Starting phenix.real_space_refine on Thu Mar 6 06:16:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8idn_35369/03_2025/8idn_35369.cif Found real_map, /net/cci-nas-00/data/ceres_data/8idn_35369/03_2025/8idn_35369.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8idn_35369/03_2025/8idn_35369.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8idn_35369/03_2025/8idn_35369.map" model { file = "/net/cci-nas-00/data/ceres_data/8idn_35369/03_2025/8idn_35369.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8idn_35369/03_2025/8idn_35369.cif" } resolution = 3.35 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= 0.001 sd= 0.044 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2169 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 14 5.16 5 C 2092 2.51 5 N 542 2.21 5 O 644 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 3292 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1544 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 11, 'TRANS': 183} Chain: "H" Number of atoms: 895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 895 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "L" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 803 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 4, 'TRANS': 103} Chain: "B" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 3.18, per 1000 atoms: 0.97 Number of scatterers: 3292 At special positions: 0 Unit cell: (68.34, 73.7, 87.77, 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 14 16.00 O 644 8.00 N 542 7.00 C 2092 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, 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=2.04 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 H 41 " - pdb=" SG CYS H 114 " distance=2.03 Simple disulfide: pdb=" SG CYS L 41 " - pdb=" SG CYS L 109 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA B 3 " - " MAN B 4 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " NAG-ASN " NAG B 1 " - " ASN H 79 " Time building additional restraints: 0.97 Conformation dependent library (CDL) restraints added in 407.8 milliseconds 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 760 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 8 sheets defined 11.2% alpha, 33.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 364 through 372 removed outlier: 4.214A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ALA A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 411 removed outlier: 4.217A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA A 411 " --> pdb=" O ARG A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.628A pdb=" N ASP A 442 " --> pdb=" O SER A 438 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 83 removed outlier: 3.871A pdb=" N LYS H 83 " --> pdb=" O SER H 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 49 through 53 Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.780A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N GLY A 431 " --> pdb=" O TYR A 380 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N TYR A 380 " --> pdb=" O GLY A 431 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL A 433 " --> pdb=" O LYS A 378 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA4, first strand: chain 'H' and resid 22 through 26 removed outlier: 3.746A pdb=" N GLN H 22 " --> pdb=" O SER H 44 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N THR H 40 " --> pdb=" O SER H 26 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 30 through 31 removed outlier: 7.117A pdb=" N VAL H 53 " --> pdb=" O MET H 69 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N MET H 69 " --> pdb=" O VAL H 53 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N TRP H 55 " --> pdb=" O LEU H 67 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 23 through 24 Processing sheet with id=AA7, first strand: chain 'L' and resid 28 through 31 removed outlier: 3.515A pdb=" N THR L 126 " --> pdb=" O LEU L 29 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE L 106 " --> pdb=" O GLU L 59 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N TRP L 56 " --> pdb=" O LEU L 68 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 28 through 31 removed outlier: 3.515A pdb=" N THR L 126 " --> pdb=" O LEU L 29 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N TYR L 113 " --> pdb=" O HIS L 116 " (cutoff:3.500A) 114 hydrogen bonds defined for protein. 264 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: 0.87 Time building geometry restraints manager: 1.