Starting phenix.real_space_refine on Thu Jul 24 15:18:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x92_33064/07_2025/7x92_33064_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x92_33064/07_2025/7x92_33064.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/7x92_33064/07_2025/7x92_33064.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x92_33064/07_2025/7x92_33064.map" model { file = "/net/cci-nas-00/data/ceres_data/7x92_33064/07_2025/7x92_33064_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x92_33064/07_2025/7x92_33064_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 15 5.16 5 C 2134 2.51 5 N 557 2.21 5 O 652 1.98 5 H 3171 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 6529 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: 1896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1896 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "L" Number of atoms: 1617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 1617 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.59, per 1000 atoms: 0.55 Number of scatterers: 6529 At special positions: 0 Unit cell: (69.636, 61.346, 101.967, 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 15 16.00 O 652 8.00 N 557 7.00 C 2134 6.00 H 3171 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=2.04 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=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " 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 BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG B 1 " - " ASN A 343 " Time building additional restraints: 1.62 Conformation dependent library (CDL) restraints added in 582.9 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: 778 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 8 sheets defined 8.5% alpha, 22.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 366 through 371 Processing helix chain 'A' and resid 383 through 390 removed outlier: 3.923A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.240A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 61 through 65 Processing sheet with id=AA1, first strand: chain 'A' and resid 355 through 358 removed outlier: 3.872A pdb=" N LYS A 356 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (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 'H' and resid 4 through 7 removed outlier: 3.712A pdb=" N THR H 69 " --> pdb=" O GLN H 82 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 49 through 51 Processing sheet with id=AA5, first strand: chain 'L' and resid 4 through 5 Processing sheet with id=AA6, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.520A pdb=" N ALA L 13 " --> pdb=" O GLU L 105 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 33 through 38 removed outlier: 3.639A pdb=" N TYR L 87 " --> pdb=" O TYR L 36 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 48 through 49 removed outlier: 3.582A pdb=" N ASN L 53 " --> pdb=" O TYR L 49 " (cutoff:3.500A) 84 hydrogen bonds defined for protein. 189 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: 1.88 Time building geometry restraints manager: 1.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 3171 1.04 - 1.24: 413 1.24 - 1.44: 1160 1.44 - 1.63: 1853 1.63 - 1.83: 18 Bond restraints: 6615 Sorted by residual: bond pdb=" CG PRO A 507 " pdb=" CD PRO A 507 " ideal model delta sigma weight residual 1.503 1.281 0.222 3.40e-02 8.65e+02 4.25e+01 bond pdb=" N PRO A 507 " pdb=" CD PRO A 507 " ideal model delta sigma weight residual 1.473 1.511 -0.038 1.40e-02 5.10e+03 7.42e+00 bond pdb=" CB PRO A 507 " pdb=" CG PRO A 507 " ideal model delta sigma weight residual 1.492 1.617 -0.125 5.00e-02 4.00e+02 6.28e+00 bond pdb=" N PRO A 507 " pdb=" CA PRO A 507 " ideal model delta sigma weight residual 1.466 1.445 0.021 1.17e-02 7.31e+03 3.28e+00 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 3.01e+00 ... (remaining 6610 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.24: 11837 6.24 - 12.49: 3 12.49 - 18.73: 2 18.73 - 24.98: 0 24.98 - 31.22: 3 Bond angle restraints: 11845 Sorted by residual: angle pdb=" CA PRO A 507 " pdb=" N PRO A 507 " pdb=" CD PRO A 507 " ideal model delta sigma weight residual 112.00 94.57 17.43 1.40e+00 5.10e-01 1.55e+02 angle pdb=" CB TYR L 96 " pdb=" CA TYR L 96 " pdb=" HA TYR L 96 " ideal model delta sigma weight residual 109.00 77.78 31.22 3.00e+00 1.11e-01 1.08e+02 angle pdb=" C TYR L 96 " pdb=" CA TYR L 96 " pdb=" HA TYR L 96 " ideal model delta sigma