Starting phenix.real_space_refine on Thu Jul 24 14:25:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x8z_33061/07_2025/7x8z_33061_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x8z_33061/07_2025/7x8z_33061.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7x8z_33061/07_2025/7x8z_33061.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x8z_33061/07_2025/7x8z_33061.map" model { file = "/net/cci-nas-00/data/ceres_data/7x8z_33061/07_2025/7x8z_33061_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x8z_33061/07_2025/7x8z_33061_trim.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 17 5.16 5 C 2114 2.51 5 N 555 2.21 5 O 647 1.98 5 H 3147 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 6480 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 2988 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 11, 'TRANS': 182} Chain: "H" Number of atoms: 1789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 1789 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 2, 'TRANS': 117} Chain: "L" Number of atoms: 1689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 1689 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 8, 'TRANS': 103} 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: 8.05, per 1000 atoms: 1.24 Number of scatterers: 6480 At special positions: 0 Unit cell: (82.071, 84.558, 75.439, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 17 16.00 O 647 8.00 N 555 7.00 C 2114 6.00 H 3147 1.00 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=2.03 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 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 94 " distance=2.04 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 NAG-ASN " NAG A1301 " - " ASN A 343 " Time building additional restraints: 2.15 Conformation dependent library (CDL) restraints added in 969.9 milliseconds 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 772 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 10 sheets defined 8.7% alpha, 29.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.623A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 369 Processing helix chain 'A' and resid 405 through 411 removed outlier: 4.077A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 3.553A 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 'H' and resid 28 through 32 Processing helix chain 'H' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 355 through 358 removed outlier: 3.950A pdb=" N ASP A 398 " --> pdb=" O VAL A 512 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N VAL A 512 " --> pdb=" O ASP A 398 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 355 through 358 removed outlier: 3.950A pdb=" N ASP A 398 " --> pdb=" O VAL A 512 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N VAL A 512 " --> pdb=" O ASP A 398 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AA4, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA5, first strand: chain 'H' and resid 3 through 7 removed outlier: 4.459A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N SER H 25 " --> pdb=" O GLN H 3 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 10 through 12 removed outlier: 5.852A pdb=" N GLY H 10 " --> pdb=" O THR H 118 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 39 through 40 removed outlier: 3.588A pdb=" N ALA H 40 " --> pdb=" O GLY H 44 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLY H 44 " --> pdb=" O ALA H 40 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'L' and resid 4 through 6 removed outlier: 3.780A pdb=" N THR L 5 " --> pdb=" O LYS L 24 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS L 24 " --> pdb=" O THR L 5 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 59 through 60 removed outlier: 3.580A pdb=" N THR L 59 " --> pdb=" O TYR L 55 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR L 55 " --> pdb=" O THR L 59 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N TRP L 41 " --> pdb=" O LEU L 53 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N TYR L 55 " --> pdb=" O LEU L 39 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N LEU L 39 " --> pdb=" O TYR L 55 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N HIS L 96 " --> pdb=" O THR L 103 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR L 103 " --> pdb=" O HIS L 96 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 59 through 60 removed outlier: 3.580A pdb=" N THR L 59 " --> pdb=" O TYR L 55 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR L 55 " --> pdb=" O THR L 59 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N TRP L 41 " --> pdb=" O LEU L 53 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N TYR L 55 " --> pdb=" O LEU L 39 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N LEU L 39 " --> pdb=" O TYR L 55 " (cutoff:3.500A) 94 hydrogen bonds defined for protein. 