Starting phenix.real_space_refine on Tue Feb 13 04:15:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e3c_30979/02_2024/7e3c_30979.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e3c_30979/02_2024/7e3c_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_30979/02_2024/7e3c_30979.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e3c_30979/02_2024/7e3c_30979.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e3c_30979/02_2024/7e3c_30979.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e3c_30979/02_2024/7e3c_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-dev-5238/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: 2.33, per 1000 atoms: 0.79 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: 1.13 Conformation dependent library (CDL) restraints added in 562.0 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: 0.35 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: 0.70 Time building geometry restraints manager: 1.24 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: 1.340 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: 6.440 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.150 Find NCS groups from input model: 0.080 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: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.920 ------------------------------------------------------------------------------- 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 : 0.345 Fit side-chains revert: symmetry clash REVERT: A 386 LYS cc_start: 0.8126 (mtmm) cc_final: 0.7756 (mtmm) REVERT: A 405 ASP cc_start: 0.8591 (m-30) cc_final: 0.8280 (m-30) REVERT: A 406 GLU cc_start: 0.8704 (pt0) cc_final: 0.8420 (pt0) REVERT: A 474 GLN cc_start: 0.6423 (tp-100) cc_final: 0.6205 (tp-100) REVERT: B 45 LEU cc_start: 0.8621 (mt) cc_final: 0.8137 (mt) REVERT: B 104 MET cc_start: 0.7456 (mtp) cc_final: 0.7089 (mtm) outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.1882 time to fit residues: 10.1592 Evaluate side-chains 41 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.339 ------------------------------------------------------------------------------- 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: 0.9980 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: 6.9990 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: 0.7835 moved from start: 0.1042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 3008 Z= 0.230 Angle : 0.696 10.237 4111 Z= 0.362 Chirality : 0.047 0.168 452 Planarity : 0.005 0.056 540 Dihedral : 6.575 46.364 463 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 16.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.11 % Favored : 85.89 % 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: -3.03 (0.67), residues: 40 sheet: -1.40 (0.48), residues: 116 loop : -2.72 (0.37), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 36 HIS 0.001 0.001 HIS A 519 PHE 0.008 0.001 PHE A 342 TYR 0.012 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 53 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 386 LYS cc_start: 0.8115 (mtmm) cc_final: 0.7638 (mtmm) REVERT: A 405 ASP cc_start: 0.8468 (m-30) cc_final: 0.8118 (m-30) REVERT: A 474 GLN cc_start: 0.6737 (tp-100) cc_final: 0.6525 (tp-100) REVERT: C 31 ASN cc_start: 0.9030 (m-40) cc_final: 0.8800 (m-40) REVERT: C 49 TYR cc_start: 0.6354 (m-10) cc_final: 0.6058 (m-10) REVERT: B 27 LEU cc_start: 0.6292 (tp) cc_final: 0.6049 (tp) REVERT: B 45 LEU cc_start: 0.8568 (mt) cc_final: 0.8097 (mt) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.1310 time to fit residues: 8.7598 Evaluate side-chains 45 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 0.358 ------------------------------------------------------------------------------- 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: 9.9990 chunk 10 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 24 optimal weight: 10.0000 chunk 9 optimal weight: 0.3980 chunk 35 optimal weight: 7.9990 chunk 38 optimal weight: 1.9990 chunk 31 optimal weight: 0.0170 chunk 12 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 overall best weight: 1.0422 ------------------------------------------------------------------------------- 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: 0.7866 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 3008 Z= 0.324 Angle : 0.731 11.113 4111 Z= 0.381 Chirality : 0.048 0.171 452 Planarity : 0.006 0.085 540 Dihedral : 6.465 35.823 463 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 18.