Starting phenix.real_space_refine on Thu Jul 24 13:45:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x90_33062/07_2025/7x90_33062_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x90_33062/07_2025/7x90_33062.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7x90_33062/07_2025/7x90_33062.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x90_33062/07_2025/7x90_33062.map" model { file = "/net/cci-nas-00/data/ceres_data/7x90_33062/07_2025/7x90_33062_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x90_33062/07_2025/7x90_33062_trim.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 16 5.16 5 C 2092 2.51 5 N 560 2.21 5 O 633 1.98 5 H 3140 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 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: 6441 Number of models: 1 Model: "" Number of chains: 4 Chain: "E" Number of atoms: 1816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 1816 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "F" Number of atoms: 1609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 1609 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "G" 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: "A" 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: 3.72, per 1000 atoms: 0.58 Number of scatterers: 6441 At special positions: 0 Unit cell: (98.651, 71.294, 71.294, 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 16 16.00 O 633 8.00 N 560 7.00 C 2092 6.00 H 3140 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.04 Simple disulfide: pdb=" SG CYS G 336 " - pdb=" SG CYS G 361 " distance=2.03 Simple disulfide: pdb=" SG CYS G 379 " - pdb=" SG CYS G 432 " distance=2.03 Simple disulfide: pdb=" SG CYS G 391 " - pdb=" SG CYS G 525 " distance=2.03 Simple disulfide: pdb=" SG CYS G 480 " - pdb=" SG CYS G 488 " 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 A 1 " - " NAG A 2 " NAG-ASN " NAG A 1 " - " ASN G 343 " Time building additional restraints: 1.67 Conformation dependent library (CDL) restraints added in 587.2 milliseconds 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 770 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 6 sheets defined 5.0% alpha, 21.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'G' and resid 337 through 341 Processing helix chain 'G' and resid 366 through 371 removed outlier: 3.624A pdb=" N SER G 371 " --> pdb=" O VAL G 367 " (cutoff:3.500A) Processing helix chain 'G' and resid 406 through 410 Processing sheet with id=AA1, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'E' and resid 10 through 11 removed outlier: 6.571A pdb=" N GLY E 10 " --> pdb=" O THR E 117 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N MET E 34 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 4 through 5 removed outlier: 3.779A pdb=" N VAL F 19 " --> pdb=" O ILE F 75 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N THR F 72 " --> pdb=" O SER F 65 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER F 65 " --> pdb=" O THR F 72 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 45 through 48 removed outlier: 6.664A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN F 38 " --> pdb=" O ALA F 85 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 356 through 358 removed outlier: 3.779A pdb=" N VAL G 395 " --> pdb=" O ILE G 358 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 361 through 362 removed outlier: 6.827A pdb=" N CYS G 361 " --> pdb=" O CYS G 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 74 hydrogen bonds defined for protein. 168 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: 1.86 Time building geometry restraints manager: 2.