1.551 1.530 0.020 1.08e-02 8.57e+03 3.50e+00 bond pdb=" N ARG B 71 " pdb=" CA ARG B 71 " ideal model delta sigma weight residual 1.457 1.482 -0.024 1.29e-02 6.01e+03 3.49e+00 bond pdb=" N HIS B 72 " pdb=" CA HIS B 72 " ideal model delta sigma weight residual 1.461 1.483 -0.022 1.20e-02 6.94e+03 3.22e+00 bond pdb=" C PRO C 95 " pdb=" N PRO C 96 " ideal model delta sigma weight residual 1.334 1.373 -0.039 2.34e-02 1.83e+03 2.74e+00 ... (remaining 3003 not shown) Histogram of bond angle deviations from ideal: 66.92 - 84.79: 2 84.79 - 102.66: 10 102.66 - 120.54: 2800 120.54 - 138.41: 1298 138.41 - 156.28: 1 Bond angle restraints: 4111 Sorted by residual: angle pdb=" O HIS B 72 " pdb=" C HIS B 72 " pdb=" N ASN B 76 " ideal model delta sigma weight residual 123.26 70.41 52.85 1.24e+00 6.50e-01 1.82e+03 angle pdb=" CA HIS B 72 " pdb=" C HIS B 72 " pdb=" N ASN B 76 " ideal model delta sigma weight residual 116.71 66.92 49.79 1.30e+00 5.92e-01 1.47e+03 angle pdb=" C HIS B 72 " pdb=" N ASN B 76 " pdb=" CA ASN B 76 " ideal model delta sigma weight residual 121.54 156.28 -34.74 1.91e+00 2.74e-01 3.31e+02 angle pdb=" N PRO C 59 " pdb=" CA PRO C 59 " pdb=" CB PRO C 59 " ideal model delta sigma weight residual 103.20 110.16 -6.96 9.50e-01 1.11e+00 5.37e+01 angle pdb=" N PRO B 14 " pdb=" CA PRO B 14 " pdb=" CB PRO B 14 " ideal model delta sigma weight residual 103.25 110.58 -7.33 1.05e+00 9.07e-01 4.87e+01 ... (remaining 4106 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.30: 1559 17.30 - 34.61: 154 34.61 - 51.91: 21 51.91 - 69.21: 7 69.21 - 86.51: 2 Dihedral angle restraints: 1743 sinusoidal: 581 harmonic: 1162 Sorted by residual: dihedral pdb=" CA HIS B 72 " pdb=" C HIS B 72 " pdb=" N ASN B 76 " pdb=" CA ASN B 76 " ideal model delta harmonic sigma weight residual -180.00 -117.44 -62.56 0 5.00e+00 4.00e-02 1.57e+02 dihedral pdb=" CB CYS A 379 " pdb=" SG CYS A 379 " pdb=" SG CYS A 432 " pdb=" CB CYS A 432 " ideal model delta sinusoidal sigma weight residual 93.00 37.09 55.91 1 1.00e+01 1.00e-02 4.22e+01 dihedral pdb=" CB CYS B 22 " pdb=" SG CYS B 22 " pdb=" SG CYS B 95 " pdb=" CB CYS B 95 " ideal model delta sinusoidal sigma weight residual 93.00 148.00 -55.00 1 1.00e+01 1.00e-02 4.09e+01 ... (remaining 1740 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 331 0.052 - 0.104: 97 0.104 - 0.156: 18 0.156 - 0.208: 3 0.208 - 0.260: 3 Chirality restraints: 452 Sorted by residual: chirality pdb=" CA PRO C 59 " pdb=" N PRO C 59 " pdb=" C PRO C 59 " pdb=" CB PRO C 59 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" C1 NAG A 601 " pdb=" ND2 ASN A 343 " pdb=" C2 NAG A 601 " pdb=" O5 NAG A 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CA PRO C 8 " pdb=" N PRO C 8 " pdb=" C PRO C 8 " pdb=" CB PRO C 8 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.21 2.00e-01 2.50e+01 1.09e+00 ... (remaining 449 not shown) Planarity restraints: 541 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS B 72 " 0.184 2.00e-02 2.50e+03 2.33e-01 5.43e+02 pdb=" C HIS B 72 " -0.351 2.00e-02 2.50e+03 pdb=" O HIS B 72 " 0.235 2.00e-02 2.50e+03 pdb=" N ASN B 76 " -0.069 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR C 94 " 0.056 5.00e-02 4.00e+02 8.55e-02 1.17e+01 pdb=" N PRO C 95 " -0.148 5.00e-02 4.00e+02 pdb=" CA PRO C 95 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO C 95 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 36 " -0.019 2.00e-02 2.50e+03 1.44e-02 5.15e+00 pdb=" CG TRP B 36 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 TRP B 36 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP B 36 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 36 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 36 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 36 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 36 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 36 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP B 36 " -0.002 2.00e-02 2.50e+03 ... (remaining 538 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 136 2.70 - 3.25: 3043 3.25 - 3.80: 4610 3.80 - 4.35: 5626 4.35 - 4.90: 9487 Nonbonded interactions: 22902 Sorted by model distance: nonbonded pdb=" NH1 ARG A 457 " pdb=" O SER A 459 " model vdw 2.151 2.520 nonbonded pdb=" O LEU B 99 " pdb=" N TYR B 102 " model vdw 2.203 2.520 nonbonded pdb=" NZ LYS A 417 " pdb=" OD2 ASP B 100 " model vdw 2.233 2.520 nonbonded pdb=" O LEU A 455 " pdb=" OH TYR B 33 " model vdw 2.253 2.440 nonbonded pdb=" O ASP C 17 " pdb=" N LEU C 78 " model vdw 2.272 2.520 ... (remaining 