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1043 1.35 - 1.47: 913 1.47 - 1.59: 1401 1.59 - 1.71: 0 1.71 - 1.84: 16 Bond restraints: 3373 Sorted by residual: bond pdb=" C1 BMA B 3 " pdb=" C2 BMA B 3 " ideal model delta sigma weight residual 1.519 1.556 -0.037 2.00e-02 2.50e+03 3.35e+00 bond pdb=" C1 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.406 1.431 -0.025 2.00e-02 2.50e+03 1.56e+00 bond pdb=" C5 MAN B 4 " pdb=" O5 MAN B 4 " ideal model delta sigma weight residual 1.418 1.443 -0.025 2.00e-02 2.50e+03 1.51e+00 bond pdb=" C5 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.413 1.436 -0.023 2.00e-02 2.50e+03 1.27e+00 bond pdb=" C5 NAG B 1 " pdb=" O5 NAG B 1 " ideal model delta sigma weight residual 1.413 1.434 -0.021 2.00e-02 2.50e+03 1.13e+00 ... (remaining 3368 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.33: 4459 1.33 - 2.65: 92 2.65 - 3.98: 29 3.98 - 5.31: 10 5.31 - 6.64: 5 Bond angle restraints: 4595 Sorted by residual: angle pdb=" C ALA L 71 " pdb=" N THR L 72 " pdb=" CA THR L 72 " ideal model delta sigma weight residual 121.54 127.51 -5.97 1.91e+00 2.74e-01 9.77e+00 angle pdb=" C3 BMA B 3 " pdb=" C2 BMA B 3 " pdb=" O2 BMA B 3 " ideal model delta sigma weight residual 112.95 106.31 6.64 3.00e+00 1.11e-01 4.89e+00 angle pdb=" CG1 ILE H 49 " pdb=" CB ILE H 49 " pdb=" CG2 ILE H 49 " ideal model delta sigma weight residual 110.70 104.21 6.49 3.00e+00 1.11e-01 4.69e+00 angle pdb=" C3 MAN B 4 " pdb=" C2 MAN B 4 " pdb=" O2 MAN B 4 " ideal model delta sigma weight residual 111.77 105.60 6.17 3.00e+00 1.11e-01 4.23e+00 angle pdb=" C4 BMA B 3 " pdb=" C5 BMA B 3 " pdb=" O5 BMA B 3 " ideal model delta sigma weight residual 113.24 107.33 5.91 3.00e+00 1.11e-01 3.88e+00 ... (remaining 4590 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.23: 1889 22.23 - 44.46: 111 44.46 - 66.68: 9 66.68 - 88.91: 8 88.91 - 111.14: 4 Dihedral angle restraints: 2021 sinusoidal: 821 harmonic: 1200 Sorted by residual: 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 49.97 43.03 1 1.00e+01 1.00e-02 2.58e+01 dihedral pdb=" O4 BMA B 3 " pdb=" C4 BMA B 3 " pdb=" C5 BMA B 3 " pdb=" O5 BMA B 3 " ideal model delta sinusoidal sigma weight residual 288.71 177.57 111.14 1 3.00e+01 1.11e-03 1.45e+01 dihedral pdb=" C3 BMA B 3 " pdb=" C4 BMA B 3 " pdb=" C5 BMA B 3 " pdb=" O5 BMA B 3 " ideal model delta sinusoidal sigma weight residual 47.62 -61.70 109.32 1 3.00e+01 1.11e-03 1.42e+01 ... (remaining 2018 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 421 0.053 - 0.106: 80 0.106 - 0.159: 15 0.159 - 0.212: 0 0.212 - 0.265: 3 Chirality restraints: 519 Sorted by residual: chirality pdb=" C5 BMA B 3 " pdb=" C4 BMA B 3 " pdb=" C6 BMA B 3 " pdb=" O5 BMA B 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" CB ILE H 49 " pdb=" CA ILE H 49 " pdb=" CG1 ILE H 49 " pdb=" CG2 ILE H 49 " both_signs ideal model delta sigma weight residual False 2.64 2.87 -0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" C1 NAG B 1 " pdb=" ND2 ASN H 79 " pdb=" C2 NAG B 1 " pdb=" O5 NAG B 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.19 -0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 516 not shown) Planarity restraints: 585 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 462 " 0.024 5.00e-02 4.00e+02 3.64e-02 2.12e+00 pdb=" N PRO A 463 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 463 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 463 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS L 60 " -0.015 5.00e-02 4.00e+02 2.31e-02 8.55e-01 pdb=" N PRO L 61 " 0.040 5.00e-02 4.00e+02 pdb=" CA PRO L 61 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO L 61 " -0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 347 " 0.006 2.00e-02 2.50e+03 6.94e-03 8.42e-01 pdb=" CG PHE A 347 " -0.016 2.00e-02 2.50e+03 pdb=" CD1 PHE A 347 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE A 347 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE A 347 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 347 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 347 " 0.001 2.00e-02 2.50e+03 ... (remaining 582 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 55 2.68 - 3.23: 2959 3.23 - 3.79: 4611 3.79 - 4.34: 6491 4.34 - 4.90: 10839 Nonbonded interactions: 24955 Sorted by model distance: nonbonded pdb=" O TYR H 120 " pdb=" OG SER L 74 " model vdw 2.120 3.040 nonbonded pdb=" O ASN A 439 " pdb=" OG SER A 443 " model vdw 2.153 3.040 nonbonded pdb=" O ALA L 71 " pdb=" OG1 THR L 72 " model vdw 2.240 3.040 nonbonded pdb=" OH TYR A 453 " pdb=" OE1 GLN A 493 " model vdw 2.262 3.040 nonbonded pdb=" O TRP A 353 " pdb=" NH2 ARG A 466 " model vdw 2.321 3.120 ... (remaining 24950 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.970 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3373 Z= 0.190 Angle : 0.579 6.637 4595 Z= 0.278 Chirality : 0.046 0.265 519 Planarity : 0.003 0.036 584 Dihedral : 14.934 111.141 1243 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.36 % Favored : 95.40 % Rotamer: Outliers : 0.56 % Allowed : 0.56 % Favored : 98.