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 3140 1.03 - 1.23: 18 1.23 - 1.43: 1484 1.43 - 1.62: 1862 1.62 - 1.82: 20 Bond restraints: 6524 Sorted by residual: bond pdb=" N ASP F 1 " pdb=" CA ASP F 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.02e+00 bond pdb=" C1 NAG A 1 " pdb=" O5 NAG A 1 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.33e+00 bond pdb=" N ASP F 1 " pdb=" H ASP F 1 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.25e+00 bond pdb=" C1 NAG A 2 " pdb=" O5 NAG A 2 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.99e+00 bond pdb=" C THR F 94 " pdb=" N PRO F 95 " ideal model delta sigma weight residual 1.335 1.351 -0.016 1.30e-02 5.92e+03 1.57e+00 ... (remaining 6519 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.07: 10928 1.07 - 2.14: 690 2.14 - 3.21: 42 3.21 - 4.27: 14 4.27 - 5.34: 4 Bond angle restraints: 11678 Sorted by residual: angle pdb=" C SER F 30 " pdb=" CA SER F 30 " pdb=" CB SER F 30 " ideal model delta sigma weight residual 110.42 115.76 -5.34 1.99e+00 2.53e-01 7.21e+00 angle pdb=" N SER F 30 " pdb=" CA SER F 30 " pdb=" C SER F 30 " ideal model delta sigma weight residual 110.80 106.54 4.26 2.13e+00 2.20e-01 3.99e+00 angle pdb=" CA SER F 30 " pdb=" C SER F 30 " pdb=" N ASN F 31 " ideal model delta sigma weight residual 116.84 119.83 -2.99 1.71e+00 3.42e-01 3.06e+00 angle pdb=" N THR F 94 " pdb=" CA THR F 94 " pdb=" C THR F 94 " ideal model delta sigma weight residual 109.81 113.40 -3.59 2.21e+00 2.05e-01 2.63e+00 angle pdb=" C TYR G 508 " pdb=" N ARG G 509 " pdb=" CA ARG G 509 " ideal model delta sigma weight residual 122.30 120.12 2.18 1.35e+00 5.49e-01 2.62e+00 ... (remaining 11673 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.68: 2768 14.68 - 29.36: 250 29.36 - 44.04: 116 44.04 - 58.72: 43 58.72 - 73.39: 5 Dihedral angle restraints: 3182 sinusoidal: 1702 harmonic: 1480 Sorted by residual: dihedral pdb=" CA CYS G 336 " pdb=" CB CYS G 336 " pdb=" SG CYS G 336 " pdb=" SG CYS G 361 " ideal model delta sinusoidal sigma weight residual -73.00 -7.14 -65.86 1 2.00e+01 2.50e-03 1.42e+01 dihedral pdb=" CA GLU G 516 " pdb=" C GLU G 516 " pdb=" N LEU G 517 " pdb=" CA LEU G 517 " ideal model delta harmonic sigma weight residual -180.00 -162.99 -17.01 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CB CYS G 391 " pdb=" SG CYS G 391 " pdb=" SG CYS G 525 " pdb=" CB CYS G 525 " ideal model delta sinusoidal sigma weight residual -86.00 -58.36 -27.64 1 1.00e+01 1.00e-02 1.10e+01 ... (remaining 3179 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 329 0.034 - 0.068: 119 0.068 - 0.101: 39 0.101 - 0.135: 14 0.135 - 0.169: 1 Chirality restraints: 502 Sorted by residual: chirality pdb=" CA ILE G 434 " pdb=" N ILE G 434 " pdb=" C ILE G 434 " pdb=" CB ILE G 434 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.12e-01 chirality pdb=" CA ILE F 21 " pdb=" N ILE F 21 " pdb=" C ILE F 21 " pdb=" CB ILE F 21 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.22e-01 chirality pdb=" CA VAL G 511 " pdb=" N VAL G 511 " pdb=" C VAL G 511 " pdb=" CB VAL G 511 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.56e-01 ... (remaining 499 not shown) Planarity restraints: 992 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR E 32 " 0.022 5.00e-02 4.00e+02 3.27e-02 1.71e+00 pdb=" N PRO E 33 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO E 33 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO E 33 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN G 506 " -0.020 5.00e-02 4.00e+02 3.01e-02 1.45e+00 pdb=" N PRO G 507 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO G 507 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO G 507 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR G 508 " -0.000 2.00e-02 2.50e+03 5.50e-03 9.07e-01 pdb=" CG TYR G 508 " 0.012 2.00e-02 2.50e+03 pdb=" CD1 TYR G 508 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR G 508 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR G 508 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR G 508 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR G 508 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR G 508 " 0.001 2.00e-02 2.50e+03 pdb=" HD1 TYR G 508 " -0.000 2.00e-02 2.50e+03 pdb=" HD2 TYR G 508 " 0.001 2.00e-02 2.50e+03 pdb=" HE1 TYR G 508 " 0.000 2.00e-02 2.50e+03 pdb=" HE2 TYR G 508 " -0.001 2.00e-02 2.50e+03 ... (remaining 989 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.18: 380 2.18 - 2.78: 12634 2.78 - 3.39: 16304 3.39 - 3.99: 21120 3.99 - 4.60: 31957 Nonbonded interactions: 82395 Sorted by model distance: nonbonded pdb=" O GLN F 79 " pdb=" H GLU F 81 " model vdw 1.575 2.450 nonbonded pdb=" OE2 GLU E 6 " pdb=" H GLY E 113 " model vdw 1.603 2.450 nonbonded pdb="HH21 ARG G 403 " pdb=" OE1 GLU G 406 " model vdw 1.651 2.450 nonbonded pdb=" O VAL G 