22897 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 6.550 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 13.430 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 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 : 0.026 1.362 3008 Z= 0.913 Angle : 1.552 52.846 4111 Z= 1.075 Chirality : 0.053 0.260 452 Planarity : 0.012 0.233 540 Dihedral : 13.929 86.511 996 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 21.49 Ramachandran Plot: Outliers : 0.51 % Allowed : 17.22 % Favored : 82.28 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.63 (0.39), residues: 395 helix: -3.32 (0.69), residues: 34 sheet: -1.46 (0.48), residues: 119 loop : -2.92 (0.37), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP B 36 HIS 0.002 0.001 HIS A 519 PHE 0.015 0.002 PHE A 342 TYR 0.022 0.002 TYR A 453 ARG 0.005 0.001 ARG B 97 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 0.364 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.1812 time to fit residues: 9.8354 Evaluate side-chains 40 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.348 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 0.8980 chunk 29 optimal weight: 6.9990 chunk 16 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 19 optimal weight: 9.9990 chunk 15 optimal weight: 0.5980 chunk 30 optimal weight: 8.9990 chunk 11 optimal weight: 0.9990 chunk 18 optimal weight: 0.3980 chunk 22 optimal weight: 0.6980 chunk 35 optimal weight: 7.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.1028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 3008 Z= 0.230 Angle : 0.699 10.322 4111 Z= 0.364 Chirality : 0.047 0.170 452 Planarity : 0.005 0.056 540 Dihedral : 6.611 46.956 463 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 16.75 Ramachandran Plot: Outliers : 0.25 % Allowed : 13.60 % Favored : 86.15 % Rotamer: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % 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: -3.44 (0.39), residues: 397 helix: -3.02 (0.68), residues: 40 sheet: -1.40 (0.48), residues: 116 loop : -2.73 (0.36), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 36 HIS 0.001 0.001 HIS A 519 PHE 0.008 0.001 PHE A 342 TYR 0.011 0.001 TYR A 453 ARG 0.002 0.000 ARG A 457 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.1318 time to fit residues: 8.4630 Evaluate side-chains 42 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.336 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 19 optimal weight: 0.0980 chunk 10 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 24 optimal weight: 9.9990 chunk 9 optimal weight: 0.5980 chunk 35 optimal weight: 10.0000 chunk 38 optimal weight: 0.9990 chunk 31 optimal weight: 0.0870 chunk 12 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 chunk 26 optimal weight: 4.9990 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 3008 Z= 0.209 Angle : 0.676 9.254 4111 Z= 0.353 Chirality : 0.047 0.158 452 Planarity : 0.005 0.083 540 Dihedral : 5.939 27.555 463 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.34 % Favored : 87.66 % Rotamer: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % 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: -3.36 (0.39), residues: 397 helix: -3.24 (0.71), residues: 34 sheet: -1.31 (0.48), residues: 117 loop : -2.67 (0.35), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 107 HIS 0.001 0.001 HIS A 519 PHE 0.010 0.001 PHE A 377 TYR 0.014 0.001 TYR A 489 ARG 0.002 0.000 ARG A 457 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.366 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.1377 time to fit residues: 9.4277 Evaluate side-chains 45 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 0.362 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 18 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 16 optimal weight: 0.0570 chunk 23 optimal weight: 2.9990 chunk 35 optimal weight: 8.9990 chunk 37 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 31 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 0 optimal weight: 1.9990 overall best weight: 1.1102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 ASN ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 3008 Z= 0.334 Angle : 0.737 11.172 4111 Z= 0.383 Chirality : 0.047 0.161 452 Planarity : 0.005 0.067 540 Dihedral : 6.035 24.707 463 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 17.