weight residual 109.00 77.92 31.08 3.00e+00 1.11e-01 1.07e+02 angle pdb=" N TYR L 96 " pdb=" CA TYR L 96 " pdb=" HA TYR L 96 " ideal model delta sigma weight residual 110.00 82.48 27.52 3.00e+00 1.11e-01 8.41e+01 angle pdb=" N PRO A 507 " pdb=" CD PRO A 507 " pdb=" CG PRO A 507 " ideal model delta sigma weight residual 103.20 90.05 13.15 1.50e+00 4.44e-01 7.68e+01 ... (remaining 11840 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.81: 2933 21.81 - 43.63: 227 43.63 - 65.44: 54 65.44 - 87.26: 4 87.26 - 109.07: 9 Dihedral angle restraints: 3227 sinusoidal: 1718 harmonic: 1509 Sorted by residual: dihedral pdb=" C TYR L 96 " pdb=" N TYR L 96 " pdb=" CA TYR L 96 " pdb=" CB TYR L 96 " ideal model delta harmonic sigma weight residual -122.60 -145.46 22.86 0 2.50e+00 1.60e-01 8.36e+01 dihedral pdb=" N TYR L 96 " pdb=" C TYR L 96 " pdb=" CA TYR L 96 " pdb=" CB TYR L 96 " ideal model delta harmonic sigma weight residual 122.80 143.62 -20.82 0 2.50e+00 1.60e-01 6.93e+01 dihedral pdb=" CB CYS A 336 " pdb=" SG CYS A 336 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual 93.00 43.61 49.39 1 1.00e+01 1.00e-02 3.35e+01 ... (remaining 3224 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.183: 506 0.183 - 0.366: 0 0.366 - 0.549: 0 0.549 - 0.732: 0 0.732 - 0.916: 1 Chirality restraints: 507 Sorted by residual: chirality pdb=" CA TYR L 96 " pdb=" N TYR L 96 " pdb=" C TYR L 96 " pdb=" CB TYR L 96 " both_signs ideal model delta sigma weight residual False 2.51 1.59 0.92 2.00e-01 2.50e+01 2.10e+01 chirality pdb=" C1 NAG B 1 " pdb=" ND2 ASN A 343 " pdb=" C2 NAG B 1 " pdb=" O5 NAG B 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-01 2.50e+01 8.10e-01 chirality pdb=" CA ILE L 39 " pdb=" N ILE L 39 " pdb=" C ILE L 39 " pdb=" CB ILE L 39 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.92e-01 ... (remaining 504 not shown) Planarity restraints: 1010 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 506 " 0.100 5.00e-02 4.00e+02 1.36e-01 2.96e+01 pdb=" N PRO A 507 " -0.235 5.00e-02 4.00e+02 pdb=" CA PRO A 507 " 0.064 5.00e-02 4.00e+02 pdb=" CD PRO A 507 " 0.070 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU L 94 " -0.026 5.00e-02 4.00e+02 3.98e-02 2.54e+00 pdb=" N PRO L 95 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO L 95 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO L 95 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL L 58 " -0.026 5.00e-02 4.00e+02 3.97e-02 2.52e+00 pdb=" N PRO L 59 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO L 59 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO L 59 " -0.022 5.00e-02 4.00e+02 ... (remaining 1007 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.24: 847 2.24 - 2.83: 13998 2.83 - 3.42: 15813 3.42 - 4.01: 21902 4.01 - 4.60: 32318 Nonbonded interactions: 84878 Sorted by model distance: nonbonded pdb=" OG SER H 30 " pdb="HD21 ASN H 74 " model vdw 1.650 2.450 nonbonded pdb=" OE1 GLN L 6 " pdb=" H GLY L 101 " model vdw 1.667 2.450 nonbonded pdb=" OD1 ASN A 448 " pdb=" H ASN A 450 " model vdw 1.679 2.450 nonbonded pdb=" H TYR L 96 " pdb=" HA TYR L 96 " model vdw 1.695 1.816 nonbonded pdb=" OH TYR A 449 " pdb="HD21 ASN H 31 " model vdw 1.697 2.450 ... (remaining 84873 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: 0.280 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: 0.120 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 17.490 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 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 : 0.005 0.222 3452 Z= 0.194 Angle : 0.749 17.433 4703 Z= 0.431 Chirality : 0.061 0.916 507 Planarity : 0.007 0.136 607 Dihedral : 17.172 109.073 1252 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.52 % Favored : 85.48 % Rotamer: Outliers : 0.27 % Allowed : 0.00 % Favored : 99.73 % Cbeta Deviations : 0.26 % 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 (0.41), residues: 420 helix: -2.72 (1.22), residues: 20 sheet: -0.96 (0.47), residues: 143 loop : -2.10 (0.37), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 47 HIS 0.001 0.000 HIS H 35 PHE 0.012 0.001 PHE A 377 TYR 0.007 0.001 TYR L 96 ARG 0.002 0.000 ARG A 509 Details of bonding type rmsd link_NAG-ASN : bond 0.00268 ( 1) link_NAG-ASN : angle 1.57768 ( 3) link_BETA1-4 : bond 0.00596 ( 1) link_BETA1-4 : angle 2.38859 ( 3) hydrogen bonds : bond 0.13598 ( 84) hydrogen bonds : angle 7.39346 ( 189) SS BOND : bond 0.00526 ( 6) SS BOND : angle 1.19856 ( 12) covalent