503 " pdb="HE21 GLN G 506 " model vdw 1.671 2.450 nonbonded pdb=" O SER F 30 " pdb=" H GLY F 68 " model vdw 1.687 2.450 ... (remaining 82390 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: 0.210 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: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 18.040 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3392 Z= 0.137 Angle : 0.581 5.343 4618 Z= 0.305 Chirality : 0.042 0.169 502 Planarity : 0.003 0.033 595 Dihedral : 13.963 73.394 1235 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.84 % Favored : 88.16 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.08 (0.37), residues: 414 helix: -3.48 (1.39), residues: 12 sheet: -0.39 (0.47), residues: 111 loop : -2.90 (0.32), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 35 HIS 0.005 0.001 HIS E 31 PHE 0.005 0.001 PHE G 456 TYR 0.012 0.001 TYR G 508 ARG 0.002 0.000 ARG G 509 Details of bonding type rmsd link_NAG-ASN : bond 0.00081 ( 1) link_NAG-ASN : angle 1.51062 ( 3) link_BETA1-4 : bond 0.00173 ( 1) link_BETA1-4 : angle 0.84138 ( 3) hydrogen bonds : bond 0.11659 ( 74) hydrogen bonds : angle 7.02936 ( 168) SS BOND : bond 0.00370 ( 6) SS BOND : angle 0.71117 ( 12) covalent geometry : bond 0.00288 ( 3384) covalent geometry : angle 0.57935 ( 4600) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 35 HIS cc_start: 0.8566 (m90) cc_final: 0.8193 (m170) REVERT: E 99 LEU cc_start: 0.8952 (mt) cc_final: 0.8632 (mt) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.3633 time to fit residues: 49.1171 Evaluate side-chains 81 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 7.9990 chunk 30 optimal weight: 8.9990 chunk 16 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 20 optimal weight: 9.9990 chunk 31 optimal weight: 1.9990 chunk 12 optimal weight: 9.9990 chunk 19 optimal weight: 4.9990 chunk 23 optimal weight: 8.9990 chunk 36 optimal weight: 0.7980 chunk 11 optimal weight: 9.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 34 ASN ** F 90 GLN ** 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 = 0.3375 r_free = 0.3375 target = 0.073461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.060476 restraints weight = 36123.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.064125 restraints weight = 16042.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.066673 restraints weight = 8830.905| |-----------------------------------------------------------------------------| r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3392 Z= 0.165 Angle : 0.563 5.836 4618 Z= 0.296 Chirality : 0.042 0.148 502 Planarity : 0.004 0.035 595 Dihedral : 5.987 50.853 507 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.77 % Favored : 86.23 % Rotamer: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % 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: -3.11 (0.37), residues: 414 helix: -2.10 (1.27), residues: 18 sheet: -0.51 (0.46), residues: 116 loop : -2.98 (0.32), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 353 HIS 0.005 0.001 HIS E 31 PHE 0.017 0.001 PHE F 71 TYR 0.007 0.001 TYR G 453 ARG 0.004 0.000 ARG G 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00090 ( 1) link_NAG-ASN : angle 1.27191 ( 3) link_BETA1-4 : bond 0.00369 ( 1) link_BETA1-4 : angle 1.03837 ( 3) hydrogen bonds : bond 0.03133 ( 74) hydrogen bonds : angle 6.17264 ( 168) SS BOND : bond 0.00377 ( 6) SS BOND : angle 0.63089 ( 12) covalent geometry : bond 0.00358 ( 3384) covalent geometry : angle 0.56119 ( 4600) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.552 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: E 46 GLU cc_start: 0.9032 (mt-10) cc_final: 0.8771 (pt0) REVERT: G 389 ASP cc_start: 0.9250 (m-30) cc_final: 0.8980 (m-30) REVERT: G 467 ASP cc_start: 0.7228 (t0) cc_final: 0.6930 (t0) outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.4619 time to fit residues: 49.5164 Evaluate side-chains 73 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 8 optimal weight: 9.9990 chunk 4 optimal weight: 10.0000 chunk 13 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 20 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 9 optimal weight: 7.9990 chunk 26 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 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 = 0.3411 r_free = 0.3411 target = 0.075511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.061925 restraints weight = 35966.