Starting phenix.real_space_refine on Tue Mar 3 14:57:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x92_33064/03_2026/7x92_33064_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x92_33064/03_2026/7x92_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_33064/03_2026/7x92_33064.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x92_33064/03_2026/7x92_33064.map" model { file = "/net/cci-nas-00/data/ceres_data/7x92_33064/03_2026/7x92_33064_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x92_33064/03_2026/7x92_33064_trim.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 1.19, per 1000 atoms: 0.18 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: 0.56 Conformation dependent library (CDL) restraints added in 284.9 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: 0.17 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: 1.09 Time building geometry restraints manager: 0.81 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: 0.010 Normalize map: mean=0, sd=1: 0.240 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: 0.040 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.590 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.030 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.002 0.000 ARG A 509 TYR 0.007 0.001 TYR L 96 PHE 0.012 0.001 PHE A 377 TRP 0.012 0.001 TRP H 47 HIS 0.001 0.000 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00529 ( 3444) covalent geometry : angle 0.74482 ( 4685) SS BOND : bond 0.00526 ( 6) SS BOND : angle 1.19856 ( 12) hydrogen bonds : bond 0.13598 ( 84) hydrogen bonds : angle 7.39346 ( 189) link_BETA1-4 : bond 0.00596 ( 1) link_BETA1-4 : angle 2.38859 ( 3) link_NAG-ASN : bond 0.00268 ( 1) link_NAG-ASN : angle 1.57768 ( 3) *********************** 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 : 0.180 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: 0.7843 (pp) REVERT: L 34 ASN cc_start: 0.7531 (m-40) cc_final: 0.7325 (m-40) REVERT: L 46 LEU cc_start: 0.8679 (tp) cc_final: 0.8444 (tp) outliers start: 1 outliers final: 1 residues processed: 135 average time/residue: 0.2043 time to fit residues: 31.7786 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 : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 24 optimal weight: 7.9990 chunk 26 optimal weight: 9.9990 chunk 2 optimal weight: 10.0000 chunk 16 optimal weight: 5.9990 chunk 32 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 19 optimal weight: 7.9990 chunk 30 optimal weight: 7.9990 chunk 22 optimal weight: 3.9990 chunk 37 optimal weight: 20.0000 overall best weight: 4.5988 ------------------------------------------------------------------------------- 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 = 0.3072 r_free = 0.3072 target = 0.053768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.042313 restraints weight = 43510.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.045309 restraints weight = 19282.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.047532 restraints weight = 10640.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.049061 restraints weight = 6569.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.050123 restraints weight = 4351.058| |-----------------------------------------------------------------------------| r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 3452 Z= 0.196 Angle : 0.650 6.835 4703 Z= 0.334 Chirality : 0.047 0.379 507 Planarity : 0.004 0.053 607 Dihedral : 11.281 78.934 512 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.00 % Favored : 85.00 % Rotamer: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.76 (0.40), residues: 420 helix: -4.49 (0.48), residues: 24 sheet: -0.72 (0.48), residues: 134 loop : -2.29 (0.36), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 509 TYR 0.010 0.002 TYR A 451 PHE 0.012 0.001 PHE A 377 TRP 0.010 0.001 TRP H 47 HIS 0.001 0.000 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00435 ( 3444) covalent geometry : angle 0.64448 ( 4685) SS BOND : bond 0.00512 ( 6) SS BOND : angle 1.41554 ( 12) hydrogen bonds : bond 0.03432 ( 84) hydrogen bonds : angle 6.86078 ( 189) link_BETA1-4 : bond 0.00538 ( 1) link_BETA1-4 : angle 1.56203 ( 3) link_NAG-ASN : bond 0.00047 ( 1) link_NAG-ASN : angle 1.71368 ( 3) *********************** 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 110 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.175 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: 0.7616 (m-30) cc_final: 0.7063 (m-30) REVERT: A 405 ASP cc_start: 0.9051 (t70) cc_final: 0.8815 (t0) REVERT: A 442 ASP cc_start: 0.9165 (m-30) cc_final: 0.8794 (m-30) REVERT: L 4 LEU cc_start: 0.9048 (mm) cc_final: 0.8782 (tt) outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 0.1789 time to fit residues: 23.1771 Evaluate side-chains 93 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 6 optimal weight: 7.9990 chunk 29 optimal weight: 0.9980 chunk 1 optimal weight: 4.9990 chunk 30 optimal weight: 10.0000 chunk 22 optimal weight: 9.9990 chunk 16 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 33 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 31 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.056295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.044897 restraints weight = 42481.