geometry : bond 0.00529 ( 3444) covalent geometry : angle 0.74482 ( 4685) *********************** 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 136 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 135 time to evaluate : 0.621 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: 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: H 45 LEU cc_start: 0.8126 (pp) cc_final: 0.7842 (pp) REVERT: L 34 ASN cc_start: 0.7531 (m-40) cc_final: 0.7317 (m-40) REVERT: L 46 LEU cc_start: 0.8679 (tp) cc_final: 0.8435 (tp) outliers start: 1 outliers final: 1 residues processed: 135 average time/residue: 0.4173 time to fit residues: 65.6180 Evaluate side-chains 106 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 105 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 6.9990 chunk 31 optimal weight: 7.9990 chunk 17 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 16 optimal weight: 10.0000 chunk 32 optimal weight: 8.9990 chunk 12 optimal weight: 9.9990 chunk 19 optimal weight: 6.9990 chunk 23 optimal weight: 9.9990 chunk 37 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.052083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.040955 restraints weight = 44814.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.043824 restraints weight = 19830.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.045949 restraints weight = 11006.758| |-----------------------------------------------------------------------------| r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 3452 Z= 0.262 Angle : 0.697 7.253 4703 Z= 0.359 Chirality : 0.047 0.368 507 Planarity : 0.005 0.046 607 Dihedral : 11.071 76.047 512 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 16.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.71 % Favored : 84.29 % Rotamer: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % 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: -2.79 (0.40), residues: 420 helix: -4.56 (0.44), residues: 24 sheet: -0.72 (0.48), residues: 137 loop : -2.33 (0.36), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP H 47 HIS 0.001 0.001 HIS A 519 PHE 0.014 0.002 PHE A 377 TYR 0.021 0.002 TYR L 96 ARG 0.005 0.001 ARG A 509 Details of bonding type rmsd link_NAG-ASN : bond 0.00125 ( 1) link_NAG-ASN : angle 2.05695 ( 3) link_BETA1-4 : bond 0.00397 ( 1) link_BETA1-4 : angle 1.51834 ( 3) hydrogen bonds : bond 0.03465 ( 84) hydrogen bonds : angle 6.94310 ( 189) SS BOND : bond 0.00553 ( 6) SS BOND : angle 1.34363 ( 12) covalent geometry : bond 0.00557 ( 3444) covalent geometry : angle 0.69187 ( 4685) *********************** 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 104 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.544 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: symmetry clash revert: symmetry clash REVERT: A 398 ASP cc_start: 0.7661 (m-30) cc_final: 0.7150 (m-30) REVERT: A 442 ASP cc_start: 0.9210 (m-30) cc_final: 0.8841 (m-30) REVERT: H 114 TYR cc_start: 0.9568 (m-80) cc_final: 0.9169 (m-10) outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.4238 time to fit residues: 52.4483 Evaluate side-chains 84 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 38 optimal weight: 10.0000 chunk 35 optimal weight: 0.9980 chunk 20 optimal weight: 4.9990 chunk 40 optimal weight: 10.0000 chunk 2 optimal weight: 9.9990 chunk 26 optimal weight: 6.9990 chunk 1 optimal weight: 7.9990 chunk 14 optimal weight: 5.9990 chunk 22 optimal weight: 10.0000 chunk 19 optimal weight: 10.0000 chunk 17 optimal weight: 0.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 31 ASN ** H 35 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 = 0.3034 r_free = 0.3034 target = 0.052056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.041238 restraints weight = 44634.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.044163 restraints weight = 19479.