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.065780 restraints weight = 15985.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.068353 restraints weight = 8798.008| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3392 Z= 0.105 Angle : 0.530 5.773 4618 Z= 0.277 Chirality : 0.042 0.148 502 Planarity : 0.004 0.026 595 Dihedral : 5.639 51.282 507 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.87 % Favored : 89.13 % Rotamer: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.97 (0.37), residues: 414 helix: -2.14 (1.25), residues: 18 sheet: -0.36 (0.46), residues: 117 loop : -2.91 (0.32), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 35 HIS 0.004 0.001 HIS E 31 PHE 0.013 0.001 PHE F 71 TYR 0.005 0.001 TYR G 453 ARG 0.002 0.000 ARG G 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00222 ( 1) link_NAG-ASN : angle 0.94961 ( 3) link_BETA1-4 : bond 0.00320 ( 1) link_BETA1-4 : angle 0.93347 ( 3) hydrogen bonds : bond 0.02993 ( 74) hydrogen bonds : angle 5.81093 ( 168) SS BOND : bond 0.00305 ( 6) SS BOND : angle 0.71890 ( 12) covalent geometry : bond 0.00247 ( 3384) covalent geometry : angle 0.52825 ( 4600) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.528 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: E 46 GLU cc_start: 0.9011 (mt-10) cc_final: 0.8733 (pt0) REVERT: E 102 MET cc_start: 0.8887 (mmm) cc_final: 0.8624 (mmm) REVERT: F 11 LEU cc_start: 0.9190 (pp) cc_final: 0.8912 (pp) REVERT: G 389 ASP cc_start: 0.9252 (m-30) cc_final: 0.8996 (m-30) REVERT: G 452 LEU cc_start: 0.9220 (mm) cc_final: 0.8990 (mm) REVERT: G 467 ASP cc_start: 0.7230 (t0) cc_final: 0.6882 (t0) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.4134 time to fit residues: 44.9276 Evaluate side-chains 77 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 23 optimal weight: 10.0000 chunk 31 optimal weight: 8.9990 chunk 2 optimal weight: 9.9990 chunk 10 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 chunk 18 optimal weight: 9.9990 chunk 39 optimal weight: 9.9990 chunk 17 optimal weight: 7.9990 chunk 3 optimal weight: 10.0000 chunk 34 optimal weight: 6.9990 chunk 4 optimal weight: 1.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 487 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.069197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.056052 restraints weight = 38894.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.059580 restraints weight = 17337.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.062009 restraints weight = 9673.311| |-----------------------------------------------------------------------------| r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.3417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 3392 Z= 0.307 Angle : 0.676 5.548 4618 Z= 0.355 Chirality : 0.043 0.142 502 Planarity : 0.005 0.034 595 Dihedral : 5.873 48.589 507 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.24 % Allowed : 16.43 % Favored : 83.33 % Rotamer: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.30 (0.36), residues: 414 helix: -2.67 (1.07), residues: 18 sheet: -0.54 (0.46), residues: 113 loop : -3.12 (0.30), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 353 HIS 0.006 0.002 HIS E 31 PHE 0.023 0.002 PHE F 71 TYR 0.010 0.001 TYR G 505 ARG 0.003 0.001 ARG F 103 Details of bonding type rmsd link_NAG-ASN : bond 0.00296 ( 1) link_NAG-ASN : angle 1.84916 ( 3) link_BETA1-4 : bond 0.00686 ( 1) link_BETA1-4 : angle 1.89579 ( 3) hydrogen bonds : bond 0.03255 ( 74) hydrogen bonds : angle 6.02820 ( 168) SS BOND : bond 0.00349 ( 6) SS BOND : angle 0.77218 ( 12) covalent geometry : bond 0.00658 ( 3384) covalent geometry : angle 0.67251 ( 4600) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.514 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: E 46 GLU cc_start: 0.9143 (mt-10) cc_final: 0.8920 (pt0) REVERT: E 102 MET cc_start: 0.9012 (mmm) cc_final: 0.8811 (mmm) REVERT: F 35 TRP cc_start: 0.8214 (m-10) cc_final: 0.7640 (m-10) REVERT: G 389 ASP cc_start: 0.9158 (m-30) cc_final: 0.8905 (m-30) REVERT: G 452 