207 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: 4.24 Time building geometry restraints manager: 2.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 3146 1.03 - 1.23: 3 1.23 - 1.42: 1529 1.42 - 1.62: 1867 1.62 - 1.81: 21 Bond restraints: 6566 Sorted by residual: bond pdb=" N ASP L 1 " pdb=" CA ASP L 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.07e+00 bond pdb=" N GLU H 1 " pdb=" CA GLU H 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.94e+00 bond pdb=" C1 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.19e+00 bond pdb=" N GLU H 1 " pdb=" H GLU H 1 " ideal model delta sigma weight residual 0.860 0.889 -0.029 2.00e-02 2.50e+03 2.13e+00 bond pdb=" N ASP L 1 " pdb=" H ASP L 1 " ideal model delta sigma weight residual 0.860 0.889 -0.029 2.00e-02 2.50e+03 2.10e+00 ... (remaining 6561 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.00: 10795 1.00 - 1.99: 866 1.99 - 2.99: 75 2.99 - 3.98: 14 3.98 - 4.98: 5 Bond angle restraints: 11755 Sorted by residual: angle pdb=" C TRP L 56 " pdb=" N ALA L 57 " pdb=" CA ALA L 57 " ideal model delta sigma weight residual 121.54 126.12 -4.58 1.91e+00 2.74e-01 5.74e+00 angle pdb=" N VAL A 524 " pdb=" CA VAL A 524 " pdb=" C VAL A 524 " ideal model delta sigma weight residual 106.55 109.94 -3.39 1.45e+00 4.76e-01 5.48e+00 angle pdb=" CA VAL H 48 " pdb=" C VAL H 48 " pdb=" N SER H 49 " ideal model delta sigma weight residual 116.60 119.90 -3.30 1.45e+00 4.76e-01 5.18e+00 angle pdb=" N VAL H 48 " pdb=" CA VAL H 48 " pdb=" C VAL H 48 " ideal model delta sigma weight residual 109.34 114.00 -4.66 2.08e+00 2.31e-01 5.01e+00 angle pdb=" N PRO L 101 " pdb=" CA PRO L 101 " pdb=" C PRO L 101 " ideal model delta sigma weight residual 110.70 112.76 -2.06 1.22e+00 6.72e-01 2.84e+00 ... (remaining 11750 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.96: 2789 15.96 - 31.92: 272 31.92 - 47.87: 90 47.87 - 63.83: 36 63.83 - 79.79: 5 Dihedral angle restraints: 3192 sinusoidal: 1689 harmonic: 1503 Sorted by residual: dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 94 " pdb=" CB CYS L 94 " ideal model delta sinusoidal sigma weight residual 93.00 167.77 -74.77 1 1.00e+01 1.00e-02 7.08e+01 dihedral pdb=" SG CYS A 391 " pdb=" CB CYS A 525 " pdb=" SG CYS A 525 " pdb=" CA CYS A 525 " ideal model delta sinusoidal sigma weight residual 79.00 6.33 72.67 1 2.00e+01 2.50e-03 1.69e+01 dihedral pdb=" CA PHE H 27 " pdb=" C PHE H 27 " pdb=" N THR H 28 " pdb=" CA THR H 28 " ideal model delta harmonic sigma weight residual 180.00 161.29 18.71 0 5.00e+00 4.00e-02 1.40e+01 ... (remaining 3189 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 254 0.027 - 0.053: 150 0.053 - 0.080: 50 0.080 - 0.107: 23 0.107 - 0.133: 15 Chirality restraints: 492 Sorted by residual: chirality pdb=" CA ILE L 21 " pdb=" N ILE L 21 " pdb=" C ILE L 21 " pdb=" CB ILE L 21 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.44e-01 chirality pdb=" CA ILE H 70 " pdb=" N ILE H 70 " pdb=" C ILE H 70 " pdb=" CB ILE H 70 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.10e-01 chirality pdb=" CA ILE A 358 " pdb=" N ILE A 358 " pdb=" C ILE A 358 " pdb=" CB ILE A 358 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.02e-01 ... (remaining 489 not shown) Planarity restraints: 1007 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 462 " 0.034 5.00e-02 4.00e+02 5.14e-02 4.22e+00 pdb=" N PRO A 463 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO A 463 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 463 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO L 100 " -0.033 5.00e-02 4.00e+02 4.89e-02 3.83e+00 pdb=" N PRO L 101 