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.11 % Favored : 84.89 % Rotamer: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % 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: -3.48 (0.39), residues: 397 helix: -2.91 (0.72), residues: 40 sheet: -1.38 (0.49), residues: 110 loop : -2.79 (0.35), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP B 107 HIS 0.002 0.002 HIS A 519 PHE 0.010 0.001 PHE A 342 TYR 0.023 0.002 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 51 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 386 LYS cc_start: 0.8104 (mtmm) cc_final: 0.7606 (mtmm) REVERT: A 405 ASP cc_start: 0.8429 (m-30) cc_final: 0.8042 (m-30) REVERT: A 406 GLU cc_start: 0.9031 (pt0) cc_final: 0.8756 (pt0) REVERT: A 474 GLN cc_start: 0.6716 (tp-100) cc_final: 0.6487 (tp-100) REVERT: B 27 LEU cc_start: 0.6350 (tp) cc_final: 0.5909 (tp) REVERT: B 45 LEU cc_start: 0.8609 (mt) cc_final: 0.8082 (mt) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.1350 time to fit residues: 8.6358 Evaluate side-chains 42 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.348 ------------------------------------------------------------------------------- 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: 0.4980 chunk 3 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 35 optimal weight: 8.9990 chunk 37 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 31 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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: 0.7837 moved from start: 0.1520 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= 0.239 Angle : 0.690 10.172 4111 Z= 0.359 Chirality : 0.046 0.155 452 Planarity : 0.005 0.071 540 Dihedral : 5.785 23.471 463 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 16.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.11 % Favored : 85.89 % Rotamer: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % 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: -3.34 (0.39), residues: 397 helix: -2.94 (0.71), residues: 40 sheet: -1.29 (0.48), residues: 116 loop : -2.68 (0.37), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 107 HIS 0.002 0.001 HIS A 519 PHE 0.007 0.001 PHE A 347 TYR 0.014 0.001 TYR C 94 ARG 0.001 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 53 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 0.354 Fit side-chains revert: symmetry clash REVERT: A 405 ASP cc_start: 0.8412 (m-30) cc_final: 0.7991 (m-30) REVERT: A 406 GLU cc_start: 0.9016 (pt0) cc_final: 0.8644 (pt0) REVERT: A 474 GLN cc_start: 0.6716 (tp-100) cc_final: 0.6442 (tp-100) REVERT: B 27 LEU cc_start: 0.6369 (tp) cc_final: 0.5966 (tp) REVERT: B 45 LEU cc_start: 0.8567 (mt) cc_final: 0.8042 (mt) REVERT: B 98 ASP cc_start: 0.7855 (m-30) cc_final: 0.7427 (m-30) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.1884 time to fit residues: 11.9632 Evaluate side-chains 44 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 0.381 ------------------------------------------------------------------------------- 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: 3.9990 chunk 15 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 chunk 26 optimal weight: 5.9990 chunk 0 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 chunk 9 optimal weight: 0.4980 chunk 12 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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: 0.7873 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 3008 Z= 0.310 Angle : 0.721 10.947 4111 Z= 0.376 Chirality : 0.048 0.177 452 Planarity : 0.005 0.058 540 Dihedral : 5.839 24.991 463 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 17.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.37 % Favored : 84.63 % Rotamer: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % 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: -3.44 (0.39), residues: 397 helix: -3.00 (0.69), residues: 40 sheet: -1.44 (0.47), residues: 116 loop : -2.70 (0.37), residues: 241 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 377 TYR 0.013 0.001 TYR B 33 ARG 0.003 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 53 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 405 ASP cc_start: 0.8480 (m-30) cc_final: 0.8053 (m-30) REVERT: A 406 GLU cc_start: 0.8959 (pt0) cc_final: 0.8592 (pt0) REVERT: B 27 LEU cc_start: 0.6672 (tp) cc_final: 0.6246 (tp) REVERT: B 45 LEU cc_start: 0.8628 (mt) cc_final: 0.8077 (mt) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.1402 time to fit residues: 9.2445 Evaluate side-chains 43 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 0.365 ------------------------------------------------------------------------------- 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: 0.9990 chunk 37 optimal weight: 0.8980 chunk 31 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 chunk 3 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 19 optimal weight: 10.0000 chunk 36 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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: 0.7845 moved from start: 0.1790 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= 0.262 Angle : 0.699 10.600 4111 Z= 0.364 Chirality : 0.047 0.169 452 Planarity : 0.005 0.062 540 Dihedral : 5.659 25.646 463 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 17.