LEU cc_start: 0.9309 (mm) cc_final: 0.9014 (mm) REVERT: G 467 ASP cc_start: 0.7465 (t0) cc_final: 0.7100 (t0) REVERT: G 516 GLU cc_start: 0.8530 (mt-10) cc_final: 0.7967 (mt-10) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.4402 time to fit residues: 43.8500 Evaluate side-chains 68 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 15 optimal weight: 0.0970 chunk 37 optimal weight: 5.9990 chunk 17 optimal weight: 6.9990 chunk 34 optimal weight: 9.9990 chunk 11 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 chunk 20 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 6 GLN F 34 ASN F 37 GLN G 487 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.072014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.058624 restraints weight = 35768.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.062306 restraints weight = 15699.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.064913 restraints weight = 8712.534| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.3453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3392 Z= 0.115 Angle : 0.559 5.414 4618 Z= 0.293 Chirality : 0.043 0.151 502 Planarity : 0.005 0.055 595 Dihedral : 5.537 50.618 507 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.63 % Favored : 89.13 % Rotamer: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.94 (0.37), residues: 414 helix: -2.29 (1.21), residues: 18 sheet: -0.38 (0.46), residues: 117 loop : -2.85 (0.32), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP F 35 HIS 0.004 0.001 HIS E 31 PHE 0.018 0.001 PHE G 400 TYR 0.010 0.001 TYR G 396 ARG 0.003 0.000 ARG G 355 Details of bonding type rmsd link_NAG-ASN : bond 0.00249 ( 1) link_NAG-ASN : angle 0.85320 ( 3) link_BETA1-4 : bond 0.00472 ( 1) link_BETA1-4 : angle 1.04326 ( 3) hydrogen bonds : bond 0.02941 ( 74) hydrogen bonds : angle 5.88992 ( 168) SS BOND : bond 0.00488 ( 6) SS BOND : angle 1.16124 ( 12) covalent geometry : bond 0.00266 ( 3384) covalent geometry : angle 0.55569 ( 4600) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 1.027 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: E 46 GLU cc_start: 0.9081 (mt-10) cc_final: 0.8865 (pt0) REVERT: E 59 HIS cc_start: 0.8421 (m90) cc_final: 0.8219 (m90) REVERT: G 354 ASN cc_start: 0.9518 (m-40) cc_final: 0.9316 (m-40) REVERT: G 389 ASP cc_start: 0.9183 (m-30) cc_final: 0.8950 (m-30) REVERT: G 452 LEU cc_start: 0.9257 (mm) cc_final: 0.8967 (mm) REVERT: G 467 ASP cc_start: 0.7367 (t0) cc_final: 0.7052 (t0) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.6656 time to fit residues: 75.1432 Evaluate side-chains 74 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 1.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 34 optimal weight: 9.9990 chunk 4 optimal weight: 9.9990 chunk 11 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 22 optimal weight: 7.9990 chunk 25 optimal weight: 5.9990 chunk 6 optimal weight: 0.4980 chunk 16 optimal weight: 9.9990 chunk 37 optimal weight: 9.9990 chunk 5 optimal weight: 3.9990 chunk 9 optimal weight: 9.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.071171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.057818 restraints weight = 36481.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.061538 restraints weight = 15991.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.064140 restraints weight = 8824.177| |-----------------------------------------------------------------------------| r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.3678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3392 Z= 0.136 Angle : 0.556 5.405 4618 Z= 0.291 Chirality : 0.042 0.174 502 Planarity : 0.004 0.036 595 Dihedral : 5.471 50.761 507 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.24 % Allowed : 12.08 % Favored : 87.68 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.00 (0.37), residues: 414 helix: -2.12 (1.27), residues: 18 sheet: -0.67 (0.45), residues: 123 loop : -2.82 (0.32), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 35 HIS 0.004 0.001 HIS E 31 PHE 0.010 0.001 PHE F 71 TYR 0.008 0.001 TYR G 396 ARG 0.003 0.000 ARG G 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00129 ( 1) link_NAG-ASN : angle 1.08255 ( 3) link_BETA1-4 : bond 0.00109 ( 