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO L 101 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO L 101 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL L 64 " -0.022 5.00e-02 4.00e+02 3.35e-02 1.79e+00 pdb=" N PRO L 65 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO L 65 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO L 65 " -0.019 5.00e-02 4.00e+02 ... (remaining 1004 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.24: 853 2.24 - 2.83: 13946 2.83 - 3.42: 15347 3.42 - 4.01: 21243 4.01 - 4.60: 31822 Nonbonded interactions: 83211 Sorted by model distance: nonbonded pdb=" O SER A 366 " pdb="HD22 ASN A 370 " model vdw 1.650 2.450 nonbonded pdb=" O PHE A 392 " pdb=" H THR A 523 " model vdw 1.657 2.450 nonbonded pdb=" OE1 GLN A 474 " pdb=" H GLN A 474 " model vdw 1.657 2.450 nonbonded pdb=" OE1 GLN H 13 " pdb=" H GLN H 13 " model vdw 1.668 2.450 nonbonded pdb=" OD1 ASP H 109 " pdb=" H VAL H 110 " model vdw 1.671 2.450 ... (remaining 83206 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 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: 93.780 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: 0.130 Extract box with map and model: 13.490 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 35.160 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 148.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 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 0.046 3426 Z= 0.139 Angle : 0.585 4.978 4662 Z= 0.327 Chirality : 0.043 0.133 492 Planarity : 0.005 0.051 605 Dihedral : 13.977 79.788 1231 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.24 % Allowed : 12.62 % Favored : 87.14 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % 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: -2.94 (0.38), residues: 420 helix: -3.67 (0.71), residues: 21 sheet: -1.29 (0.47), residues: 122 loop : -2.24 (0.35), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 41 HIS 0.002 0.001 HIS L 96 PHE 0.014 0.001 PHE L 77 TYR 0.013 0.001 TYR A 380 ARG 0.001 0.000 ARG L 67 Details of bonding type rmsd link_NAG-ASN : bond 0.00333 ( 1) link_NAG-ASN : angle 0.87456 ( 3) hydrogen bonds : bond 0.14705 ( 79) hydrogen bonds : angle 9.17299 ( 207) SS BOND : bond 0.00345 ( 6) SS BOND : angle 0.84173 ( 12) covalent geometry : bond 0.00299 ( 3419) covalent geometry : angle 0.58412 ( 4647) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 389 ASP cc_start: 0.8760 (m-30) cc_final: 0.8492 (m-30) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.7413 time to fit residues: 73.7908 Evaluate side-chains 65 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 1.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 9.9990 chunk 31 optimal weight: 6.9990 chunk 17 optimal weight: 9.9990 chunk 10 optimal weight: 5.9990 chunk 21 optimal weight: 0.9980 chunk 32 optimal weight: 9.9990 chunk 12 optimal weight: 9.9990 chunk 20 optimal weight: 1.9990 chunk 24 optimal weight: 10.0000 chunk 38 optimal weight: 10.0000 chunk 11 optimal weight: 1.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 34 ASN ** L 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.053261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.044117 restraints weight = 50251.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.046876 restraints weight = 21421.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.048758 restraints weight = 11499.326| |-----------------------------------------------------------------------------| r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 3426 Z= 0.154 Angle : 0.570 4.837 4662 Z= 0.308 Chirality : 0.041 0.134 492 Planarity : 0.005 0.049 605 Dihedral : 5.645 42.684 494 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.57 % Favored : 86.43 % Rotamer: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % 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: -2.86 (0.39), residues: 420 helix: -3.01 (0.80), residues: 27 sheet: -1.31 (0.47), residues: 123 loop : -2.17 (0.36), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 36 HIS 0.002 0.001 HIS A 519 PHE 0.011 0.001 PHE L 77 TYR 0.019 0.001 TYR A 489 ARG 0.002 0.000 ARG A 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00251 ( 1) link_NAG-ASN : angle 