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.048072 restraints weight = 18432.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.050351 restraints weight = 10071.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.051933 restraints weight = 6097.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.053049 restraints weight = 3962.507| |-----------------------------------------------------------------------------| r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 3452 Z= 0.110 Angle : 0.620 7.714 4703 Z= 0.314 Chirality : 0.048 0.342 507 Planarity : 0.004 0.042 607 Dihedral : 8.403 49.377 512 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.24 % Allowed : 13.81 % Favored : 85.95 % Rotamer: Outliers : 0.27 % Allowed : 1.37 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.78 (0.39), residues: 420 helix: -4.87 (0.34), residues: 18 sheet: -0.72 (0.47), residues: 134 loop : -2.36 (0.35), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 509 TYR 0.012 0.001 TYR L 32 PHE 0.008 0.001 PHE A 377 TRP 0.006 0.001 TRP A 436 HIS 0.000 0.000 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 3444) covalent geometry : angle 0.61441 ( 4685) SS BOND : bond 0.00511 ( 6) SS BOND : angle 1.11695 ( 12) hydrogen bonds : bond 0.02953 ( 84) hydrogen bonds : angle 6.57252 ( 189) link_BETA1-4 : bond 0.00534 ( 1) link_BETA1-4 : angle 2.71449 ( 3) link_NAG-ASN : bond 0.00327 ( 1) link_NAG-ASN : angle 0.94440 ( 3) *********************** 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 112 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 111 time to evaluate : 0.174 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: A 398 ASP cc_start: 0.7645 (m-30) cc_final: 0.7272 (m-30) REVERT: A 442 ASP cc_start: 0.9106 (m-30) cc_final: 0.8711 (m-30) REVERT: H 28 THR cc_start: 0.9548 (t) cc_final: 0.8730 (t) REVERT: H 31 ASN cc_start: 0.9476 (OUTLIER) cc_final: 0.8942 (p0) REVERT: H 35 HIS cc_start: 0.8910 (m90) cc_final: 0.8270 (m90) outliers start: 1 outliers final: 0 residues processed: 112 average time/residue: 0.1701 time to fit residues: 22.5460 Evaluate side-chains 95 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 94 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 8.9990 chunk 21 optimal weight: 20.0000 chunk 32 optimal weight: 10.0000 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 9.9990 chunk 18 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 chunk 17 optimal weight: 8.9990 chunk 0 optimal weight: 0.8980 chunk 8 optimal weight: 10.0000 chunk 16 optimal weight: 9.9990 overall best weight: 6.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 77 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 = 0.3068 r_free = 0.3068 target = 0.052724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.042311 restraints weight = 47705.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.045167 restraints weight = 20305.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.047192 restraints weight = 10999.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.048581 restraints weight = 6722.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.049545 restraints weight = 4414.265| |-----------------------------------------------------------------------------| r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.3722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 3452 Z= 0.242 Angle : 0.678 6.432 4703 Z= 0.352 Chirality : 0.046 0.323 507 Planarity : 0.004 0.042 607 Dihedral : 7.288 48.083 512 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 17.08 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.56 (0.40), residues: 420 helix: -4.45 (0.51), residues: 18 sheet: -0.25 (0.50), residues: 128 loop : -2.38 (0.35), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 509 TYR 0.016 0.002 TYR H 53 PHE 0.012 0.002 PHE H 112 TRP 0.039 0.003 TRP H 36 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00520 ( 3444) covalent geometry : angle 0.67116 ( 4685) SS BOND : bond 0.00864 ( 6) SS BOND : angle 1.13467 ( 12) hydrogen bonds : bond 0.03326 ( 84) hydrogen bonds : angle 6.98352 ( 189) link_BETA1-4 : bond 0.00272 ( 1) link_BETA1-4 : angle 3.17997 ( 3) link_NAG-ASN : bond 0.00229 ( 1) link_NAG-ASN : angle 1.28446 ( 3) *********************** 