1) link_BETA1-4 : angle 1.12517 ( 3) hydrogen bonds : bond 0.02929 ( 74) hydrogen bonds : angle 5.72827 ( 168) SS BOND : bond 0.00475 ( 6) SS BOND : angle 0.98317 ( 12) covalent geometry : bond 0.00313 ( 3384) covalent geometry : angle 0.55333 ( 4600) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.532 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: E 59 HIS cc_start: 0.8403 (m90) cc_final: 0.8115 (m90) REVERT: G 345 THR cc_start: 0.9091 (m) cc_final: 0.8480 (m) REVERT: G 389 ASP cc_start: 0.9165 (m-30) cc_final: 0.8936 (m-30) REVERT: G 452 LEU cc_start: 0.9208 (mm) cc_final: 0.8950 (mm) REVERT: G 467 ASP cc_start: 0.7360 (t0) cc_final: 0.7055 (t0) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.3862 time to fit residues: 39.4564 Evaluate side-chains 73 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 26 optimal weight: 0.0370 chunk 3 optimal weight: 10.0000 chunk 4 optimal weight: 4.9990 chunk 9 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 30 optimal weight: 7.9990 overall best weight: 3.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 59 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 = 0.3329 r_free = 0.3329 target = 0.070999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.057632 restraints weight = 36676.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.061332 restraints weight = 16148.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.063894 restraints weight = 8921.993| |-----------------------------------------------------------------------------| r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.3888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3392 Z= 0.146 Angle : 0.550 5.497 4618 Z= 0.287 Chirality : 0.042 0.162 502 Planarity : 0.004 0.032 595 Dihedral : 5.413 50.367 507 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.24 % Allowed : 11.59 % Favored : 88.16 % Rotamer: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % 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 (0.37), residues: 414 helix: -2.95 (0.93), residues: 25 sheet: -0.66 (0.44), residues: 128 loop : -2.81 (0.33), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 35 HIS 0.004 0.001 HIS E 31 PHE 0.011 0.001 PHE F 71 TYR 0.009 0.001 TYR G 396 ARG 0.005 0.000 ARG G 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00102 ( 1) link_NAG-ASN : angle 1.16584 ( 3) link_BETA1-4 : bond 0.00173 ( 1) link_BETA1-4 : angle 1.26127 ( 3) hydrogen bonds : bond 0.02740 ( 74) hydrogen bonds : angle 5.59739 ( 168) SS BOND : bond 0.00397 ( 6) SS BOND : angle 0.76253 ( 12) covalent geometry : bond 0.00325 ( 3384) covalent geometry : angle 0.54811 ( 4600) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.959 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: E 59 HIS cc_start: 0.8531 (m90) cc_final: 0.8115 (m90) REVERT: G 345 THR cc_start: 0.9113 (m) cc_final: 0.8486 (m) REVERT: G 354 ASN cc_start: 0.9539 (m-40) cc_final: 0.9338 (m-40) REVERT: G 389 ASP cc_start: 0.9128 (m-30) cc_final: 0.8894 (m-30) REVERT: G 406 GLU cc_start: 0.8988 (pm20) cc_final: 0.8746 (pm20) REVERT: G 452 LEU cc_start: 0.9176 (mm) cc_final: 0.8907 (mm) REVERT: G 467 ASP cc_start: 0.7346 (t0) cc_final: 0.7027 (t0) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.5365 time to fit residues: 55.3786 Evaluate side-chains 72 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 23 optimal weight: 10.0000 chunk 27 optimal weight: 1.9990 chunk 4 optimal weight: 10.0000 chunk 8 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 chunk 15 optimal weight: 2.9990 chunk 11 optimal weight: 10.0000 chunk 37 optimal weight: 9.9990 chunk 32 optimal weight: 6.9990 chunk 12 optimal weight: 4.9990 chunk 21 optimal weight: 0.0670 overall best weight: 3.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 59 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 = 0.3327 r_free = 0.3327 target = 0.070990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.057411 restraints weight = 36746.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.061130 restraints weight = 16203.