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.046275 restraints weight = 10650.453| |-----------------------------------------------------------------------------| r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.3319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 3452 Z= 0.169 Angle : 0.648 7.831 4703 Z= 0.332 Chirality : 0.047 0.336 507 Planarity : 0.004 0.041 607 Dihedral : 8.431 46.815 512 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.24 % Favored : 84.76 % Rotamer: Outliers : 0.27 % Allowed : 1.65 % Favored : 98.08 % 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: -2.84 (0.40), residues: 420 helix: -3.81 (0.67), residues: 26 sheet: -0.64 (0.48), residues: 140 loop : -2.53 (0.36), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 436 HIS 0.001 0.001 HIS H 35 PHE 0.010 0.001 PHE A 377 TYR 0.014 0.001 TYR H 53 ARG 0.003 0.000 ARG A 509 Details of bonding type rmsd link_NAG-ASN : bond 0.00051 ( 1) link_NAG-ASN : angle 1.26010 ( 3) link_BETA1-4 : bond 0.00186 ( 1) link_BETA1-4 : angle 2.64073 ( 3) hydrogen bonds : bond 0.03111 ( 84) hydrogen bonds : angle 6.69026 ( 189) SS BOND : bond 0.00510 ( 6) SS BOND : angle 1.25047 ( 12) covalent geometry : bond 0.00380 ( 3444) covalent geometry : angle 0.64204 ( 4685) *********************** 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 105 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 104 time to evaluate : 0.927 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: symmetry clash REVERT: A 398 ASP cc_start: 0.7619 (m-30) cc_final: 0.7281 (m-30) REVERT: A 405 ASP cc_start: 0.9105 (t0) cc_final: 0.8656 (t0) REVERT: A 442 ASP cc_start: 0.9094 (m-30) cc_final: 0.8733 (m-30) REVERT: H 31 ASN cc_start: 0.9513 (OUTLIER) cc_final: 0.9310 (m110) REVERT: H 35 HIS cc_start: 0.9257 (m90) cc_final: 0.8957 (m90) REVERT: H 73 ASP cc_start: 0.8221 (t0) cc_final: 0.7992 (t0) REVERT: H 114 TYR cc_start: 0.9541 (m-80) cc_final: 0.9201 (m-10) REVERT: L 4 LEU cc_start: 0.8875 (mm) cc_final: 0.8665 (tt) REVERT: L 31 ASN cc_start: 0.9230 (t0) cc_final: 0.9024 (t0) REVERT: L 49 TYR cc_start: 0.9582 (p90) cc_final: 0.9353 (p90) outliers start: 1 outliers final: 0 residues processed: 105 average time/residue: 0.4226 time to fit residues: 52.7712 Evaluate side-chains 94 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 93 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 39 optimal weight: 8.9990 chunk 27 optimal weight: 10.0000 chunk 22 optimal weight: 9.9990 chunk 16 optimal weight: 9.9990 chunk 25 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 10 optimal weight: 7.9990 chunk 13 optimal weight: 8.9990 chunk 26 optimal weight: 7.9990 chunk 23 optimal weight: 0.9990 chunk 36 optimal weight: 9.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.051222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.040549 restraints weight = 48200.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.043449 restraints weight = 20921.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.045525 restraints weight = 11416.719| |-----------------------------------------------------------------------------| r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.3829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 3452 Z= 0.199 Angle : 0.664 6.823 4703 Z= 0.343 Chirality : 0.046 0.301 507 Planarity : 0.004 0.041 607 Dihedral : 7.012 48.193 512 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.24 % Allowed : 15.95 % Favored : 83.81 % Rotamer: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.97 (0.40), residues: 420 helix: -3.92 (0.63), residues: 26 sheet: -0.78 (0.47), residues: 144 loop : -2.61 (0.36), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 436 HIS 0.001 0.001 HIS A 519 PHE 0.011 0.002 PHE A 377 TYR 0.016 0.002 TYR H 53 ARG 0.003 0.000 ARG A 509 Details of bonding type rmsd link_NAG-ASN : bond 0.00071 ( 1) link_NAG-ASN : angle 1.40595 ( 3) link_BETA1-4 : bond 0.00010 ( 1) link_BETA1-4 : angle 3.12798 ( 3) hydrogen bonds : bond 0.02982 ( 84) hydrogen bonds : angle 6.56881 ( 189) SS BOND : bond 0.00475 ( 6) SS BOND : angle 1.07895 ( 12) covalent geometry : bond 0.00429 ( 3444) covalent geometry : angle 0.65727 ( 4685) *********************** 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 98 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.558 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 398 ASP cc_start: 0.7538 (m-30) cc_final: 0.7169 (m-30) REVERT: A 405 ASP cc_start: 0.9006 (t0) cc_final: 0.8732 (t0) REVERT: A 442 ASP cc_start: 0.9078 (m-30) cc_final: 0.8706 (m-30) REVERT: H 34 MET cc_start: 0.8040 (pmm) cc_final: 0.7818 (pmm) REVERT: H 35 HIS cc_start: 0.9304 (m90) cc_final: 0.8855 (m90) REVERT: H 114 TYR cc_start: 0.9577 (m-80) cc_final: 0.8565 (m-10) REVERT: L 31 ASN cc_start: 0.9261 (t0) cc_final: 0.9059 (t0) REVERT: L 97 THR cc_start: 0.8811 (t) cc_final: 0.8508 (t) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.3406 time to fit residues: 39.9508 Evaluate side-chains 85 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 9.9990 chunk 27 optimal weight: 0.9990 chunk 10 optimal weight: 0.4980 chunk 16 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 6 optimal weight: 10.0000 chunk 40 optimal weight: 0.0040 chunk 39 optimal weight: 0.9980 chunk 21 optimal weight: 10.0000 chunk 31 optimal weight: 8.9990 chunk 7 optimal weight: 2.9990 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.054175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.043241 restraints weight = 44811.