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.42), residues: 413 helix: -1.63 (1.06), residues: 27 sheet: 1.39 (0.44), residues: 146 loop : -0.79 (0.40), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 127 HIS 0.000 0.000 HIS L 116 PHE 0.016 0.001 PHE A 347 TYR 0.010 0.001 TYR A 505 ARG 0.004 0.001 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 76 time to evaluate : 0.355 Fit side-chains REVERT: A 509 ARG cc_start: 0.6952 (mtt90) cc_final: 0.6531 (mtt90) outliers start: 2 outliers final: 2 residues processed: 77 average time/residue: 0.1635 time to fit residues: 15.5823 Evaluate side-chains 67 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 65 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 439 ASN Chi-restraints excluded: chain L residue 73 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 0.2980 chunk 30 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 chunk 10 optimal weight: 0.2980 chunk 20 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 11 optimal weight: 0.0370 overall best weight: 0.6660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 115 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.192175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.149843 restraints weight = 4107.014| |-----------------------------------------------------------------------------| r_work (start): 0.3945 rms_B_bonded: 3.43 r_work: 0.3718 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.1247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 3373 Z= 0.167 Angle : 0.596 7.017 4595 Z= 0.322 Chirality : 0.046 0.201 519 Planarity : 0.004 0.036 584 Dihedral : 10.437 74.478 540 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.39 % Favored : 96.37 % Rotamer: Outliers : 1.41 % Allowed : 10.17 % Favored : 88.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.42), residues: 413 helix: -1.63 (1.04), residues: 27 sheet: 1.40 (0.43), residues: 145 loop : -0.64 (0.40), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 66 HIS 0.001 0.000 HIS L 63 PHE 0.011 0.001 PHE L 65 TYR 0.008 0.001 TYR A 505 ARG 0.004 0.001 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 73 time to evaluate : 0.751 Fit side-chains revert: symmetry clash REVERT: A 398 ASP cc_start: 0.7783 (m-30) cc_final: 0.7532 (m-30) REVERT: A 505 TYR cc_start: 0.6814 (m-10) cc_final: 0.6599 (m-80) REVERT: A 509 ARG cc_start: 0.7327 (mtt90) cc_final: 0.7001 (mtt90) REVERT: L 75 ARG cc_start: 0.8160 (ttp80) cc_final: 0.7834 (mtp-110) outliers start: 5 outliers final: 2 residues processed: 76 average time/residue: 0.1818 time to fit residues: 16.9913 Evaluate side-chains 69 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 67 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 73 ASN Chi-restraints excluded: chain L residue 115 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 34 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 439 ASN H 54 ASN H 123 GLN L 25 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.190335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.147266 restraints weight = 4104.069| |-----------------------------------------------------------------------------| r_work (start): 0.3920 rms_B_bonded: 3.66 r_work: 0.3707 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3373 Z= 0.194 Angle : 0.574 6.785 4595 Z= 0.302 Chirality : 0.045 0.181 519 Planarity : 0.004 0.051 584 Dihedral : 9.293 61.404 538 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.87 % Favored : 95.88 % Rotamer: Outliers : 1.98 % Allowed : 12.71 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.42), residues: 413 helix: -1.74 (1.01), residues: 27 sheet: 1.44 (0.43), residues: 144 loop : -0.72 (0.40), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 66 HIS 0.003 0.001 HIS L 116 PHE 0.010 0.001 PHE L 65 TYR 0.011 0.001 TYR H 113 ARG 0.003 0.000 ARG H 116 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 68 time to evaluate : 0.342 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 72 average time/residue: 0.1565 time to fit residues: 13.7727 Evaluate side-chains 69 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 65 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 49 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 3.9990 chunk 24 optimal weight: 0.0020 chunk 21 optimal weight: 1.9990 chunk 12 optimal weight: 0.0970 chunk 23 optimal weight: 0.8980 chunk 31 optimal weight: 0.3980 chunk 17 optimal weight: 4.9990 chunk 4 optimal weight: 8.9990 chunk 11 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 32 optimal weight: 7.9990 overall best weight: 0.