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 97 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.238 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: A 398 ASP cc_start: 0.7553 (m-30) cc_final: 0.7184 (m-30) REVERT: A 405 ASP cc_start: 0.8873 (t70) cc_final: 0.8471 (t0) REVERT: A 442 ASP cc_start: 0.9134 (m-30) cc_final: 0.8763 (m-30) REVERT: H 34 MET cc_start: 0.7829 (pmm) cc_final: 0.7627 (pmm) REVERT: H 35 HIS cc_start: 0.8980 (m90) cc_final: 0.8673 (m90) REVERT: L 36 TYR cc_start: 0.9049 (m-80) cc_final: 0.8694 (m-80) REVERT: L 49 TYR cc_start: 0.9522 (p90) cc_final: 0.9254 (p90) outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.1838 time to fit residues: 21.0764 Evaluate side-chains 89 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 30 optimal weight: 7.9990 chunk 27 optimal weight: 3.9990 chunk 37 optimal weight: 20.0000 chunk 36 optimal weight: 6.9990 chunk 35 optimal weight: 5.9990 chunk 6 optimal weight: 9.9990 chunk 26 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 39 optimal weight: 10.0000 chunk 11 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.053408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.042876 restraints weight = 46384.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.045906 restraints weight = 19252.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.048052 restraints weight = 10252.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.049491 restraints weight = 6122.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.050468 restraints weight = 3964.350| |-----------------------------------------------------------------------------| r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.4055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3452 Z= 0.156 Angle : 0.649 6.947 4703 Z= 0.333 Chirality : 0.047 0.316 507 Planarity : 0.004 0.041 607 Dihedral : 6.637 47.637 512 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.48 % Allowed : 14.76 % Favored : 84.76 % Rotamer: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.73 (0.39), residues: 420 helix: -4.46 (0.45), residues: 24 sheet: -0.36 (0.49), residues: 130 loop : -2.46 (0.34), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 408 TYR 0.016 0.001 TYR H 53 PHE 0.010 0.001 PHE A 377 TRP 0.011 0.002 TRP H 36 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 3444) covalent geometry : angle 0.64320 ( 4685) SS BOND : bond 0.00658 ( 6) SS BOND : angle 0.97831 ( 12) hydrogen bonds : bond 0.03135 ( 84) hydrogen bonds : angle 6.82765 ( 189) link_BETA1-4 : bond 0.00091 ( 1) link_BETA1-4 : angle 3.13463 ( 3) link_NAG-ASN : bond 0.00074 ( 1) link_NAG-ASN : angle 1.17134 ( 3) *********************** 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 98 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.174 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: A 398 ASP cc_start: 0.7451 (m-30) cc_final: 0.7059 (m-30) REVERT: A 405 ASP cc_start: 0.8775 (t70) cc_final: 0.8391 (t0) REVERT: A 442 ASP cc_start: 0.9076 (m-30) cc_final: 0.8700 (m-30) REVERT: H 34 MET cc_start: 0.7862 (pmm) cc_final: 0.7589 (pmm) REVERT: L 49 TYR cc_start: 0.9515 (p90) cc_final: 0.9246 (p90) REVERT: L 97 THR cc_start: 0.8840 (t) cc_final: 0.8602 (t) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.1703 time to fit residues: 19.7368 Evaluate side-chains 91 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 10 optimal weight: 8.9990 chunk 31 optimal weight: 7.9990 chunk 25 optimal weight: 0.9980 chunk 8 optimal weight: 9.9990 chunk 4 optimal weight: 10.0000 chunk 7 optimal weight: 4.9990 chunk 28 optimal weight: 8.9990 chunk 15 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 33 optimal weight: 8.9990 chunk 1 optimal weight: 1.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- 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 = 0.3097 r_free = 0.3097 target = 0.053659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.043212 restraints weight = 44857.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.046200 restraints weight = 18541.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.048294 restraints weight = 9841.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.049719 restraints weight = 5870.