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.046272 restraints weight = 19052.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.048417 restraints weight = 10285.374| |-----------------------------------------------------------------------------| r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.4040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 3452 Z= 0.106 Angle : 0.611 7.429 4703 Z= 0.312 Chirality : 0.048 0.321 507 Planarity : 0.003 0.040 607 Dihedral : 6.494 45.143 512 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.48 % Allowed : 14.52 % Favored : 85.00 % Rotamer: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.94 (0.39), residues: 420 helix: -3.87 (0.62), residues: 26 sheet: -0.86 (0.47), residues: 136 loop : -2.48 (0.35), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 436 HIS 0.001 0.001 HIS H 35 PHE 0.008 0.001 PHE A 377 TYR 0.013 0.001 TYR H 53 ARG 0.002 0.000 ARG A 509 Details of bonding type rmsd link_NAG-ASN : bond 0.00344 ( 1) link_NAG-ASN : angle 1.40639 ( 3) link_BETA1-4 : bond 0.00215 ( 1) link_BETA1-4 : angle 3.29752 ( 3) hydrogen bonds : bond 0.02706 ( 84) hydrogen bonds : angle 6.40781 ( 189) SS BOND : bond 0.00469 ( 6) SS BOND : angle 0.96738 ( 12) covalent geometry : bond 0.00256 ( 3444) covalent geometry : angle 0.60315 ( 4685) *********************** 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 106 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.770 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: symmetry clash revert: symmetry clash REVERT: A 398 ASP cc_start: 0.7599 (m-30) cc_final: 0.7232 (m-30) REVERT: A 405 ASP cc_start: 0.8775 (t0) cc_final: 0.8498 (t0) REVERT: A 442 ASP cc_start: 0.8969 (m-30) cc_final: 0.8581 (m-30) REVERT: H 35 HIS cc_start: 0.9157 (m90) cc_final: 0.8495 (m90) REVERT: H 73 ASP cc_start: 0.8182 (t0) cc_final: 0.7977 (t0) REVERT: H 114 TYR cc_start: 0.9531 (m-80) cc_final: 0.9322 (m-80) REVERT: L 97 THR cc_start: 0.8676 (t) cc_final: 0.8417 (t) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.3809 time to fit residues: 48.9853 Evaluate side-chains 87 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 9.9990 chunk 1 optimal weight: 10.0000 chunk 35 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 27 optimal weight: 7.9990 chunk 29 optimal weight: 10.0000 chunk 11 optimal weight: 3.9990 chunk 37 optimal weight: 20.0000 chunk 25 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 HIS ** 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 = 0.3075 r_free = 0.3075 target = 0.052697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.042174 restraints weight = 45089.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.045073 restraints weight = 19193.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.047123 restraints weight = 10373.339| |-----------------------------------------------------------------------------| r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.4333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3452 Z= 0.144 Angle : 0.627 7.311 4703 Z= 0.323 Chirality : 0.047 0.327 507 Planarity : 0.004 0.061 607 Dihedral : 6.341 43.013 512 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.71 % Allowed : 16.19 % Favored : 83.10 % Rotamer: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % 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 (0.39), residues: 420 helix: -4.11 (0.57), residues: 26 sheet: -0.57 (0.49), residues: 130 loop : -2.60 (0.34), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 35 HIS 0.001 0.001 HIS H 35 PHE 0.021 0.002 PHE H 112 TYR 0.013 0.001 TYR H 53 ARG 0.008 0.000 ARG A 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00006 ( 1) link_NAG-ASN : angle 1.24450 ( 3) link_BETA1-4 : bond 0.00336 ( 1) link_BETA1-4 : angle 3.52291 ( 3) hydrogen bonds : bond 0.02746 ( 84) hydrogen bonds : angle 6.47049 ( 189) SS BOND : bond 0.00446 ( 6) SS BOND : angle 1.05813 ( 12) covalent geometry : bond 0.00323 ( 3444) covalent geometry : angle 0.61886 ( 4685) *********************** 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 101 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.555 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 386 LYS cc_start: 0.9677 (mttp) cc_final: 0.9461 (mttm) REVERT: A 398 ASP cc_start: 0.7523 (m-30) cc_final: 0.7149 (m-30) REVERT: A 442 ASP cc_start: 0.9012 (m-30) cc_final: 0.8619 (m-30) REVERT: H 35 HIS cc_start: 0.9241 (m90) cc_final: 0.8942 (m-70) REVERT: H 114 TYR cc_start: 0.9518 (m-80) cc_final: 0.8553 (m-10) REVERT: L 31 ASN cc_start: 0.9320 (t0) cc_final: 0.9086 (t0) REVERT: L 93 ASN cc_start: 0.9628 (t0) cc_final: 0.9410 (t0) REVERT: L 97 THR cc_start: 0.8324 (t) cc_final: 0.8100 (t) outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.3004 time to fit residues: 37.2796 Evaluate side-chains 87 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 12 optimal weight: 0.9990 chunk 17 optimal weight: 8.9990 chunk 29 optimal weight: 3.9990 chunk 31 optimal weight: 9.9990 chunk 6 optimal weight: 9.9990 chunk 9 optimal weight: 3.9990 chunk 22 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 chunk 3 optimal weight: 0.9990 chunk 36 optimal weight: 9.9990 chunk 11 optimal weight: 9.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 HIS ** 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 = 0.3055 r_free = 0.3055 target = 0.052022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.041569 restraints weight = 47069.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.044426 restraints weight = 20078.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.046463 restraints weight = 10847.077| |-----------------------------------------------------------------------------| r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.4537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3452 Z= 0.161 Angle : 0.634 7.174 4703 Z= 0.329 Chirality : 0.046 0.306 507 Planarity : 0.004 0.040 607 Dihedral : 6.190 41.604 512 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.71 % Allowed : 14.76 % Favored : 84.52 % Rotamer: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.99 (0.40), residues: 420 helix: -3.97 (0.63), residues: 26 sheet: -0.96 (0.46), residues: 148 loop : -2.51 (0.36), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP L 35 HIS 0.003 0.001 HIS H 35 PHE 0.025 0.002 PHE H 111 TYR 0.013 0.002 TYR H 53 ARG 0.006 0.001 ARG A 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00045 ( 1) link_NAG-ASN : angle 1.29778 ( 3) link_BETA1-4 : bond 0.00251 ( 1) link_BETA1-4 : angle 3.62691 ( 3) hydrogen bonds : bond 0.02783 ( 84) hydrogen bonds : angle 6.47703 ( 189) SS BOND : bond 0.00567 ( 6) SS BOND : angle 1.35016 ( 12) covalent geometry : bond 0.00354 ( 3444) covalent geometry : angle 0.62404 ( 4685) *********************** 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 102 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.538 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: symmetry clash REVERT: A 398 ASP cc_start: 0.7464 (m-30) cc_final: 0.7099 (m-30) REVERT: A 405 ASP cc_start: 0.8741 (t70) cc_final: 0.8423 (t0) REVERT: A 442 ASP cc_start: 0.8995 (m-30) cc_final: 0.8610 (m-30) REVERT: H 101 THR cc_start: 0.8356 (t) cc_final: 0.8078 (t) REVERT: H 111 PHE cc_start: 0.9130 (t80) cc_final: 0.8679 (t80) REVERT: H 114 TYR cc_start: 0.9515 (m-80) cc_final: 0.8546 (m-10) REVERT: L 31 ASN cc_start: 0.9329 (t0) cc_final: 0.9110 (t0) REVERT: L 49 TYR cc_start: 0.9577 (p90) cc_final: 0.9325 (p90) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.2986 time to fit residues: 37.5256 Evaluate side-chains 84 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 38 optimal weight: 4.9990 chunk 29 optimal weight: 8.9990 chunk 31 optimal weight: 10.0000 chunk 8 optimal weight: 8.9990 chunk 28 optimal weight: 10.0000 chunk 9 optimal weight: 5.9990 chunk 26 optimal weight: 9.9990 chunk 32 optimal weight: 3.9990 chunk 25 optimal weight: 7.9990 chunk 37 optimal weight: 9.9990 chunk 34 optimal weight: 9.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 ASN L 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.049335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.039377 restraints weight = 48729.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.042085 restraints weight = 20526.