1.23146 ( 3) hydrogen bonds : bond 0.03140 ( 79) hydrogen bonds : angle 6.46711 ( 207) SS BOND : bond 0.00295 ( 6) SS BOND : angle 1.24047 ( 12) covalent geometry : bond 0.00345 ( 3419) covalent geometry : angle 0.56684 ( 4647) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 466 ARG cc_start: 0.9455 (ttm110) cc_final: 0.9041 (mtp85) outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.5177 time to fit residues: 43.6989 Evaluate side-chains 62 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 8 optimal weight: 10.0000 chunk 22 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 chunk 27 optimal weight: 6.9990 chunk 32 optimal weight: 10.0000 chunk 41 optimal weight: 10.0000 chunk 11 optimal weight: 10.0000 chunk 39 optimal weight: 8.9990 chunk 33 optimal weight: 7.9990 chunk 3 optimal weight: 8.9990 chunk 37 optimal weight: 10.0000 overall best weight: 5.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 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 = 0.3183 r_free = 0.3183 target = 0.050422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.041469 restraints weight = 51923.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.044078 restraints weight = 22050.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.045868 restraints weight = 11905.898| |-----------------------------------------------------------------------------| r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 3426 Z= 0.188 Angle : 0.580 5.268 4662 Z= 0.313 Chirality : 0.040 0.126 492 Planarity : 0.006 0.079 605 Dihedral : 5.459 35.679 494 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.81 % Favored : 86.19 % Rotamer: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % 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: -2.72 (0.39), residues: 420 helix: -3.20 (0.81), residues: 27 sheet: -1.24 (0.47), residues: 123 loop : -2.02 (0.36), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 436 HIS 0.003 0.002 HIS L 96 PHE 0.020 0.002 PHE A 486 TYR 0.017 0.002 TYR A 489 ARG 0.018 0.001 ARG A 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00382 ( 1) link_NAG-ASN : angle 1.22287 ( 3) hydrogen bonds : bond 0.03300 ( 79) hydrogen bonds : angle 6.03835 ( 207) SS BOND : bond 0.00258 ( 6) SS BOND : angle 0.82551 ( 12) covalent geometry : bond 0.00408 ( 3419) covalent geometry : angle 0.57846 ( 4647) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 474 GLN cc_start: 0.9398 (pm20) cc_final: 0.8826 (tt0) REVERT: A 484 GLU cc_start: 0.7737 (tp30) cc_final: 0.7493 (tp30) REVERT: H 59 TYR cc_start: 0.8730 (m-80) cc_final: 0.8227 (m-80) outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.4903 time to fit residues: 39.4234 Evaluate side-chains 59 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 33 optimal weight: 10.0000 chunk 13 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 20 optimal weight: 0.4980 chunk 16 optimal weight: 10.0000 chunk 11 optimal weight: 7.9990 chunk 10 optimal weight: 9.9990 chunk 27 optimal weight: 4.9990 chunk 29 optimal weight: 8.9990 chunk 25 optimal weight: 7.9990 chunk 6 optimal weight: 2.9990 overall best weight: 3.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** 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 = 0.3195 r_free = 0.3195 target = 0.050330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.041529 restraints weight = 52146.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.044053 restraints weight = 22200.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.045841 restraints weight = 12000.642| |-----------------------------------------------------------------------------| r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.3194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 3426 Z= 0.142 Angle : 0.546 5.114 4662 Z= 0.294 Chirality : 0.040 0.138 492 Planarity : 0.006 0.075 605 Dihedral : 5.322 35.962 494 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.38 % Favored : 87.62 % Rotamer: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % 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: -2.53 (0.40), residues: 420 helix: -3.12 (0.81), residues: 27 sheet: -1.10 (0.46), residues: 123 loop : -1.88 (0.37), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 36 HIS 0.003 0.001 HIS L 96 PHE 0.016 0.001 PHE L 77 TYR 0.012 0.001 TYR A 489 ARG 0.004 0.000 ARG A 466 Details of bonding type rmsd link_NAG-ASN : bond 0.00360 ( 1) link_NAG-ASN : angle 1.24092 ( 3) hydrogen bonds : bond 0.02946 ( 79) hydrogen bonds : angle 5.83522 ( 207) SS BOND : bond 0.00238 ( 6) SS BOND : angle 0.82028 ( 12) covalent geometry : bond 0.00316 ( 3419) covalent geometry : angle 0.54439 ( 4647) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 1.