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.36 % Favored : 85.64 % Rotamer: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % 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: -3.30 (0.39), residues: 397 helix: -3.00 (0.68), residues: 40 sheet: -1.37 (0.47), residues: 116 loop : -2.57 (0.37), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP B 36 HIS 0.002 0.001 HIS A 519 PHE 0.006 0.001 PHE A 377 TYR 0.012 0.001 TYR B 33 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 50 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 386 LYS cc_start: 0.8016 (mtmm) cc_final: 0.7475 (mtmm) REVERT: A 405 ASP cc_start: 0.8489 (m-30) cc_final: 0.8094 (m-30) REVERT: A 406 GLU cc_start: 0.9025 (pt0) cc_final: 0.8617 (pt0) REVERT: B 27 LEU cc_start: 0.6781 (tp) cc_final: 0.6336 (tp) REVERT: B 46 GLU cc_start: 0.8053 (mm-30) cc_final: 0.7839 (mm-30) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.1423 time to fit residues: 8.8716 Evaluate side-chains 43 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 0.343 ------------------------------------------------------------------------------- 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: 4.9990 chunk 31 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 17 optimal weight: 0.5980 chunk 15 optimal weight: 0.8980 chunk 11 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 18 optimal weight: 0.2980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 3008 Z= 0.212 Angle : 0.675 8.811 4111 Z= 0.350 Chirality : 0.046 0.160 452 Planarity : 0.005 0.054 540 Dihedral : 5.465 23.823 463 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 17.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.85 % Favored : 87.15 % 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: -3.18 (0.39), residues: 397 helix: -3.09 (0.63), residues: 40 sheet: -1.28 (0.47), residues: 119 loop : -2.47 (0.38), residues: 238 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 0.007 0.001 PHE A 377 TYR 0.021 0.001 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 52 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.333 Fit side-chains revert: symmetry clash REVERT: A 386 LYS cc_start: 0.8426 (mtmm) cc_final: 0.7878 (mtmm) REVERT: A 405 ASP cc_start: 0.8487 (m-30) cc_final: 0.8053 (m-30) REVERT: A 406 GLU cc_start: 0.8930 (pt0) cc_final: 0.8446 (pt0) REVERT: B 27 LEU cc_start: 0.6859 (tp) cc_final: 0.6388 (tp) REVERT: B 45 LEU cc_start: 0.8561 (mt) cc_final: 0.8013 (mt) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.1637 time to fit residues: 10.2844 Evaluate side-chains 43 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 0.341 ------------------------------------------------------------------------------- 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: 1.9990 chunk 29 optimal weight: 0.1980 chunk 34 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 31 optimal weight: 0.0170 overall best weight: 0.6220 ------------------------------------------------------------------------------- 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: 0.7818 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 3008 Z= 0.224 Angle : 0.689 8.519 4111 Z= 0.355 Chirality : 0.047 0.206 452 Planarity : 0.005 0.057 540 Dihedral : 5.513 25.819 463 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 15.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.35 % Favored : 86.65 % 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: -3.10 (0.40), residues: 397 helix: -3.04 (0.64), residues: 40 sheet: -1.21 (0.47), residues: 119 loop : -2.42 (0.38), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 107 HIS 0.002 0.001 HIS A 519 PHE 0.011 0.001 PHE A 377 TYR 0.014 0.001 TYR A 453 ARG 0.003 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 53 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 386 LYS cc_start: 0.8434 (mtmm) cc_final: 0.7883 (mtmm) REVERT: A 405 ASP cc_start: 0.8488 (m-30) cc_final: 0.8083 (m-30) REVERT: A 406 GLU cc_start: 0.8864 (pt0) cc_final: 0.8408 (pt0) REVERT: A 474 GLN cc_start: 0.6747 (tp-100) cc_final: 0.6532 (tp-100) REVERT: B 45 LEU cc_start: 0.8536 (mt) cc_final: 0.7975 (mt) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.1422 time to fit residues: 9.3148 Evaluate side-chains 42 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.339 ------------------------------------------------------------------------------- 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: 1.9990 chunk 34 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 25 optimal weight: 10.0000 chunk 38 optimal weight: 0.5980 chunk 35 optimal weight: 4.9990 chunk 30 optimal weight: 7.9990 chunk 3 optimal weight: 0.8980 overall best weight: 1.0986 ------------------------------------------------------------------------------- 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: 0.7860 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 3008 Z= 0.330 Angle : 0.736 9.779 4111 Z= 0.381 Chirality : 0.047 0.167 452 Planarity : 0.005 0.052 540 Dihedral : 5.709 23.486 463 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 18.