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.050718 restraints weight = 3785.902| |-----------------------------------------------------------------------------| r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.4147 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= 0.119 Angle : 0.613 6.484 4703 Z= 0.313 Chirality : 0.047 0.334 507 Planarity : 0.003 0.041 607 Dihedral : 6.159 43.439 512 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.48 % Allowed : 14.52 % Favored : 85.00 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.56 (0.40), residues: 420 helix: -3.81 (0.66), residues: 26 sheet: -0.39 (0.49), residues: 140 loop : -2.36 (0.35), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 408 TYR 0.019 0.001 TYR A 495 PHE 0.009 0.001 PHE A 377 TRP 0.010 0.002 TRP H 36 HIS 0.001 0.000 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 3444) covalent geometry : angle 0.60460 ( 4685) SS BOND : bond 0.00571 ( 6) SS BOND : angle 0.92712 ( 12) hydrogen bonds : bond 0.03057 ( 84) hydrogen bonds : angle 6.46116 ( 189) link_BETA1-4 : bond 0.00451 ( 1) link_BETA1-4 : angle 3.51998 ( 3) link_NAG-ASN : bond 0.00254 ( 1) link_NAG-ASN : angle 1.40653 ( 3) *********************** 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 100 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.141 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: 0.9642 (mttp) cc_final: 0.9434 (mttm) REVERT: A 398 ASP cc_start: 0.7483 (m-30) cc_final: 0.7088 (m-30) REVERT: A 405 ASP cc_start: 0.8754 (t70) cc_final: 0.8322 (t70) REVERT: A 442 ASP cc_start: 0.8976 (m-30) cc_final: 0.8582 (m-30) REVERT: H 34 MET cc_start: 0.7962 (pmm) cc_final: 0.7700 (pmm) REVERT: H 114 TYR cc_start: 0.9424 (m-80) cc_final: 0.9022 (m-80) REVERT: L 49 TYR cc_start: 0.9524 (p90) cc_final: 0.9287 (p90) REVERT: L 97 THR cc_start: 0.8834 (t) cc_final: 0.8456 (t) outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 0.1679 time to fit residues: 19.8152 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 : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 16 optimal weight: 10.0000 chunk 4 optimal weight: 9.9990 chunk 13 optimal weight: 9.9990 chunk 38 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 22 optimal weight: 10.0000 chunk 40 optimal weight: 0.0570 chunk 1 optimal weight: 8.9990 chunk 8 optimal weight: 5.9990 overall best weight: 3.0104 ------------------------------------------------------------------------------- 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 = 0.3084 r_free = 0.3084 target = 0.053282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.042577 restraints weight = 45773.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.045591 restraints weight = 19471.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.047711 restraints weight = 10475.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.049110 restraints weight = 6344.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.050095 restraints weight = 4201.288| |-----------------------------------------------------------------------------| r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.4451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3452 Z= 0.140 Angle : 0.616 6.024 4703 Z= 0.316 Chirality : 0.048 0.392 507 Planarity : 0.004 0.041 607 Dihedral : 6.013 41.574 512 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.48 % Allowed : 14.52 % Favored : 85.00 % Rotamer: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Cbeta Deviations : 0.26 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.51 (0.40), residues: 420 helix: -3.80 (0.67), residues: 26 sheet: -0.31 (0.49), residues: 140 loop : -2.35 (0.36), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 408 TYR 0.013 0.001 TYR H 53 PHE 0.009 0.001 PHE A 377 TRP 0.032 0.003 TRP H 47 HIS 0.001 0.000 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 3444) covalent geometry : angle 0.60601 ( 4685) SS BOND : bond 0.00612 ( 6) SS BOND : angle 1.26923 ( 12) hydrogen bonds : bond 0.03400 ( 84) hydrogen bonds : angle 6.48419 ( 189) link_BETA1-4 : bond 0.00313 ( 1) link_BETA1-4 : angle 3.56790 ( 3) link_NAG-ASN : bond 0.00110 ( 1) link_NAG-ASN : angle 1.50763 ( 3) *********************** 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 97 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.153 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: 0.7382 (m-30) cc_final: 0.6998 (m-30) REVERT: A 405 ASP cc_start: 0.8724 (t70) cc_final: 0.8313 (t70) REVERT: A 442 ASP cc_start: 0.8984 (m-30) cc_final: 0.8592 (m-30) REVERT: H 34 MET cc_start: 0.8001 (pmm) cc_final: 0.7722 (pmm) REVERT: L 49 TYR cc_start: 0.9503 (p90) cc_final: 0.9258 (p90) outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.1706 time to fit residues: 19.5616 Evaluate side-chains 89 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 8 optimal weight: 9.9990 chunk 10 optimal weight: 7.9990 chunk 35 optimal weight: 0.5980 chunk 23 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 31 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 chunk 29 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 25 optimal weight: 8.9990 chunk 15 optimal weight: 0.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.052942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.042448 restraints weight = 47191.