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 388 ASN cc_start: 0.9030 (t0) cc_final: 0.8796 (t0) REVERT: A 471 GLU cc_start: 0.8597 (mm-30) cc_final: 0.7980 (mm-30) REVERT: A 484 GLU cc_start: 0.7865 (tp30) cc_final: 0.7494 (tp30) REVERT: H 59 TYR cc_start: 0.8728 (m-80) cc_final: 0.8238 (m-80) outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.9358 time to fit residues: 79.4519 Evaluate side-chains 60 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 1.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 0 optimal weight: 10.0000 chunk 27 optimal weight: 8.9990 chunk 22 optimal weight: 10.0000 chunk 40 optimal weight: 10.0000 chunk 13 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 19 optimal weight: 0.3980 chunk 6 optimal weight: 9.9990 chunk 20 optimal weight: 10.0000 chunk 4 optimal weight: 6.9990 chunk 24 optimal weight: 7.9990 overall best weight: 5.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** 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 = 0.3162 r_free = 0.3162 target = 0.048865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.040300 restraints weight = 53775.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.042718 restraints weight = 23093.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.044404 restraints weight = 12611.828| |-----------------------------------------------------------------------------| r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.3568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 3426 Z= 0.189 Angle : 0.566 4.878 4662 Z= 0.304 Chirality : 0.040 0.134 492 Planarity : 0.006 0.070 605 Dihedral : 5.345 34.941 494 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.52 % Favored : 85.48 % Rotamer: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % 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: -2.49 (0.40), residues: 420 helix: -3.29 (0.78), residues: 27 sheet: -1.01 (0.46), residues: 123 loop : -1.87 (0.38), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 436 HIS 0.004 0.001 HIS L 96 PHE 0.017 0.002 PHE L 77 TYR 0.010 0.001 TYR A 489 ARG 0.005 0.001 ARG A 466 Details of bonding type rmsd link_NAG-ASN : bond 0.00394 ( 1) link_NAG-ASN : angle 1.28547 ( 3) hydrogen bonds : bond 0.03198 ( 79) hydrogen bonds : angle 5.81389 ( 207) SS BOND : bond 0.00336 ( 6) SS BOND : angle 0.86989 ( 12) covalent geometry : bond 0.00406 ( 3419) covalent geometry : angle 0.56404 ( 4647) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 1.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 388 ASN cc_start: 0.9074 (t0) cc_final: 0.8834 (t0) REVERT: A 471 GLU cc_start: 0.8655 (mm-30) cc_final: 0.7952 (mm-30) REVERT: A 484 GLU cc_start: 0.7901 (tp30) cc_final: 0.7515 (tp30) REVERT: H 59 TYR cc_start: 0.8793 (m-80) cc_final: 0.8181 (m-80) outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.7948 time to fit residues: 60.1943 Evaluate side-chains 57 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 27 optimal weight: 10.0000 chunk 33 optimal weight: 4.9990 chunk 19 optimal weight: 6.9990 chunk 30 optimal weight: 7.9990 chunk 2 optimal weight: 0.8980 chunk 37 optimal weight: 9.9990 chunk 10 optimal weight: 9.9990 chunk 32 optimal weight: 10.0000 chunk 40 optimal weight: 6.9990 chunk 26 optimal weight: 7.9990 chunk 28 optimal weight: 5.9990 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** 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 = 0.3146 r_free = 0.3146 target = 0.048094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.039864 restraints weight = 54023.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.042233 restraints weight = 23564.