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.043992 restraints weight = 11046.919| |-----------------------------------------------------------------------------| r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.4893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 3452 Z= 0.250 Angle : 0.698 7.915 4703 Z= 0.367 Chirality : 0.046 0.297 507 Planarity : 0.004 0.040 607 Dihedral : 6.309 39.631 512 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 20.28 Ramachandran Plot: Outliers : 0.71 % Allowed : 17.38 % Favored : 81.90 % Rotamer: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.05 (0.40), residues: 420 helix: -4.12 (0.56), residues: 26 sheet: -0.95 (0.47), residues: 144 loop : -2.56 (0.37), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 436 HIS 0.005 0.002 HIS H 35 PHE 0.023 0.002 PHE H 112 TYR 0.017 0.002 TYR L 96 ARG 0.005 0.001 ARG A 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00227 ( 1) link_NAG-ASN : angle 1.46264 ( 3) link_BETA1-4 : bond 0.00030 ( 1) link_BETA1-4 : angle 3.80939 ( 3) hydrogen bonds : bond 0.03122 ( 84) hydrogen bonds : angle 6.58268 ( 189) SS BOND : bond 0.00577 ( 6) SS BOND : angle 1.27343 ( 12) covalent geometry : bond 0.00526 ( 3444) covalent geometry : angle 0.68870 ( 4685) *********************** 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 92 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.574 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 398 ASP cc_start: 0.7307 (m-30) cc_final: 0.6974 (m-30) REVERT: A 442 ASP cc_start: 0.8990 (m-30) cc_final: 0.8640 (m-30) REVERT: H 70 ILE cc_start: 0.8726 (tt) cc_final: 0.8503 (tt) REVERT: L 91 TYR cc_start: 0.9284 (p90) cc_final: 0.8977 (p90) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.3154 time to fit residues: 35.6168 Evaluate side-chains 78 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 2 optimal weight: 8.9990 chunk 22 optimal weight: 6.9990 chunk 14 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 39 optimal weight: 10.0000 chunk 17 optimal weight: 7.9990 chunk 33 optimal weight: 9.9990 chunk 40 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 ASN L 38 GLN L 100 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.051193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.040276 restraints weight = 45546.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.043148 restraints weight = 19335.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.045199 restraints weight = 10528.408| |-----------------------------------------------------------------------------| r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.4985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3452 Z= 0.145 Angle : 0.636 7.628 4703 Z= 0.330 Chirality : 0.046 0.291 507 Planarity : 0.004 0.040 607 Dihedral : 6.001 35.851 512 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 16.77 Ramachandran Plot: Outliers : 0.71 % Allowed : 14.52 % Favored : 84.76 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.10 (0.40), residues: 420 helix: -3.95 (0.61), residues: 26 sheet: -1.24 (0.45), residues: 150 loop : -2.45 (0.38), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 35 HIS 0.001 0.001 HIS H 35 PHE 0.024 0.002 PHE A 392 TYR 0.012 0.001 TYR H 53 ARG 0.005 0.001 ARG A 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00183 ( 1) link_NAG-ASN : angle 1.59757 ( 3) link_BETA1-4 : bond 0.00388 ( 1) link_BETA1-4 : angle 3.65692 ( 3) hydrogen bonds : bond 0.02755 ( 84) hydrogen bonds : angle 6.46895 ( 189) SS BOND : bond 0.00602 ( 6) SS BOND : angle 1.18943 ( 12) covalent geometry : bond 0.00328 ( 3444) covalent geometry : angle 0.62640 ( 4685) *********************** 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 94 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.557 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 398 ASP cc_start: 0.7356 (m-30) cc_final: 0.6985 (m-30) REVERT: A 442 ASP cc_start: 0.8863 (m-30) cc_final: 0.8489 (m-30) REVERT: H 108 MET cc_start: 0.9163 (mtm) cc_final: 0.8931 (mtm) REVERT: L 91 TYR cc_start: 0.9289 (p90) cc_final: 0.8906 (p90) outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.2928 time to fit residues: 34.0036 Evaluate side-chains 79 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 8.9990 chunk 22 optimal weight: 0.0770 chunk 31 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 19 optimal weight: 10.0000 chunk 35 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 25 optimal weight: 7.9990 chunk 7 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 overall best weight: 1.1542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.052642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.042002 restraints weight = 46198.