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.045398 restraints weight = 19864.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.047469 restraints weight = 10656.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.048815 restraints weight = 6447.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.049826 restraints weight = 4289.815| |-----------------------------------------------------------------------------| r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.4465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3452 Z= 0.135 Angle : 0.628 6.988 4703 Z= 0.322 Chirality : 0.048 0.372 507 Planarity : 0.004 0.041 607 Dihedral : 5.905 39.314 512 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.71 % Allowed : 14.76 % Favored : 84.52 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.56 (0.40), residues: 420 helix: -3.74 (0.69), residues: 26 sheet: -0.43 (0.49), residues: 140 loop : -2.33 (0.36), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 408 TYR 0.016 0.002 TYR L 91 PHE 0.009 0.001 PHE A 377 TRP 0.017 0.002 TRP H 47 HIS 0.001 0.000 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 3444) covalent geometry : angle 0.61796 ( 4685) SS BOND : bond 0.00646 ( 6) SS BOND : angle 1.20241 ( 12) hydrogen bonds : bond 0.03346 ( 84) hydrogen bonds : angle 6.44890 ( 189) link_BETA1-4 : bond 0.00381 ( 1) link_BETA1-4 : angle 3.60939 ( 3) link_NAG-ASN : bond 0.00141 ( 1) link_NAG-ASN : angle 1.55762 ( 3) *********************** 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 95 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.192 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: 0.7399 (m-30) cc_final: 0.7001 (m-30) REVERT: A 405 ASP cc_start: 0.8714 (t70) cc_final: 0.8293 (t70) REVERT: A 442 ASP cc_start: 0.8937 (m-30) cc_final: 0.8538 (m-30) REVERT: H 4 LEU cc_start: 0.9041 (tp) cc_final: 0.8837 (tp) REVERT: H 34 MET cc_start: 0.7987 (pmm) cc_final: 0.7722 (pmm) REVERT: H 73 ASP cc_start: 0.8305 (t0) cc_final: 0.7898 (t0) REVERT: L 49 TYR cc_start: 0.9501 (p90) cc_final: 0.9289 (p90) REVERT: L 50 ASP cc_start: 0.9604 (m-30) cc_final: 0.9375 (m-30) outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.1675 time to fit residues: 19.1092 Evaluate side-chains 86 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 14 optimal weight: 8.9990 chunk 10 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 21 optimal weight: 9.9990 chunk 1 optimal weight: 10.0000 chunk 5 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 33 optimal weight: 9.9990 chunk 0 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.053020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.042687 restraints weight = 47166.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.045612 restraints weight = 19803.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.047676 restraints weight = 10576.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.049080 restraints weight = 6357.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.050020 restraints weight = 4143.687| |-----------------------------------------------------------------------------| r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.4690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3452 Z= 0.141 Angle : 0.624 6.753 4703 Z= 0.321 Chirality : 0.048 0.366 507 Planarity : 0.003 0.042 607 Dihedral : 5.766 37.010 512 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.71 % Allowed : 13.57 % Favored : 85.71 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.57 (0.41), residues: 420 helix: -3.79 (0.67), residues: 26 sheet: -0.46 (0.49), residues: 140 loop : -2.33 (0.36), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 408 TYR 0.013 0.001 TYR H 53 PHE 0.009 0.001 PHE A 377 TRP 0.041 0.003 TRP L 35 HIS 0.004 0.002 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 3444) covalent geometry : angle 0.61424 ( 4685) SS BOND : bond 0.00598 ( 6) SS BOND : angle 1.20867 ( 12) hydrogen bonds : bond 0.03418 ( 84) hydrogen bonds : angle 6.39004 ( 189) link_BETA1-4 : bond 0.00375 ( 1) link_BETA1-4 : angle 3.65202 ( 3) link_NAG-ASN : bond 0.00135 ( 1) link_NAG-ASN : angle 1.54013 ( 3) *********************** 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 95 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.179 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: 0.7390 (m-30) cc_final: 0.6978 (m-30) REVERT: A 405 ASP cc_start: 0.8715 (t70) cc_final: 0.8436 (t70) REVERT: A 442 ASP cc_start: 0.8944 (m-30) cc_final: 0.8549 (m-30) REVERT: H 34 MET cc_start: 0.8013 (pmm) cc_final: 0.7738 (pmm) REVERT: H 73 ASP cc_start: 0.8194 (t0) cc_final: 0.7992 (t0) outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.1720 time to fit residues: 19.4292 Evaluate side-chains 86 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 9.9990 chunk 2 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 29 optimal weight: 7.9990 chunk 1 optimal weight: 6.9990 chunk 35 optimal weight: 6.9990 chunk 20 optimal weight: 0.9980 chunk 16 optimal weight: 5.9990 chunk 37 optimal weight: 20.0000 chunk 32 optimal weight: 9.9990 chunk 22 optimal weight: 10.0000 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 31 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.050243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.040420 restraints weight = 49020.