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.063695 restraints weight = 8976.317| |-----------------------------------------------------------------------------| r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.4006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3392 Z= 0.154 Angle : 0.550 5.516 4618 Z= 0.287 Chirality : 0.042 0.151 502 Planarity : 0.004 0.039 595 Dihedral : 5.383 50.409 507 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.24 % Allowed : 12.08 % Favored : 87.68 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.04 (0.37), residues: 414 helix: -2.90 (0.93), residues: 25 sheet: -0.65 (0.44), residues: 128 loop : -2.82 (0.33), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 35 HIS 0.005 0.001 HIS E 31 PHE 0.011 0.001 PHE F 71 TYR 0.010 0.001 TYR G 396 ARG 0.005 0.000 ARG G 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00088 ( 1) link_NAG-ASN : angle 1.16264 ( 3) link_BETA1-4 : bond 0.00072 ( 1) link_BETA1-4 : angle 1.16633 ( 3) hydrogen bonds : bond 0.02664 ( 74) hydrogen bonds : angle 5.60066 ( 168) SS BOND : bond 0.00440 ( 6) SS BOND : angle 0.74911 ( 12) covalent geometry : bond 0.00341 ( 3384) covalent geometry : angle 0.54831 ( 4600) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 1.792 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: E 59 HIS cc_start: 0.8626 (m90) cc_final: 0.8104 (m90) REVERT: G 345 THR cc_start: 0.9126 (m) cc_final: 0.8497 (m) REVERT: G 354 ASN cc_start: 0.9551 (m-40) cc_final: 0.9347 (m-40) REVERT: G 389 ASP cc_start: 0.9131 (m-30) cc_final: 0.8907 (m-30) REVERT: G 452 LEU cc_start: 0.9158 (mm) cc_final: 0.8885 (mm) REVERT: G 467 ASP cc_start: 0.7377 (t0) cc_final: 0.7053 (t0) outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.6049 time to fit residues: 63.2908 Evaluate side-chains 71 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 17 optimal weight: 0.9990 chunk 4 optimal weight: 7.9990 chunk 21 optimal weight: 2.9990 chunk 2 optimal weight: 9.9990 chunk 25 optimal weight: 5.9990 chunk 33 optimal weight: 8.9990 chunk 32 optimal weight: 10.0000 chunk 31 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 20 optimal weight: 0.5980 chunk 39 optimal weight: 10.0000 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 6 GLN F 34 ASN ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.071955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.058707 restraints weight = 36652.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.062446 restraints weight = 16047.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.065055 restraints weight = 8798.932| |-----------------------------------------------------------------------------| r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.4132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3392 Z= 0.124 Angle : 0.537 5.514 4618 Z= 0.279 Chirality : 0.042 0.150 502 Planarity : 0.004 0.037 595 Dihedral : 5.366 51.150 507 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.63 % Favored : 89.13 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.93 (0.37), residues: 414 helix: -2.13 (1.25), residues: 18 sheet: -0.63 (0.45), residues: 125 loop : -2.77 (0.32), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP F 35 HIS 0.004 0.001 HIS E 31 PHE 0.009 0.001 PHE F 71 TYR 0.008 0.001 TYR F 36 ARG 0.004 0.000 ARG G 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00163 ( 1) link_NAG-ASN : angle 1.03065 ( 3) link_BETA1-4 : bond 0.00021 ( 1) link_BETA1-4 : angle 1.02926 ( 3) hydrogen bonds : bond 0.02685 ( 74) hydrogen bonds : angle 5.62793 ( 168) SS BOND : bond 0.00356 ( 6) SS BOND : angle 0.65398 ( 12) covalent geometry : bond 0.00282 ( 3384) covalent geometry : angle 0.53601 ( 4600) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.546 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: G 345 THR cc_start: 0.9139 (m) cc_final: 0.8512 (m) REVERT: G 354 ASN cc_start: 0.9553 (m-40) cc_final: 0.9352 (m-40) REVERT: G 389 ASP cc_start: 0.9163 (m-30) cc_final: 0.8944 (m-30) REVERT: G 406 GLU cc_start: 0.9005 (pm20) cc_final: 0.8762 (pm20) REVERT: G 452 LEU cc_start: 0.9144 (mm) cc_final: 0.8867 (mm) REVERT: G 467 ASP cc_start: 0.7329 (t0) cc_final: 0.7057 (t0) outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.4754 time to fit residues: 47.5175 Evaluate side-chains 70 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 8 optimal weight: 10.0000 chunk 29 optimal weight: 8.9990 chunk 13 optimal weight: 7.9990 chunk 14 optimal weight: 8.9990 chunk 20 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 30 optimal weight: 0.8980 chunk 5 optimal weight: 8.9990 chunk 32 optimal weight: 9.9990 chunk 26 optimal weight: 8.