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.044906 restraints weight = 19508.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.046964 restraints weight = 10541.371| |-----------------------------------------------------------------------------| r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.5049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3452 Z= 0.115 Angle : 0.617 7.311 4703 Z= 0.318 Chirality : 0.047 0.305 507 Planarity : 0.004 0.039 607 Dihedral : 5.591 31.955 512 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.71 % Allowed : 14.05 % Favored : 85.24 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % 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: -2.96 (0.40), residues: 420 helix: -4.10 (0.54), residues: 26 sheet: -0.93 (0.46), residues: 142 loop : -2.46 (0.37), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP L 35 HIS 0.001 0.000 HIS H 35 PHE 0.017 0.002 PHE A 392 TYR 0.014 0.001 TYR L 36 ARG 0.005 0.001 ARG A 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00340 ( 1) link_NAG-ASN : angle 1.71028 ( 3) link_BETA1-4 : bond 0.00441 ( 1) link_BETA1-4 : angle 3.67333 ( 3) hydrogen bonds : bond 0.02791 ( 84) hydrogen bonds : angle 6.34792 ( 189) SS BOND : bond 0.00477 ( 6) SS BOND : angle 1.12823 ( 12) covalent geometry : bond 0.00272 ( 3444) covalent geometry : angle 0.60719 ( 4685) ********************** 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 97 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.519 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: symmetry clash revert: symmetry clash REVERT: A 398 ASP cc_start: 0.7384 (m-30) cc_final: 0.6992 (m-30) REVERT: A 405 ASP cc_start: 0.8705 (t70) cc_final: 0.8483 (t0) REVERT: A 442 ASP cc_start: 0.8828 (m-30) cc_final: 0.8457 (m-30) REVERT: H 96 CYS cc_start: 0.1736 (p) cc_final: 0.1290 (p) REVERT: H 101 THR cc_start: 0.8389 (t) cc_final: 0.8074 (t) REVERT: H 108 MET cc_start: 0.9152 (mtm) cc_final: 0.8887 (mtm) REVERT: H 111 PHE cc_start: 0.8947 (t80) cc_final: 0.8469 (t80) REVERT: H 114 TYR cc_start: 0.9345 (m-80) cc_final: 0.8997 (m-80) REVERT: L 50 ASP cc_start: 0.9486 (t0) cc_final: 0.9248 (t0) outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.2812 time to fit residues: 33.8454 Evaluate side-chains 84 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 8.9990 chunk 24 optimal weight: 10.0000 chunk 28 optimal weight: 10.0000 chunk 12 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 chunk 40 optimal weight: 5.9990 chunk 3 optimal weight: 6.9990 chunk 14 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 chunk 21 optimal weight: 20.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 89 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 = 0.3052 r_free = 0.3052 target = 0.051540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.041494 restraints weight = 47843.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.044352 restraints weight = 20014.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.046397 restraints weight = 10637.996| |-----------------------------------------------------------------------------| r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.5219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3452 Z= 0.174 Angle : 0.640 9.014 4703 Z= 0.334 Chirality : 0.046 0.304 507 Planarity : 0.004 0.041 607 Dihedral : 5.601 30.498 512 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 17.69 Ramachandran Plot: Outliers : 0.71 % Allowed : 15.24 % Favored : 84.05 % 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: -2.93 (0.40), residues: 420 helix: -4.04 (0.56), residues: 26 sheet: -0.95 (0.46), residues: 142 loop : -2.41 (0.37), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP L 35 HIS 0.001 0.001 HIS H 35 PHE 0.014 0.002 PHE A 392 TYR 0.015 0.002 TYR H 53 ARG 0.004 0.001 ARG A 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00028 ( 1) link_NAG-ASN : angle 1.78184 ( 3) link_BETA1-4 : bond 0.00233 ( 1) link_BETA1-4 : angle 3.68787 ( 3) hydrogen bonds : bond 0.02969 ( 84) hydrogen bonds : angle 6.44470 ( 189) SS BOND : bond 0.00536 ( 6) SS BOND : angle 1.09859 ( 12) covalent geometry : bond 0.00380 ( 3444) covalent geometry : angle 0.63002 ( 4685) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3051.73 seconds wall clock time: 53 minutes 25.94 seconds (3205.94 seconds total)