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.043203 restraints weight = 20689.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.045151 restraints weight = 11057.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.046448 restraints weight = 6670.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.047324 restraints weight = 4381.714| |-----------------------------------------------------------------------------| r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.4972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 3452 Z= 0.228 Angle : 0.666 6.321 4703 Z= 0.351 Chirality : 0.047 0.369 507 Planarity : 0.004 0.042 607 Dihedral : 6.019 34.943 512 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 20.13 Ramachandran Plot: Outliers : 0.71 % Allowed : 15.48 % Favored : 83.81 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.74 (0.40), residues: 420 helix: -3.86 (0.63), residues: 26 sheet: -0.60 (0.48), residues: 142 loop : -2.44 (0.36), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 509 TYR 0.028 0.002 TYR H 53 PHE 0.011 0.002 PHE A 392 TRP 0.023 0.003 TRP H 47 HIS 0.006 0.002 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00482 ( 3444) covalent geometry : angle 0.65610 ( 4685) SS BOND : bond 0.00629 ( 6) SS BOND : angle 1.28307 ( 12) hydrogen bonds : bond 0.03415 ( 84) hydrogen bonds : angle 6.49709 ( 189) link_BETA1-4 : bond 0.00120 ( 1) link_BETA1-4 : angle 3.72857 ( 3) link_NAG-ASN : bond 0.00170 ( 1) link_NAG-ASN : angle 1.70468 ( 3) ********************** 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 89 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.226 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: 0.7260 (m-30) cc_final: 0.6898 (m-30) REVERT: A 442 ASP cc_start: 0.9007 (m-30) cc_final: 0.8639 (m-30) REVERT: H 34 MET cc_start: 0.8191 (pmm) cc_final: 0.7875 (pmm) REVERT: H 73 ASP cc_start: 0.8259 (t0) cc_final: 0.8038 (t0) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.1789 time to fit residues: 18.8480 Evaluate side-chains 73 residues out of total 364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 31 optimal weight: 0.9990 chunk 11 optimal weight: 10.0000 chunk 19 optimal weight: 10.0000 chunk 34 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 33 optimal weight: 0.0870 chunk 21 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 3 optimal weight: 9.9990 chunk 12 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 overall best weight: 2.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.051437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.041346 restraints weight = 48263.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.044179 restraints weight = 20305.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.046158 restraints weight = 10905.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.047523 restraints weight = 6601.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.048399 restraints weight = 4309.749| |-----------------------------------------------------------------------------| r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.5033 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= 0.142 Angle : 0.619 6.193 4703 Z= 0.320 Chirality : 0.047 0.361 507 Planarity : 0.003 0.041 607 Dihedral : 5.693 31.707 512 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 16.32 Ramachandran Plot: Outliers : 0.71 % Allowed : 14.52 % Favored : 84.76 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.74 (0.40), residues: 420 helix: -3.95 (0.58), residues: 26 sheet: -0.65 (0.47), residues: 140 loop : -2.38 (0.37), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 509 TYR 0.014 0.001 TYR H 53 PHE 0.022 0.002 PHE A 392 TRP 0.020 0.002 TRP L 35 HIS 0.006 0.002 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 3444) covalent geometry : angle 0.60919 ( 4685) SS BOND : bond 0.00659 ( 6) SS BOND : angle 1.15475 ( 12) hydrogen bonds : bond 0.03269 ( 84) hydrogen bonds : angle 6.40247 ( 189) link_BETA1-4 : bond 0.00402 ( 1) link_BETA1-4 : angle 3.58167 ( 3) link_NAG-ASN : bond 0.00180 ( 1) link_NAG-ASN : angle 1.76206 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1596.14 seconds wall clock time: 27 minutes 48.94 seconds (1668.94 seconds total)