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 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 = 0.3295 r_free = 0.3295 target = 0.069528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.056247 restraints weight = 37356.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.059922 restraints weight = 16462.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.062468 restraints weight = 9063.012| |-----------------------------------------------------------------------------| r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.4245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3392 Z= 0.194 Angle : 0.570 5.528 4618 Z= 0.299 Chirality : 0.042 0.142 502 Planarity : 0.005 0.041 595 Dihedral : 5.476 50.687 507 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.24 % Allowed : 13.53 % Favored : 86.23 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.07 (0.37), residues: 414 helix: -2.27 (1.14), residues: 18 sheet: -0.62 (0.44), residues: 128 loop : -2.95 (0.32), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP F 35 HIS 0.005 0.001 HIS E 31 PHE 0.015 0.001 PHE F 71 TYR 0.011 0.001 TYR G 396 ARG 0.004 0.001 ARG G 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00076 ( 1) link_NAG-ASN : angle 1.40822 ( 3) link_BETA1-4 : bond 0.00218 ( 1) link_BETA1-4 : angle 1.44290 ( 3) hydrogen bonds : bond 0.02667 ( 74) hydrogen bonds : angle 5.65875 ( 168) SS BOND : bond 0.00338 ( 6) SS BOND : angle 0.72005 ( 12) covalent geometry : bond 0.00423 ( 3384) covalent geometry : angle 0.56807 ( 4600) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.521 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: G 345 THR cc_start: 0.9164 (m) cc_final: 0.8507 (m) REVERT: G 389 ASP cc_start: 0.9162 (m-30) cc_final: 0.8949 (m-30) REVERT: G 406 GLU cc_start: 0.9048 (pm20) cc_final: 0.8822 (pm20) REVERT: G 452 LEU cc_start: 0.9161 (mm) cc_final: 0.8878 (mm) REVERT: G 467 ASP cc_start: 0.7450 (t0) cc_final: 0.7114 (t0) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.5895 time to fit residues: 59.9405 Evaluate side-chains 69 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 8 optimal weight: 7.9990 chunk 30 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 12 optimal weight: 7.9990 chunk 33 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 4 optimal weight: 0.5980 chunk 14 optimal weight: 9.9990 chunk 20 optimal weight: 0.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.073276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.059922 restraints weight = 36513.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.063684 restraints weight = 16017.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.066279 restraints weight = 8822.686| |-----------------------------------------------------------------------------| r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.4294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3392 Z= 0.095 Angle : 0.537 5.657 4618 Z= 0.279 Chirality : 0.043 0.158 502 Planarity : 0.004 0.037 595 Dihedral : 5.425 52.058 507 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.87 % Favored : 88.89 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.93 (0.37), residues: 414 helix: -2.02 (1.24), residues: 18 sheet: -0.73 (0.44), residues: 130 loop : -2.75 (0.33), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP F 35 HIS 0.006 0.001 HIS E 31 PHE 0.008 0.001 PHE G 400 TYR 0.013 0.001 TYR E 32 ARG 0.004 0.000 ARG G 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00304 ( 1) link_NAG-ASN : angle 0.75825 ( 3) link_BETA1-4 : bond 0.00370 ( 1) link_BETA1-4 : angle 0.86716 ( 3) hydrogen bonds : bond 0.02535 ( 74) hydrogen bonds : angle 5.54016 ( 168) SS BOND : bond 0.00402 ( 6) SS BOND : angle 0.70202 ( 12) covalent geometry : bond 0.00224 ( 3384) covalent geometry : angle 0.53619 ( 4600) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4100.54 seconds wall clock time: 76 minutes 22.68 seconds (4582.68 seconds total)