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.043873 restraints weight = 12907.649| |-----------------------------------------------------------------------------| r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.3900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 3426 Z= 0.190 Angle : 0.573 5.094 4662 Z= 0.309 Chirality : 0.040 0.135 492 Planarity : 0.006 0.068 605 Dihedral : 5.382 34.971 494 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.62 % Favored : 87.38 % Rotamer: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % 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: -2.47 (0.40), residues: 420 helix: -3.38 (0.75), residues: 27 sheet: -0.84 (0.46), residues: 124 loop : -1.92 (0.38), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 436 HIS 0.002 0.001 HIS L 96 PHE 0.020 0.002 PHE L 77 TYR 0.012 0.001 TYR L 93 ARG 0.007 0.001 ARG A 466 Details of bonding type rmsd link_NAG-ASN : bond 0.00400 ( 1) link_NAG-ASN : angle 1.32556 ( 3) hydrogen bonds : bond 0.03260 ( 79) hydrogen bonds : angle 5.91536 ( 207) SS BOND : bond 0.00253 ( 6) SS BOND : angle 0.98872 ( 12) covalent geometry : bond 0.00411 ( 3419) covalent geometry : angle 0.57039 ( 4647) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 388 ASN cc_start: 0.9087 (t0) cc_final: 0.8867 (t0) REVERT: A 428 ASP cc_start: 0.9532 (t0) cc_final: 0.9224 (t0) REVERT: A 484 GLU cc_start: 0.7794 (tp30) cc_final: 0.7326 (tp30) REVERT: H 59 TYR cc_start: 0.8850 (m-80) cc_final: 0.8257 (m-80) REVERT: L 55 TYR cc_start: 0.9477 (p90) cc_final: 0.9152 (p90) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.4109 time to fit residues: 29.5262 Evaluate side-chains 54 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 21 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 18 optimal weight: 6.9990 chunk 8 optimal weight: 7.9990 chunk 34 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 chunk 26 optimal weight: 0.9980 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** 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 = 0.3179 r_free = 0.3179 target = 0.049143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.040790 restraints weight = 53645.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.043256 restraints weight = 23357.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.044948 restraints weight = 12743.958| |-----------------------------------------------------------------------------| r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.3987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3426 Z= 0.110 Angle : 0.536 5.204 4662 Z= 0.288 Chirality : 0.041 0.140 492 Planarity : 0.005 0.068 605 Dihedral : 5.250 37.789 494 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.67 % Favored : 88.33 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % 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: -2.32 (0.41), residues: 420 helix: -3.17 (0.83), residues: 26 sheet: -0.82 (0.46), residues: 124 loop : -1.79 (0.39), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 436 HIS 0.001 0.001 HIS A 519 PHE 0.015 0.001 PHE L 77 TYR 0.010 0.001 TYR A 489 ARG 0.004 0.001 ARG A 466 Details of bonding type rmsd link_NAG-ASN : bond 0.00306 ( 1) link_NAG-ASN : angle 1.35774 ( 3) hydrogen bonds : bond 0.02706 ( 79) hydrogen bonds : angle 5.59732 ( 207) SS BOND : bond 0.00292 ( 6) SS BOND : angle 0.97880 ( 12) covalent geometry : bond 0.00257 ( 3419) covalent geometry : angle 0.53339 ( 4647) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 388 ASN cc_start: 0.9036 (t0) cc_final: 0.8824 (t0) REVERT: A 484 GLU cc_start: 0.7866 (tp30) cc_final: 0.7470 (tp30) REVERT: H 34 MET cc_start: 0.9323 (mtm) cc_final: 0.8903 (mmm) REVERT: H 59 TYR cc_start: 0.8806 (m-80) cc_final: 0.8334 (m-80) outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.3938 time to fit residues: 29.2699 Evaluate side-chains 54 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 25 optimal weight: 9.9990 chunk 31 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 36 optimal weight: 8.9990 chunk 1 optimal weight: 0.0170 chunk 9 optimal weight: 9.9990 chunk 12 optimal weight: 7.9990 chunk 24 optimal weight: 9.9990 chunk 16 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 overall best weight: 3.