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.37 % Favored : 84.63 % 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: -3.18 (0.39), residues: 397 helix: -3.00 (0.67), residues: 39 sheet: -1.13 (0.48), residues: 110 loop : -2.54 (0.37), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.004 TRP B 36 HIS 0.003 0.002 HIS A 519 PHE 0.006 0.001 PHE A 342 TYR 0.018 0.002 TYR A 453 ARG 0.002 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 47 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 386 LYS cc_start: 0.8557 (mtmm) cc_final: 0.8010 (mtmm) REVERT: A 405 ASP cc_start: 0.8524 (m-30) cc_final: 0.8118 (m-30) REVERT: A 406 GLU cc_start: 0.8861 (pt0) cc_final: 0.8440 (pt0) REVERT: B 45 LEU cc_start: 0.8592 (mt) cc_final: 0.8010 (mt) outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.1362 time to fit residues: 8.1139 Evaluate side-chains 39 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.343 ------------------------------------------------------------------------------- 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: 0.9980 chunk 18 optimal weight: 0.8980 chunk 24 optimal weight: 0.0050 chunk 32 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 28 optimal weight: 0.0970 chunk 4 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 30 optimal weight: 10.0000 chunk 12 optimal weight: 0.7980 chunk 31 optimal weight: 0.0270 overall best weight: 0.3050 ------------------------------------------------------------------------------- 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: 0.7788 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= 0.167 Angle : 0.661 8.865 4111 Z= 0.341 Chirality : 0.045 0.149 452 Planarity : 0.005 0.056 540 Dihedral : 5.327 24.975 463 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.59 % Favored : 88.41 % 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: -2.99 (0.40), residues: 397 helix: -3.19 (0.71), residues: 34 sheet: -1.17 (0.47), residues: 120 loop : -2.33 (0.37), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.003 TRP B 36 HIS 0.001 0.001 HIS A 519 PHE 0.009 0.001 PHE A 377 TYR 0.010 0.001 TYR A 365 ARG 0.002 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 53 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 386 LYS cc_start: 0.8488 (mtmm) cc_final: 0.7945 (mtmm) REVERT: A 405 ASP cc_start: 0.8513 (m-30) cc_final: 0.8067 (m-30) REVERT: A 406 GLU cc_start: 0.8918 (pt0) cc_final: 0.8330 (pt0) REVERT: A 474 GLN cc_start: 0.6755 (tp-100) cc_final: 0.6421 (tp-100) REVERT: B 45 LEU cc_start: 0.8485 (mt) cc_final: 0.7963 (mt) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.1308 time to fit residues: 8.7522 Evaluate side-chains 42 residues out of total 340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.348 ------------------------------------------------------------------------------- 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: 1.9990 chunk 5 optimal weight: 0.0060 chunk 27 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 35 optimal weight: 4.9990 chunk 20 optimal weight: 9.9990 chunk 26 optimal weight: 1.9990 chunk 24 optimal weight: 10.0000 chunk 23 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 overall best weight: 0.9602 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.061271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.051477 restraints weight = 11946.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.053207 restraints weight = 7191.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.054512 restraints weight = 4928.568| |-----------------------------------------------------------------------------| r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 3008 Z= 0.295 Angle : 0.710 9.489 4111 Z= 0.367 Chirality : 0.047 0.157 452 Planarity : 0.005 0.052 540 Dihedral : 5.548 23.661 463 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 18.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.11 % Favored : 85.89 % 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: -3.10 (0.39), residues: 397 helix: -2.89 (0.68), residues: 40 sheet: -1.12 (0.48), residues: 113 loop : -2.49 (0.37), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.003 TRP B 36 HIS 0.003 0.002 HIS A 519 PHE 0.008 0.001 PHE A 377 TYR 0.016 0.002 TYR A 453 ARG 0.002 0.000 ARG B 97 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1097.57 seconds wall clock time: 20 minutes 30.14 seconds (1230.14 seconds total)