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.191951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.148872 restraints weight = 4166.753| |-----------------------------------------------------------------------------| r_work (start): 0.3932 rms_B_bonded: 3.83 r_work: 0.3705 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3373 Z= 0.137 Angle : 0.547 6.183 4595 Z= 0.283 Chirality : 0.044 0.171 519 Planarity : 0.004 0.044 584 Dihedral : 7.399 43.225 536 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.15 % Favored : 96.61 % Rotamer: Outliers : 1.41 % Allowed : 15.54 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.42), residues: 413 helix: -1.96 (0.97), residues: 27 sheet: 1.37 (0.43), residues: 145 loop : -0.73 (0.40), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 66 HIS 0.001 0.000 HIS L 116 PHE 0.009 0.001 PHE L 65 TYR 0.013 0.001 TYR L 53 ARG 0.004 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 66 time to evaluate : 0.388 Fit side-chains REVERT: H 69 MET cc_start: 0.8211 (tpp) cc_final: 0.7891 (tpp) outliers start: 5 outliers final: 5 residues processed: 69 average time/residue: 0.1685 time to fit residues: 14.4803 Evaluate side-chains 68 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 63 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 49 THR Chi-restraints excluded: chain L residue 73 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 12 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 30 optimal weight: 7.9990 chunk 35 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 14 optimal weight: 8.9990 chunk 17 optimal weight: 0.6980 chunk 27 optimal weight: 0.0770 overall best weight: 1.3142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN L 73 ASN L 115 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.188751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.145767 restraints weight = 4173.451| |-----------------------------------------------------------------------------| r_work (start): 0.3903 rms_B_bonded: 3.35 r_work: 0.3669 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3373 Z= 0.217 Angle : 0.580 7.382 4595 Z= 0.301 Chirality : 0.045 0.172 519 Planarity : 0.004 0.041 584 Dihedral : 6.895 45.136 536 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.87 % Favored : 95.88 % Rotamer: Outliers : 2.82 % Allowed : 15.54 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.42), residues: 413 helix: -1.95 (0.98), residues: 27 sheet: 1.27 (0.43), residues: 145 loop : -0.79 (0.40), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP H 127 HIS 0.001 0.000 HIS L 116 PHE 0.011 0.001 PHE L 65 TYR 0.020 0.001 TYR L 53 ARG 0.007 0.001 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.349 Fit side-chains revert: symmetry clash REVERT: L 88 ILE cc_start: 0.8594 (OUTLIER) cc_final: 0.8299 (mp) outliers start: 10 outliers final: 8 residues processed: 72 average time/residue: 0.2177 time to fit residues: 19.6553 Evaluate side-chains 73 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 64 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 49 THR Chi-restraints excluded: chain L residue 73 ASN Chi-restraints excluded: chain L residue 88 ILE Chi-restraints excluded: chain L residue 115 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 31 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 12 optimal weight: 0.0870 chunk 34 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 18 optimal weight: 8.9990 chunk 16 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 13 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 overall best weight: 0.8960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 73 ASN L 115 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.189587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.147208 restraints weight = 4281.745| |-----------------------------------------------------------------------------| r_work (start): 0.3919 rms_B_bonded: 3.18 r_work: 0.3676 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3373 Z= 0.178 Angle : 0.567 7.740 4595 Z= 0.295 Chirality : 0.045 0.168 519 Planarity : 0.004 0.039 584 Dihedral : 6.394 44.471 536 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.12 % Favored : 95.64 % Rotamer: Outliers : 3.39 % Allowed : 15.25 