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** 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 = 0.3164 r_free = 0.3164 target = 0.048442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.040390 restraints weight = 54398.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.042775 restraints weight = 23476.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.044304 restraints weight = 12777.166| |-----------------------------------------------------------------------------| r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.4296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 3426 Z= 0.135 Angle : 0.542 4.825 4662 Z= 0.291 Chirality : 0.040 0.133 492 Planarity : 0.005 0.066 605 Dihedral : 5.254 38.064 494 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.10 % Favored : 86.90 % Rotamer: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % 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: -2.35 (0.40), residues: 420 helix: -3.23 (0.81), residues: 26 sheet: -0.83 (0.46), residues: 124 loop : -1.82 (0.39), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 436 HIS 0.001 0.001 HIS L 96 PHE 0.015 0.001 PHE L 77 TYR 0.009 0.001 TYR H 80 ARG 0.006 0.001 ARG A 466 Details of bonding type rmsd link_NAG-ASN : bond 0.00363 ( 1) link_NAG-ASN : angle 1.24452 ( 3) hydrogen bonds : bond 0.02790 ( 79) hydrogen bonds : angle 5.52365 ( 207) SS BOND : bond 0.00237 ( 6) SS BOND : angle 0.84240 ( 12) covalent geometry : bond 0.00307 ( 3419) covalent geometry : angle 0.54046 ( 4647) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 484 GLU cc_start: 0.7852 (tp30) cc_final: 0.7476 (tp30) REVERT: H 34 MET cc_start: 0.9458 (mtm) cc_final: 0.8881 (mmm) REVERT: H 59 TYR cc_start: 0.8840 (m-80) cc_final: 0.8245 (m-80) outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.4006 time to fit residues: 29.3080 Evaluate side-chains 54 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 23 optimal weight: 9.9990 chunk 28 optimal weight: 10.0000 chunk 41 optimal weight: 0.0040 chunk 32 optimal weight: 0.9990 chunk 34 optimal weight: 10.0000 chunk 20 optimal weight: 7.9990 chunk 3 optimal weight: 9.9990 chunk 22 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 6 optimal weight: 10.0000 chunk 7 optimal weight: 0.3980 overall best weight: 1.8798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** 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 = 0.3178 r_free = 0.3178 target = 0.048927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.040473 restraints weight = 54212.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.042938 restraints weight = 23624.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.044657 restraints weight = 12917.566| |-----------------------------------------------------------------------------| r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.4322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 3426 Z= 0.101 Angle : 0.533 4.952 4662 Z= 0.283 Chirality : 0.041 0.142 492 Planarity : 0.005 0.066 605 Dihedral : 5.185 40.034 494 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.90 % Favored : 88.10 % 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: -2.28 (0.41), residues: 420 helix: -3.18 (0.82), residues: 26 sheet: -0.72 (0.47), residues: 118 loop : -1.78 (0.39), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 436 HIS 0.001 0.000 HIS A 519 PHE 0.013 0.001 PHE L 77 TYR 0.008 0.001 TYR L 93 ARG 0.007 0.001 ARG A 466 Details of bonding type rmsd link_NAG-ASN : bond 0.00318 ( 1) link_NAG-ASN : angle 1.28266 ( 3) hydrogen bonds : bond 0.02536 ( 79) hydrogen bonds : angle 5.38945 ( 207) SS BOND : bond 0.00265 ( 6) SS BOND : angle 0.74629 ( 12) covalent geometry : bond 0.00243 ( 3419) covalent geometry : angle 0.53108 ( 4647) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 484 GLU cc_start: 0.7906 (tp30) cc_final: 0.7447 (tp30) REVERT: H 34 MET cc_start: 0.9414 (mtm) cc_final: 0.8871 (mmm) REVERT: H 59 TYR cc_start: 0.8797 (m-80) cc_final: 0.8350 (m-80) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.4299 time to fit residues: 30.7888 Evaluate side-chains 50 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 34 optimal weight: 8.9990 chunk 2 optimal weight: 4.9990 chunk 7 optimal weight: 0.7980 chunk 30 optimal weight: 8.9990 chunk 13 optimal weight: 2.9990 chunk 23 optimal weight: 9.9990 chunk 9 optimal weight: 9.9990 chunk 8 optimal weight: 1.9990 chunk 11 optimal weight: 9.9990 chunk 15 optimal weight: 9.9990 chunk 18 optimal weight: 0.8980 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** 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 = 0.3165 r_free = 0.3165 target = 0.048464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.040205 restraints weight = 54925.