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.62 % Favored : 84.38 % Rotamer: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.36 (0.39), residues: 397 helix: -3.12 (0.63), residues: 40 sheet: -1.20 (0.48), residues: 110 loop : -2.70 (0.36), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 107 HIS 0.003 0.002 HIS A 519 PHE 0.008 0.001 PHE A 342 TYR 0.016 0.002 TYR A 453 ARG 0.003 0.000 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.1613 time to fit residues: 10.0006 Evaluate side-chains 42 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.353 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 28 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 0 optimal weight: 1.9990 chunk 19 optimal weight: 6.9990 chunk 33 optimal weight: 0.9990 chunk 9 optimal weight: 0.2980 chunk 12 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 3008 Z= 0.260 Angle : 0.708 10.610 4111 Z= 0.368 Chirality : 0.047 0.180 452 Planarity : 0.005 0.059 540 Dihedral : 5.754 24.815 463 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 18.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.60 % Favored : 86.40 % Rotamer: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % 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: -3.27 (0.39), residues: 397 helix: -3.05 (0.65), residues: 40 sheet: -1.25 (0.48), residues: 114 loop : -2.59 (0.37), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 36 HIS 0.002 0.001 HIS A 519 PHE 0.009 0.001 PHE A 377 TYR 0.013 0.001 TYR A 453 ARG 0.004 0.000 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.1752 time to fit residues: 11.1503 Evaluate side-chains 44 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 0.400 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 9 optimal weight: 0.4980 chunk 37 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 19 optimal weight: 9.9990 chunk 36 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 3008 Z= 0.259 Angle : 0.699 10.417 4111 Z= 0.361 Chirality : 0.047 0.167 452 Planarity : 0.005 0.055 540 Dihedral : 5.595 25.831 463 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 16.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.36 % Favored : 85.64 % Rotamer: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % 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: -3.26 (0.39), residues: 397 helix: -3.07 (0.63), residues: 40 sheet: -1.36 (0.47), residues: 116 loop : -2.52 (0.38), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 36 HIS 0.002 0.002 HIS A 519 PHE 0.006 0.001 PHE A 464 TYR 0.013 0.001 TYR A 453 ARG 0.002 0.000 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.348 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.1572 time to fit residues: 9.9369 Evaluate side-chains 43 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 0.325 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 21 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 22 optimal weight: 0.5980 chunk 17 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 chunk 7 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 3008 Z= 0.247 Angle : 0.700 9.105 4111 Z= 0.365 Chirality : 0.047 0.163 452 Planarity : 0.004 0.054 540 Dihedral : 5.585 23.984 463 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 18.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.10 % Favored : 86.90 % Rotamer: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % 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: -3.22 (0.39), residues: 397 helix: -3.13 (0.59), residues: 40 sheet: -1.35 (0.47), residues: 116 loop : -2.45 (0.38), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 36 HIS 0.002 0.001 HIS A 519 PHE 0.010 0.001 PHE A 377 TYR 0.021 0.002 TYR A 365 ARG 0.002 0.000 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.1426 time to fit residues: 9.0418 Evaluate side-chains 41 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.375 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 34 optimal weight: 0.2980 chunk 36 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 21 optimal weight: 0.0070 chunk 15 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 31 optimal weight: 0.0270 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 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3008 Z= 0.176 Angle : 0.675 8.494 4111 Z= 0.347 Chirality : 0.046 0.207 452 Planarity : 0.004 0.052 540 Dihedral : 5.340 25.355 463 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.59 % Favored : 88.41 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % 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: -3.06 (0.40), residues: 397 helix: -3.30 (0.65), residues: 34 sheet: -1.28 (0.47), residues: 120 loop : -2.33 (0.38), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.003 TRP B 36 HIS 0.001 0.001 HIS A 519 PHE 0.007 0.001 PHE A 377 TYR 0.012 0.001 TYR A 365 ARG 0.002 0.000 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.1632 time to fit residues: 10.1285 Evaluate side-chains 43 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 0.330 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 33 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 37 optimal weight: 0.0980 chunk 22 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 25 optimal weight: 10.0000 chunk 38 optimal weight: 0.5980 chunk 35 optimal weight: 3.9990 chunk 30 optimal weight: 7.9990 chunk 3 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3008 Z= 0.209 Angle : 0.676 8.940 4111 Z= 0.346 Chirality : 0.046 0.152 452 Planarity : 0.004 0.051 540 Dihedral : 5.294 23.833 463 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 16.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.84 % Favored : 88.16 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % 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: -3.05 (0.39), residues: 397 helix: -3.06 (0.63), residues: 40 sheet: -1.22 (0.47), residues: 119 loop : -2.35 (0.38), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP B 36 HIS 0.002 0.001 HIS A 519 PHE 0.010 0.001 PHE A 377 TYR 0.012 0.001 TYR A 365 ARG 0.003 0.000 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.1392 time to fit residues: 8.9022 Evaluate side-chains 42 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.334 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 23 optimal weight: 0.4980 chunk 18 optimal weight: 0.4980 chunk 24 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 9 optimal weight: 0.4980 chunk 28 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 30 optimal weight: 9.9990 chunk 12 optimal weight: 0.2980 chunk 31 optimal weight: 0.7980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3008 Z= 0.201 Angle : 0.669 9.226 4111 Z= 0.345 Chirality : 0.045 0.151 452 Planarity : 0.004 0.049 540 Dihedral : 5.292 26.401 463 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 15.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.09 % Favored : 87.91 % Rotamer: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % 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: -3.00 (0.40), residues: 397 helix: -3.18 (0.67), residues: 34 sheet: -1.23 (0.47), residues: 120 loop : -2.30 (0.38), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP B 36 HIS 0.002 0.001 HIS A 519 PHE 0.008 0.001 PHE A 377 TYR 0.011 0.001 TYR A 453 ARG 0.003 0.000 ARG A 346 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 794 Ramachandran restraints generated. 397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.1449 time to fit residues: 9.1411 Evaluate side-chains 41 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.347 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 0.9990 chunk 5 optimal weight: 0.0270 chunk 27 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 22 optimal weight: 0.5980 chunk 35 optimal weight: 7.9990 chunk 20 optimal weight: 5.9990 chunk 26 optimal weight: 0.5980 chunk 24 optimal weight: 10.0000 chunk 23 optimal weight: 0.0970 chunk 15 optimal weight: 0.9990 overall best weight: 0.4436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 GLN B 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.063604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.053558 restraints weight = 11702.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.055340 restraints weight = 6999.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.056726 restraints weight = 4772.386| |-----------------------------------------------------------------------------| r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3008 Z= 0.188 Angle : 0.663 9.461 4111 Z= 0.340 Chirality : 0.045 0.136 452 Planarity : 0.004 0.050 540 Dihedral : 5.321 24.167 463 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.83 % Favored : 89.17 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % 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: -2.97 (0.40), residues: 397 helix: -3.22 (0.66), residues: 34 sheet: -1.21 (0.47), residues: 120 loop : -2.28 (0.38), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 36 HIS 0.002 0.001 HIS A 519 PHE 0.011 0.001 PHE A 347 TYR 0.010 0.001 TYR A 365 ARG 0.008 0.001 ARG A 457 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1126.51 seconds wall clock time: 21 minutes 12.89 seconds (1272.89 seconds total)