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.42), residues: 413 helix: -1.99 (0.97), residues: 27 sheet: 1.22 (0.43), residues: 145 loop : -0.84 (0.40), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 127 HIS 0.000 0.000 HIS L 116 PHE 0.012 0.001 PHE L 65 TYR 0.014 0.001 TYR L 53 ARG 0.002 0.000 ARG H 116 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 68 time to evaluate : 0.373 Fit side-chains revert: symmetry clash REVERT: A 471 GLU cc_start: 0.7390 (tm-30) cc_final: 0.7108 (tm-30) outliers start: 12 outliers final: 9 residues processed: 75 average time/residue: 0.1503 time to fit residues: 14.1751 Evaluate side-chains 71 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 49 THR Chi-restraints excluded: chain L residue 73 ASN Chi-restraints excluded: chain L residue 115 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 30 optimal weight: 6.9990 chunk 14 optimal weight: 0.7980 chunk 36 optimal weight: 0.3980 chunk 15 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 1 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 8 optimal weight: 3.9990 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 394 ASN ** H 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 73 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.189663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.147628 restraints weight = 4192.626| |-----------------------------------------------------------------------------| r_work (start): 0.3914 rms_B_bonded: 3.16 r_work: 0.3674 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3373 Z= 0.161 Angle : 0.574 8.412 4595 Z= 0.296 Chirality : 0.044 0.167 519 Planarity : 0.004 0.038 584 Dihedral : 5.945 43.754 536 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.87 % Favored : 95.88 % Rotamer: Outliers : 3.39 % Allowed : 14.41 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.41), residues: 413 helix: -1.99 (0.97), residues: 27 sheet: 1.22 (0.43), residues: 145 loop : -0.84 (0.40), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 127 HIS 0.002 0.001 HIS L 116 PHE 0.012 0.001 PHE L 65 TYR 0.018 0.001 TYR L 53 ARG 0.006 0.001 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 67 time to evaluate : 0.360 Fit side-chains REVERT: A 471 GLU cc_start: 0.7372 (tm-30) cc_final: 0.7105 (tm-30) outliers start: 12 outliers final: 8 residues processed: 75 average time/residue: 0.1388 time to fit residues: 12.9481 Evaluate side-chains 70 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 62 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 49 THR Chi-restraints excluded: chain L residue 73 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 0.5980 chunk 24 optimal weight: 0.5980 chunk 7 optimal weight: 0.5980 chunk 9 optimal weight: 4.9990 chunk 12 optimal weight: 0.0040 chunk 14 optimal weight: 0.6980 chunk 21 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 5 optimal weight: 5.9990 chunk 2 optimal weight: 0.8980 chunk 27 optimal weight: 0.5980 overall best weight: 0.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 25 GLN L 73 ASN L 115 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.190807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.148215 restraints weight = 4177.894| |-----------------------------------------------------------------------------| r_work (start): 0.3931 rms_B_bonded: 3.09 r_work: 0.3694 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 3373 Z= 0.148 Angle : 0.578 8.218 4595 Z= 0.301 Chirality : 0.044 0.162 519 Planarity : 0.004 0.037 584 Dihedral : 5.532 42.724 536 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.87 % Favored : 95.88 % Rotamer: Outliers : 2.54 % Allowed : 15.82 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.42), residues: 413 helix: -1.95 (0.98), residues: 27 sheet: 1.03 (0.42), residues: 150 loop : -0.72 (0.41), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 66 HIS 0.001 0.000 HIS L 116 PHE 0.012 0.001 PHE L 65 TYR 0.016 0.001 TYR L 53 ARG 0.004 0.000 ARG L 75 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 64 time to evaluate : 0.495 Fit side-chains revert: symmetry clash REVERT: A 398 ASP cc_start: 0.7472 (m-30) cc_final: 0.7181 (m-30) REVERT: A 471 GLU cc_start: 0.7458 (tm-30) cc_final: 0.7207 (tm-30) REVERT: H 69 MET cc_start: 0.8148 (tpp) cc_final: 0.7933 (ttm) outliers start: 9 outliers final: 9 residues processed: 70 average time/residue: 0.1508 time to fit residues: 13.1396 Evaluate side-chains 72 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 49 THR Chi-restraints excluded: chain L residue 73 ASN Chi-restraints excluded: chain L residue 115 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 