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.042636 restraints weight = 23644.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.044313 restraints weight = 12873.685| |-----------------------------------------------------------------------------| r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.4496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3426 Z= 0.112 Angle : 0.534 5.051 4662 Z= 0.285 Chirality : 0.041 0.136 492 Planarity : 0.006 0.072 605 Dihedral : 5.169 39.836 494 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.67 % Favored : 88.33 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % 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: -2.34 (0.41), residues: 420 helix: -3.18 (0.82), residues: 26 sheet: -0.75 (0.47), residues: 114 loop : -1.83 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 36 HIS 0.001 0.000 HIS A 519 PHE 0.012 0.001 PHE L 77 TYR 0.008 0.001 TYR L 93 ARG 0.008 0.001 ARG A 466 Details of bonding type rmsd link_NAG-ASN : bond 0.00458 ( 1) link_NAG-ASN : angle 1.00919 ( 3) hydrogen bonds : bond 0.02580 ( 79) hydrogen bonds : angle 5.30852 ( 207) SS BOND : bond 0.00229 ( 6) SS BOND : angle 0.80005 ( 12) covalent geometry : bond 0.00265 ( 3419) covalent geometry : angle 0.53219 ( 4647) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 388 ASN cc_start: 0.8937 (t0) cc_final: 0.8731 (t0) REVERT: A 484 GLU cc_start: 0.7900 (tp30) cc_final: 0.7486 (tp30) REVERT: H 34 MET cc_start: 0.9407 (mtm) cc_final: 0.8816 (mmm) REVERT: H 59 TYR cc_start: 0.8853 (m-80) cc_final: 0.8273 (m-80) REVERT: L 42 TYR cc_start: 0.8209 (m-10) cc_final: 0.7945 (m-10) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.3606 time to fit residues: 25.8152 Evaluate side-chains 53 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 16 optimal weight: 0.7980 chunk 11 optimal weight: 6.9990 chunk 19 optimal weight: 9.9990 chunk 41 optimal weight: 0.5980 chunk 4 optimal weight: 0.0270 chunk 0 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 chunk 6 optimal weight: 10.0000 chunk 36 optimal weight: 9.9990 chunk 18 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 overall best weight: 2.2842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 6 GLN ** 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 = 0.3171 r_free = 0.3171 target = 0.048719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.040330 restraints weight = 53947.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.042748 restraints weight = 23312.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.044485 restraints weight = 12813.087| |-----------------------------------------------------------------------------| r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.4494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3426 Z= 0.106 Angle : 0.522 4.584 4662 Z= 0.277 Chirality : 0.041 0.138 492 Planarity : 0.005 0.061 605 Dihedral : 5.155 40.886 494 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.19 % Favored : 88.81 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % 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: -2.27 (0.41), residues: 420 helix: -3.19 (0.82), residues: 26 sheet: -0.74 (0.46), residues: 114 loop : -1.76 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 436 HIS 0.001 0.000 HIS A 519 PHE 0.014 0.001 PHE H 29 TYR 0.008 0.001 TYR L 93 ARG 0.009 0.001 ARG A 466 Details of bonding type rmsd link_NAG-ASN : bond 0.00368 ( 1) link_NAG-ASN : angle 1.10856 ( 3) hydrogen bonds : bond 0.02534 ( 79) hydrogen bonds : angle 5.27528 ( 207) SS BOND : bond 0.00220 ( 6) SS BOND : angle 0.78089 ( 12) covalent geometry : bond 0.00252 ( 3419) covalent geometry : angle 0.52031 ( 4647) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3898.90 seconds wall clock time: 72 minutes 26.23 seconds (4346.23 seconds total)