7 optimal weight: 0.0270 chunk 29 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 21 optimal weight: 7.9990 chunk 24 optimal weight: 0.0370 chunk 9 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 chunk 26 optimal weight: 0.6980 overall best weight: 0.7518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN A 439 ASN L 73 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.190341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.148421 restraints weight = 4196.114| |-----------------------------------------------------------------------------| r_work (start): 0.3927 rms_B_bonded: 3.73 r_work: 0.3669 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3373 Z= 0.171 Angle : 0.591 8.294 4595 Z= 0.308 Chirality : 0.044 0.164 519 Planarity : 0.004 0.054 584 Dihedral : 5.341 43.060 536 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.12 % Favored : 95.64 % Rotamer: Outliers : 2.54 % Allowed : 16.67 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.42), residues: 413 helix: -1.91 (0.99), residues: 27 sheet: 0.93 (0.43), residues: 152 loop : -0.70 (0.41), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 127 HIS 0.002 0.000 HIS L 116 PHE 0.011 0.001 PHE L 65 TYR 0.017 0.001 TYR L 53 ARG 0.006 0.001 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.399 Fit side-chains revert: symmetry clash REVERT: A 471 GLU cc_start: 0.7461 (tm-30) cc_final: 0.7232 (tm-30) outliers start: 9 outliers final: 8 residues processed: 73 average time/residue: 0.1421 time to fit residues: 12.8847 Evaluate side-chains 75 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 49 THR Chi-restraints excluded: chain L residue 73 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 0 optimal weight: 10.0000 chunk 17 optimal weight: 3.9990 chunk 37 optimal weight: 9.9990 chunk 19 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 13 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN ** H 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 73 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.187214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.145446 restraints weight = 4237.430| |-----------------------------------------------------------------------------| r_work (start): 0.3900 rms_B_bonded: 3.13 r_work: 0.3658 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3373 Z= 0.250 Angle : 0.627 8.062 4595 Z= 0.325 Chirality : 0.045 0.170 519 Planarity : 0.004 0.043 584 Dihedral : 5.453 45.933 536 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.60 % Favored : 95.16 % Rotamer: Outliers : 2.54 % Allowed : 16.38 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.42), residues: 413 helix: -1.91 (1.00), residues: 27 sheet: 0.94 (0.43), residues: 150 loop : -0.81 (0.41), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP H 127 HIS 0.001 0.000 HIS L 116 PHE 0.010 0.001 PHE L 65 TYR 0.023 0.002 TYR L 53 ARG 0.004 0.001 ARG L 82 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 67 time to evaluate : 0.530 Fit side-chains revert: symmetry clash REVERT: A 471 GLU cc_start: 0.7419 (tm-30) cc_final: 0.7193 (tm-30) outliers start: 9 outliers final: 8 residues processed: 72 average time/residue: 0.1735 time to fit residues: 16.1684 Evaluate side-chains 71 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 49 THR Chi-restraints excluded: chain L residue 73 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 36 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 16 optimal weight: 0.0980 chunk 11 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 21 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.189432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.148957 restraints weight = 4241.403| |-----------------------------------------------------------------------------| r_work (start): 0.3927 rms_B_bonded: 3.21 r_work: 0.3691 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3373 Z= 0.176 Angle : 0.612 8.407 4595 Z= 0.317 Chirality : 0.044 0.162 519 Planarity : 0.004 0.040 584 Dihedral : 5.234 44.442 536 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.60 % Favored : 95.16 % Rotamer: Outliers : 1.98 % Allowed : 16.67 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.42), residues: 413 helix: -1.88 (1.00), residues: 27 sheet: 0.84 (0.43), residues: 152 loop : -0.68 (0.42), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 66 HIS 0.001 0.000 HIS L 116 PHE 0.012 0.001 PHE L 65 TYR 0.019 0.001 TYR L 53 ARG 0.004 0.000 ARG L 82 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2522.91 seconds wall clock time: 46 minutes 12.41 seconds (2772.41 seconds total)